WorldWideScience

Sample records for atlas web server

  1. The Medicago truncatula gene expression atlas web server

    Directory of Open Access Journals (Sweden)

    Tang Yuhong

    2009-12-01

    Full Text Available Abstract Background Legumes (Leguminosae or Fabaceae play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA web server for this purpose. Description The Medicago truncatula Gene Expression Atlas (MtGEA web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible

  2. The RNAsnp web server

    DEFF Research Database (Denmark)

    Radhakrishnan, Sabarinathan; Tafer, Hakim; Seemann, Ernst Stefan;

    2013-01-01

    , are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected...... to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/....

  3. HDF-EOS Web Server

    Science.gov (United States)

    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.

  4. What's New in Apache Web Server 22?

    CERN Document Server

    Bowen, Rich

    2007-01-01

    What's New in Apache Web Server 2.2? shows you all the new features you'll know to set up and administer the Apache 2.2 web server. Learn how to take advantage of its improved caching, proxying, authentication, and other improvements in your Web 2.0 applications.

  5. Parallel Computing Using Web Servers and "Servlets".

    Science.gov (United States)

    Lo, Alfred; Bloor, Chris; Choi, Y. K.

    2000-01-01

    Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

  6. FPGA Implementation of Modified Secured Web Server

    Directory of Open Access Journals (Sweden)

    Dr.K.V.Karthikeyan

    2013-10-01

    Full Text Available Demand for High speed portable networks impels compulsory optimization in various aspects. A common web server is to act as a central control point which responds to the user request, and employing a high sophisticated computer for this purpose is not obligatory. This Paper focuses on a portable low power automated web server in a FPGA platform by accomplish the Network on chip concept. This web server has the capability to adapt multipurpose operation, a client can share the web content not only the HTML files but also can control a device operated in a remote place through this web server. In accession a modified Elliptic curve cryptographic architecture is implemented to fortify the communication of server to client system. The ECC is coalition with Montgomery multiplication for certain advantage like minimum register usage.

  7. APPRIS WebServer and WebServices

    OpenAIRE

    Rodriguez, Jose Manuel; Carro, Angel; Valencia, Alfonso; Tress, Michael L.

    2015-01-01

    This paper introduces the APPRIS WebServer (http://appris.bioinfo.cnio.es) and WebServices (http://apprisws.bioinfo.cnio.es). Both the web servers and the web services are based around the APPRIS Database, a database that presently houses annotations of splice isoforms for five different vertebrate genomes. The APPRIS WebServer and WebServices provide access to the computational methods implemented in the APPRIS Database, while the APPRIS WebServices also allows retrieval of the annotations. ...

  8. ATLAS Tags Web Service calls Athena via Athenaeum Framework

    CERN Document Server

    Hrivnac, J; The ATLAS collaboration

    2011-01-01

    High Energy Physics experiments start using a Web Service style application to access functionality of their main frameworks. Those frameworks, however, are not ready to be executed in a standard Web Service environment as frameworks are too complex, monolithic and use non-standard and non-portable technologies. ATLAS Tag Browser is one of those Web Service. To provide the possibility to extract full ATLAS events from the standard Web Service, we need to access to full ATLAS offline framework - Athena. As Athena cannot run directly within any Web Service, the client server approach has been chosen. Web Service calls Athena remotely over XML-RPC connection using Athenaeum framework.

  9. MICROSOFT SHAREPOINT SERVER 2013 : Web-julkaisualustana

    OpenAIRE

    Mäkelä, Marko

    2013-01-01

    Opinnäytetyön tutkimuksen aiheena on Microsoft SharePoint Enterprise 2013. Tarkoituksena työssäni oli tutustua uuteen SharePoint Server 2013 Enterprise versioon, sen käyttöliittymään, joihinkin uusiin ominaisuuksiin ja toimintoihin. Työssä pystytettiin SharePoint 2013 sivusto valmiin SharePoint Server 2013 Enterprise ja SQL Server 2012 asennuksen päälle, käyttöjärjestelmänä on Windows Server 2012. Sharepoint -ympäristö on pystytetty pilveen, Amazon Web Serviceen, joka tarjoaa laajan skaala...

  10. Web server with ATMEGA 2560 microcontroller

    Science.gov (United States)

    Răduca, E.; Ungureanu-Anghel, D.; Nistor, L.; Haţiegan, C.; Drăghici, S.; Chioncel, C.; Spunei, E.; Lolea, R.

    2016-02-01

    This paper presents the design and building of a Web Server to command, control and monitor at a distance lots of industrial or personal equipments and/or sensors. The server works based on a personal software. The software can be written by users and can work with many types of operating system. The authors were realized the Web server based on two platforms, an UC board and a network board. The source code was written in "open source" language Arduino 1.0.5.

  11. APPRIS WebServer and WebServices.

    Science.gov (United States)

    Rodriguez, Jose Manuel; Carro, Angel; Valencia, Alfonso; Tress, Michael L

    2015-07-01

    This paper introduces the APPRIS WebServer (http://appris.bioinfo.cnio.es) and WebServices (http://apprisws.bioinfo.cnio.es). Both the web servers and the web services are based around the APPRIS Database, a database that presently houses annotations of splice isoforms for five different vertebrate genomes. The APPRIS WebServer and WebServices provide access to the computational methods implemented in the APPRIS Database, while the APPRIS WebServices also allows retrieval of the annotations. The APPRIS WebServer and WebServices annotate splice isoforms with protein structural and functional features, and with data from cross-species alignments. In addition they can use the annotations of structure, function and conservation to select a single reference isoform for each protein-coding gene (the principal protein isoform). APPRIS principal isoforms have been shown to agree overwhelmingly with the main protein isoform detected in proteomics experiments. The APPRIS WebServer allows for the annotation of splice isoforms for individual genes, and provides a range of visual representations and tools to allow researchers to identify the likely effect of splicing events. The APPRIS WebServices permit users to generate annotations automatically in high throughput mode and to interrogate the annotations in the APPRIS Database. The APPRIS WebServices have been implemented using REST architecture to be flexible, modular and automatic. PMID:25990727

  12. Solution for an Improved WEB Server

    Directory of Open Access Journals (Sweden)

    George PECHERLE

    2009-12-01

    Full Text Available We want to present a solution with maximum performance from a web server,in terms of services that the server provides. We do not always know what tools to useor how to configure what we have in order to get what we need. Keeping the Internetrelatedservices you provide in working condition can sometimes be a real challenge.And with the increasing demand in Internet services, we need to come up with solutionsto problems that occur every day.

  13. Instant Debian build a web server

    CERN Document Server

    Parrella, Jose Miguel

    2013-01-01

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. A concise guide full of step-by-step recipes to teach you how to install and configure a Debian web server.This is an ideal book if you are an administrator on a Development Operations team or infrastructure management, who is passionate about Linux and their Web applications but have no previous experience with Debian or APT-based systems.

  14. Swiss EMBnet node web server

    OpenAIRE

    Falquet, Laurent; Bordoli, Lorenza; Ioannidis, Vassilios; Pagni, Marco; Jongeneel, C. Victor

    2003-01-01

    EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node’, a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets bio...

  15. DISTRIBUTION OF LOAD USING MOBILE AGENT IN DISTRIBUTED WEB SERVERS

    OpenAIRE

    VijayaKumar G. Dhas; V. Rhymend Uthariaraj

    2014-01-01

    The continuing growth of the World-Wide Web is placing increasing demands on popular Web servers. Many of the sites are now using distributed Web servers (i.e., groups of machines) to service the increasing number of client requests, as a single server cannot handle the workload. Incoming client requests must be distributed in some fashion among the machines in the distributed Web server to improve the performance. In the existing work, reducing the high message complexity is a challenge. Thi...

  16. Weather station with a web server

    OpenAIRE

    Repinc, Matej

    2013-01-01

    In this diploma thesis we present the process of making a cheap weather station using Arduino prototyping platform and its functionality. The weather station monitors current temperature, humidity of air and air pressure. The station has its own simple HTTP server that is used to relay current data in two different formats: JSON encoded data and simple HTML website. The weather station can also send data to a pre-defined server used for data collection. We implemented a web site where data an...

  17. ATLAS Tags Web Service calls Athena via Athenaeum Framework

    CERN Document Server

    Hrivnac, J; The ATLAS collaboration

    2010-01-01

    High Energy Physics experiments start using a Web Service style application to access functionality of their main frameworks. Those frameworks, however, are not ready to be executed in a standard Web Service environment as frameworks are too complex, monolithic and use non-standard and non-portable technologies. ATLAS Tag Browser is one of those Web Service. To provide the possibility to extract full ATLAS events from the standard Web Service, we need to access to full ATLAS offline framework - Athena. As Athena cannot run directly within any Web Service, the client server approach has been chosen. Web Service calls Athena remotely over XML-RPC connection using Athenaeum framework. The paper will discuss integration of Athenaeum framework with ATLAS Tag database service, its distributed deployment, monitoring and performance.

  18. Detecting Malicious Web Servers with Honeyclients

    OpenAIRE

    Mahmoud T Qassrawi; Hongli Zhang

    2011-01-01

    Using malicious sites to launch attacks against client user applications is a growing threat in recent years. This led to emergence of new technologies to counter and detect attacks against end user. One of these technologies is honeyclient (aka client honeypot). Honeyclients crawl the Internet to find and identify web servers that exploit client-side vulnerabilities. In this paper, we address honeyclients by studying and analyzing low-interaction and high-interaction honeyclients. We introdu...

  19. UPGRADE OF THE CENTRAL WEB SERVERS

    CERN Multimedia

    WEB Services

    2000-01-01

    During the weekend of the 25-26 March, the infrastructure of the CERN central web servers will undergo a major upgrade.As a result, the web services hosted by the central servers (that is, the services the address of which starts with www.cern.ch) will be unavailable Friday 24th, from 17:30 to 18:30, and may suffer from short interruptions until 20:00. This includes access to the CERN top-level page as well as the services referenced by this page (such as access to the scientific program and events information, or training, recruitment, housing services).After the upgrade, the change will be transparent to the users. Expert readers may however notice that when they connect to a web page starting with www.cern.ch this address is slightly changed when the page is actually displayed on their screen (e.g. www.cern.ch/Press will be changed to Press.web.cern.ch/Press). They should not worry: this behaviour, necessary for technical reasons, is normal.web.services@cern.chTel 74989

  20. A Web Server for MACCS Magnetometer Data

    Science.gov (United States)

    Engebretson, Mark J.

    1998-01-01

    NASA Grant NAG5-3719 was provided to Augsburg College to support the development of a web server for the Magnetometer Array for Cusp and Cleft Studies (MACCS), a two-dimensional array of fluxgate magnetometers located at cusp latitudes in Arctic Canada. MACCS was developed as part of the National Science Foundation's GEM (Geospace Environment Modeling) Program, which was designed in part to complement NASA's Global Geospace Science programs during the decade of the 1990s. This report describes the successful use of these grant funds to support a working web page that provides both daily plots and file access to any user accessing the worldwide web. The MACCS home page can be accessed at http://space.augsburg.edu/space/MaccsHome.html.

  1. A Web-Based Airborne Remote Sensing Telemetry Server Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A Web-based Airborne Remote Sensing Telemetry Server (WARSTS) is proposed to integrate UAV telemetry and web-technology into an innovative communication, command,...

  2. An efficient solution to Web server based automatic packaging

    Institute of Scientific and Technical Information of China (English)

    JIANG Jian-ping; DING Xing-miao

    2004-01-01

    The manfully packaging the content of the web server for down loading is much inefficient.The paper introduced a Web server agent for packaging automitization, which makes self-organization of the content of the pages and free the site administrator from the heavy burden of the manually packaging the web pages downloaded by web browsers. An example was illustrated to show the details of the solution, which was implemented in J2EE architecture.

  3. Detecting Malicious Web Servers with Honeyclients

    Directory of Open Access Journals (Sweden)

    Mahmoud T Qassrawi

    2011-01-01

    Full Text Available Using malicious sites to launch attacks against client user applications is a growing threat in recent years. This led to emergence of new technologies to counter and detect attacks against end user. One of these technologies is honeyclient (aka client honeypot. Honeyclients crawl the Internet to find and identify web servers that exploit client-side vulnerabilities. In this paper, we address honeyclients by studying and analyzing low-interaction and high-interaction honeyclients. We introduce a comparison attributes to evaluate honeyclients by comparing between the two types. Moreover, we present techniques can be used by malicious websites to evade and fingerprint honeyclients, and we make recommendations to overcome these evasion techniques. By analyzing characteristics of honeyclients, we introduce factors to define and measure honeyclients effectiveness.Using malicious sites to launch attacks against client user applications is a growing threat in recent years. This led to emergence of new technologies to counter and detect attacks against end user. One of these technologies is honeyclient (aka client honeypot. Honeyclients crawl the Internet to find and identify web servers that exploit client-side vulnerabilities. In this paper, we address honeyclients by studying and analyzing low-interaction and high-interaction honeyclients. We introduce a comparison attributes to evaluate honeyclients by comparing between the two types. Moreover, we present techniques can be used by malicious websites to evade and fingerprint honeyclients, and we make recommendations to overcome these evasion techniques. By analyzing characteristics of honeyclients, we introduce factors to define and measure honeyclients effectiveness.

  4. IBM WebSphere Application Server 80 Administration Guide

    CERN Document Server

    Robinson, Steve

    2011-01-01

    IBM WebSphere Application Server 8.0 Administration Guide is a highly practical, example-driven tutorial. You will be introduced to WebSphere Application Server 8.0, and guided through configuration, deployment, and tuning for optimum performance. If you are an administrator who wants to get up and running with IBM WebSphere Application Server 8.0, then this book is not to be missed. Experience with WebSphere and Java would be an advantage, but is not essential.

  5. A RESTful Web service interface to the ATLAS COOL database

    International Nuclear Information System (INIS)

    The COOL database in ATLAS is primarily used for storing detector conditions data, but also status flags which are uploaded summaries of information to indicate the detector reliability during a run. This paper introduces the use of CherryPy, a Python application server which acts as an intermediate layer between a web interface and the database, providing a simple means of storing to and retrieving from the COOL database which has found use in many web applications. The software layer is designed to be RESTful, implementing the common CRUD (Create, Read, Update, Delete) database methods by means of interpreting the HTTP method (POST, GET, PUT, DELETE) on the server along with a URL identifying the database resource to be operated on. The format of the data (text, xml etc) is also determined by the HTTP protocol. The details of this layer are described along with a popular application demonstrating its use, the ATLAS run list web page.

  6. Web Server Security on Open Source Environments

    Science.gov (United States)

    Gkoutzelis, Dimitrios X.; Sardis, Manolis S.

    Administering critical resources has never been more difficult that it is today. In a changing world of software innovation where major changes occur on a daily basis, it is crucial for the webmasters and server administrators to shield their data against an unknown arsenal of attacks in the hands of their attackers. Up until now this kind of defense was a privilege of the few, out-budgeted and low cost solutions let the defender vulnerable to the uprising of innovating attacking methods. Luckily, the digital revolution of the past decade left its mark, changing the way we face security forever: open source infrastructure today covers all the prerequisites for a secure web environment in a way we could never imagine fifteen years ago. Online security of large corporations, military and government bodies is more and more handled by open source application thus driving the technological trend of the 21st century in adopting open solutions to E-Commerce and privacy issues. This paper describes substantial security precautions in facing privacy and authentication issues in a totally open source web environment. Our goal is to state and face the most known problems in data handling and consequently propose the most appealing techniques to face these challenges through an open solution.

  7. DISTRIBUTION OF LOAD USING MOBILE AGENT IN DISTRIBUTED WEB SERVERS

    Directory of Open Access Journals (Sweden)

    Vijayakumar G. Dhas

    2014-01-01

    Full Text Available The continuing growth of the World-Wide Web is placing increasing demands on popular Web servers. Many of the sites are now using distributed Web servers (i.e., groups of machines to service the increasing number of client requests, as a single server cannot handle the workload. Incoming client requests must be distributed in some fashion among the machines in the distributed Web server to improve the performance. In the existing work, reducing the high message complexity is a challenge. This study introduces a novel algorithm, which has low message complexity named Load Distribution by dynamically Fixing input to the server using Mobile agent (LDFM which distributes the incoming request, as it arrives from the client world, to avoid overloading of the distributed web servers. LDFM uses prefetch techniques to balance the load among the distributed web servers. Mobile agents are susceptible to failure. This issue is also addressed to bring reliability to the algorithm. The simulation results confirm that the proposed method is reliable. The relative improvement in throughput, comparing with the exiting methods is appreciable.

  8. AN ANALYTICAL STUDY AND SYNTHESIS ON WEB SERVER SECURITY

    Directory of Open Access Journals (Sweden)

    Jyoti Pandey

    2015-10-01

    Full Text Available Web servers are being as a viable means to access Internet-based applications. Latest Approaches to secure Web servers are not much efficient or robust enough to protect and their applications from hackers. There are several approaches and analogies to examine the minimum-security requirements of a system. But The Highly efficient Techniques approaches as Protection profile, a systematic approach Therefore, we derive the Web security components that make a secure Web server from the Web Server Protection Profile. Study of A component-based framework as well as an open source solution has been done subsequently in this paper We believe that after the studying of such a system (implemented and deployed later, it will function reliably and effectively. This work aims at establishing the provable reliability of construction and the feasibility of component-based solutions for the secure Web server. This paper gives a theoretical approach and analogy of Profiling a web server including All three basic security models together( System security, Transmission security & Access Control Systemetc.

  9. GEOGRAPHIC INFORMATION SYSTEM (GIS) WEB SERVER FOR BIODIVERSITY INFORMATION SYSTEM

    OpenAIRE

    IBRAHIM DJAMALUDDIN; POPPY INDRAYANI; YASUHIRO MITANI; SHUICHIRO TAGANE; TETSUKAZU YAHARA

    2016-01-01

    DJAMALUDDIN, I., INDRAYANI, P., MITANI, Y., TAGANE, S. & YAHARA, T. 2015. Geographic Information System (GIS) web server for biodiversity information system. Reinwardtia 14 (2): 249 – 258. — Ecological protection strategies, designed by sharing information and integrating data, play an important role in defining interconnections and interdependencies in research as well as in increasing global awareness. The Geographic Information System (GIS) web server is one technology  solution to imp...

  10. Web Lectures - ATLAS Overview Week

    CERN Multimedia

    Tushar Bhatnagar; Jeremy Herr; Mitch McLachlan; Homer A. Neal

    2007-01-01

    ATLAS Web Archives Web Archives of the ATLAS Overview Week in Glasgow are now available from the University of Michigan portal here. Archives of ATLAS Plenary Sessions, Workshops, Meetings, and Tutorials recorded over the past two years are available via the University of Michigan Lecture Portal. Other recent additions include the ROOT Workshop held at CERN on March 26-27, the Physics Analysis Tools Workshop held in Bergen, Norway on April 23-27, and the CTEQ Workshop: "Physics at the LHC: Early Challenges" held at Michigan State University on May 14-15. Viewing requires a standard Web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the Web or downloaded locally. In addition, you will find access to a variety of general tutorials and events via the portal. Feedback & Suggestions Welcome Suggestions for events or tutorials to record in 2007, as well as feedback on existing archives, is always welcome...

  11. Web server's reliability improvements using recurrent neural networks

    DEFF Research Database (Denmark)

    Madsen, Henrik; Albu, Rǎzvan-Daniel; Felea, Ioan;

    2012-01-01

    In this paper we describe an interesting approach to error prediction illustrated by experimental results. The application consists of monitoring the activity for the web servers in order to collect the specific data. Predicting an error with severe consequences for the performance of a server (the...... result of which is that its functionality becomes totally inaccessible or hard to access for clients) requires measuring the capacity of a server at any given time. This measurement is highly complex, if not impossible. There are several variables which we can measure on a running system, such as: CPU...

  12. Proactive Web Server Protocol for Complaint Assessment

    OpenAIRE

    2014-01-01

    Vulnerability Discovery with attack Injection security threats are increasing for the server software, when software is developed, the software tested for the functionality. Due to unawareness of software vulnerabilities most of the software before pre-Release the software should be thoroughly tested for not only functionality reliability, but should be tested for the security flows (or) vulnerabilities. The approaches such as fuzzers, Fault injection, vulnerabilities scanners, static vulnera...

  13. The Configuration Strategies on Caching for Web Servers

    Institute of Scientific and Technical Information of China (English)

    GUO Chengcheng; ZHANG Li; YAN Puliu

    2006-01-01

    The Web cluster has been a popular solution of network server system because of its scalability and cost effective ness. The cache configured in servers can result in increasing significantly performance. In this paper, we discuss the suitable configuration strategies for caching dynamic content by our experimental results. Considering the system itself can provide support for caching static Web page, such as computer memory cache and disk's own cache, we adopt a special pattern that only caches dynamic Web page in some experiments to enlarge cache space. The paper is introduced three different replacement algorithms in our cache proxy module to test the practical effects of caching dynamic pages under different conditions. The paper is chiefly analyzed the influences of generated time and accessed frequency on caching dynamic Web pages. The paper is also provided the detailed experiment results and main conclusions in the paper.

  14. Improving web server efficiency on commodity hardware

    OpenAIRE

    Beltrán Querol, Vicenç

    2008-01-01

    El ràpid creixement de la Web requereix una gran quantitat de recursos computacionals que han de ser utilitzats eficientment. Avui en dia, els servidors basats en hardware estendard son les plataformes preferides per executar els servidors web, ja que són les plataformes amb millor relació rendiment/cost. El treball presentat en aquesta tesi esta dirigit a millorar la eficàcia en la gestió de recursos dels servidors web actuals. Per assolir els objectius d'aquesta tesis s'ha caracteritzat e...

  15. EarthServer - 3D Visualization on the Web

    Science.gov (United States)

    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

  16. TBI server: a web server for predicting ion effects in RNA folding.

    Directory of Open Access Journals (Sweden)

    Yuhong Zhu

    Full Text Available Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects.The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects.By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

  17. A New Web-based Application Optimization Model in Multicore Web Server

    Science.gov (United States)

    You, Guohua; Zhao, Ying

    More and more web servers adopt multi-core CPUs to improve performance because of the development of multi-core technology. However, web applications couldn't exploit the potential of multi-core web server efficiently because of traditional processing algorithm of requests and scheduling strategies of threads in O/S. In this paper, a new web-based application optimization model was proposed, which could classify and schedule the dynamic requests and static requests on scheduling core, and process the dynamic requests on the other cores. By this way, a simulation program, which is called SIM, was developed. Experiments have been done to validate the new model, and the results show that the new model can effectively improve the performance of multi-core web servers, and avoid the problems of ping-pong effect.

  18. Kelayakan Raspberry Pi sebagai Web Server: Perbandingan Kinerja Nginx, Apache, dan Lighttpd pada Platform Raspberry Pi

    Directory of Open Access Journals (Sweden)

    Rahmad Dawood

    2014-04-01

    Full Text Available Raspberry Pi is a small-sized computer, but it can function like an ordinary computer. Because it can function like a regular PC then it is also possible to run a web server application on the Raspberry Pi. This paper will report results from testing the feasibility and performance of running a web server on the Raspberry Pi. The test was conducted on the current top three most popular web servers, which are: Apache, Nginx, and Lighttpd. The parameters used to evaluate the feasibility and performance of these web servers were: maximum request and reply time. The results from the test showed that it is feasible to run all three web servers on the Raspberry Pi but Nginx gave the best performance followed by Lighttpd and Apache.Keywords: Raspberry Pi, web server, Apache, Lighttpd, Nginx, web server performance

  19. Web Server Suite for Complex Mixture Analysis by Covariance NMR

    OpenAIRE

    Zhang, Fengli; Robinette, Steve; Bruschweiler-Li, Lei; Brüschweiler, Rafael

    2009-01-01

    Elucidation of the chemical composition of biological samples is a main focus of systems biology and metabolomics. Their comprehensive study requires reliable, efficient, and automatable methods to identify and quantify the underlying metabolites. Because nuclear magnetic resonance (NMR) spectroscopy is a rich source of molecular information, it has a unique potential for this task. Here we present a suite of public web servers (http://spinportal.magnet.fsu.edu), termed COLMAR, that facilitat...

  20. Software Aging Analysis of Web Server Using Neural Networks

    Directory of Open Access Journals (Sweden)

    G.Sumathi

    2012-05-01

    Full Text Available Software aging is a phenomenon that refers to progressive performance degradation or transient failures or even crashes in long running software systems such as web servers. It mainly occurs due to the deterioration of operating system resource, fragmentation and numerical error accumulation. A primitive method to fight against software aging is software rejuvenation. Software rejuvenation is a proactive fault management technique aimed at cleaning up the system internal state to prevent the occurrence of more severe crash failures in the future. It involves occasionally stopping the running software, cleaning its internal state and restarting it. An optimized schedule for performing the software rejuvenation has to be derived in advance because a long running application could not be put down now and then as it may lead to waste of cost. This paper proposes a method to derive an accurate and optimized schedule for rejuvenation of a web server (Apache by using Radial Basis Function (RBF based Feed Forward Neural Network, a variant of Artificial Neural Networks (ANN. Aging indicators are obtained through experimental setup involving Apache web server and clients, which acts as input to the neural network model. This method is better than existing ones because usage of RBF leads to better accuracy and speed in convergence.

  1. Software Aging Analysis of Web Server Using Neural Networks

    Directory of Open Access Journals (Sweden)

    G.Sumathi

    2012-06-01

    Full Text Available Software aging is a phenomenon that refers to progressive performance degradation or transient failures or even crashes in long running software systems such as web servers. It mainly occurs due to the deterioration of operating system resource, fragmentation and numerical error accumulation. A primitive method to fight against software aging is software rejuvenation. Software rejuvenation is a proactive fault management technique aimed at cleaning up the system internal state to prevent the occurrence of more severe crash failures in the future. It involves occasionally stopping the running software, cleaning its internal state and restarting it. An optimized schedule for performing the software rejuvenation has to be derived in advance because a long running application could not be put down now and then as it may lead to waste of cost. This paper proposes a method to derive an accurate and optimized schedule for rejuvenation of a web server (Apache by using Radial Basis Function (RBF based Feed Forward Neural Network, a variant of Artificial Neural Networks (ANN. Aging indicators are obtained through experimental setup involving Apache web server and clients, which acts as input to the neural network model. This method is better than existing ones because usage of RBF leads to better accuracy and speed in convergence.

  2. Web application for monitoring mainframe computer, Linux operating systems and application servers

    OpenAIRE

    DIMNIK, TOMAŽ

    2016-01-01

    This work presents the idea and the realization of web application for monitoring the operation of the mainframe computer, servers with Linux operating system and application servers. Web application is intended for administrators of these systems, as an aid to better understand the current state, load and operation of the individual components of the server systems.

  3. Design and Implementation of A Dynamic Content Cache Module for Web Server

    Institute of Scientific and Technical Information of China (English)

    LIU Dan; GUO Cheng-cheng; ZHANG Li

    2004-01-01

    Web offers a very convenient way to access remote information resources, an important measurement of evaluating Web services quality is how long it takes to search and get information.By caching the Web server's dynamic content, it can avoid repeated queries for database and reduce the access frequency of original resources, thus to improve the speed of server's response.This paper describes the concept, advantages, principles and concrete realization procedure of a dynamic content cache module for Web server.

  4. ACFIS: a web server for fragment-based drug discovery.

    Science.gov (United States)

    Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

    2016-07-01

    In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown 'chemical space' to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for 'chemical space', which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. PMID:27150808

  5. Oracle WebLogic Server 12c advanced administration cookbook

    CERN Document Server

    Iwazaki, Dalton

    2013-01-01

    Using real life problems and simple solutions this book will make any issue seem small. WebLogic Server books can be a bit dry but Dalton keeps the tone light and ensures no matter how complex the problem you always feel like you have someone right there with you helping you along.This book is ideal for those who know the basics of WebLogic but want to dive deeper and get to grips with more advanced topics. So if you are a datacenter operator, system administrator or even a Java developer this book could be exactly what you are looking for to take you one step further with Oracle WebLogic Serv

  6. CloudGenius: Decision Support for Web Server Cloud Migration

    CERN Document Server

    Menzel, Michael

    2012-01-01

    Cloud computing is the latest computing paradigm that delivers hardware and software resources as virtualized services in which users are free from the burden of worrying about the low-level system administration details. Migrating Web applications to Cloud services and integrating Cloud services into existing computing infrastructures is non-trivial. It leads to new challenges that often require innovation of paradigms and practices at all levels: technical, cultural, legal, regulatory, and social. The key problem in mapping Web applications to virtualized Cloud services is selecting the best and compatible mix of software images (e.g., Web server image) and infrastructure services to ensure that Quality of Service (QoS) targets of an application are achieved. The fact that, when selecting Cloud services, engineers must consider heterogeneous sets of criteria and complex dependencies between infrastructure services and software images, which are impossible to resolve manually, is a critical issue. To overcom...

  7. High-Performance Tiled WMS and KML Web Server

    Science.gov (United States)

    Plesea, Lucian

    2007-01-01

    This software is an Apache 2.0 module implementing a high-performance map server to support interactive map viewers and virtual planet client software. It can be used in applications that require access to very-high-resolution geolocated images, such as GIS, virtual planet applications, and flight simulators. It serves Web Map Service (WMS) requests that comply with a given request grid from an existing tile dataset. It also generates the KML super-overlay configuration files required to access the WMS image tiles.

  8. WebSphere Application Server Step by Step

    CERN Document Server

    Cline, Owen; Van Sickel, Peter

    2012-01-01

    WebSphere Application Server (WAS) is complex and multifaceted middleware used by huge enterprises as well as small businesses. In this book, the authors do an excellent job of covering the many aspects of the software. While other books merely cover installation and configuration, this book goes beyond that to cover the critical verification and management process to ensure a successful installation and implementation. It also addresses all of the different packages-from Express to Network-so that no matter what size your company is, you will be able to successfully implement WAS V6. To de

  9. The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences

    DEFF Research Database (Denmark)

    Seemann, Ernst Stefan; Menzel, Karl Peter; Backofen, Rolf;

    2011-01-01

    to interactive usage of the predictors. Additionally, the web servers provide direct access to annotated RNA alignments, such as the Rfam 10.0 database and multiple alignments of 16 vertebrate genomes with human. The web servers are freely available at: http://rth.dk/resources/petfold/...... gene. We present web servers to analyze multiple RNA sequences for common RNA structure and for RNA interaction sites. The web servers are based on the recent PET (Probabilistic Evolutionary and Thermodynamic) models PETfold and PETcofold, but add user friendly features ranging from a graphical layer...

  10. Weighted fair queueing scheduling for World Wide Web proxy servers

    Science.gov (United States)

    El Abdouni Khayari, Rachid; Sadre, Ramin; Haverkort, Boudewijn R.; Zoschke, Norman

    2002-07-01

    Current world-wide web servers as well as proxy servers rely for their scheduling on services provided by the underlying operating system. In practice, this means that some form of first-come-first-served (FCFS) scheduling is utilised. Although FCFS is a reasonable scheduling strategy for job sequences that do not show much variance, in the world-wide web (WWW), however, it has been shown that the typical object sizes requested do exhibit heavy tails. This means that the probability to observe very long jobs (very large objects) is much higher than typically predicted using an exponential model. Under these circumstances, job scheduling on the basis of shortest-job first (SJF) has been shown to perform much better, in fact, to minimise the total average waiting time, simply by avoiding situations in which short jobs have to wait for very long one. However, SJF has as disadvantage that long jobs might suffer from starvation. In order to avoid the problems of both FCFS and SJF we present in this paper a new scheduling algorithm called class-based interleaving weighted fair queueing (CI-WFQ). This algorithm uses the specific characteristics of the job stream being served, that is, the distribution of the sizes of the objects being requested, to set its parameters such that good mean reponse times are obtained and starvation does not occur. In the paper, the new scheduling approach is introduced and compared, using trace-driven simulations, with existing scheduling approaches.

  11. A Web-Server of Cell Type Discrimination System

    Directory of Open Access Journals (Sweden)

    Anyou Wang

    2014-01-01

    Full Text Available Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs, induced pluripotent stem cells (iPSCs, and somatic cells (SCs. Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

  12. A web-server of cell type discrimination system.

    Science.gov (United States)

    Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

    2014-01-01

    Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

  13. WAMI: a web server for the analysis of minisatellite maps

    Directory of Open Access Journals (Sweden)

    El-Kalioby Mohamed

    2010-06-01

    Full Text Available Abstract Background Minisatellites are genomic loci composed of tandem arrays of short repetitive DNA segments. A minisatellite map is a sequence of symbols that represents the tandem repeat array such that the set of symbols is in one-to-one correspondence with the set of distinct repeats. Due to variations in repeat type and organization as well as copy number, the minisatellite maps have been widely used in forensic and population studies. In either domain, researchers need to compare the set of maps to each other, to build phylogenetic trees, to spot structural variations, and to study duplication dynamics. Efficient algorithms for these tasks are required to carry them out reliably and in reasonable time. Results In this paper we present WAMI, a web-server for the analysis of minisatellite maps. It performs the above mentioned computational tasks using efficient algorithms that take the model of map evolution into account. The WAMI interface is easy to use and the results of each analysis task are visualized. Conclusions To the best of our knowledge, WAMI is the first server providing all these computational facilities to the minisatellite community. The WAMI web-interface and the source code of the underlying programs are available at http://www.nubios.nileu.edu.eg/tools/wami.

  14. WebMGA: a customizable web server for fast metagenomic sequence analysis

    Directory of Open Access Journals (Sweden)

    Niu Beifang

    2011-09-01

    Full Text Available Abstract Background The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. Results We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis. Conclusions WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.

  15. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Lyngsø, Rune B.; Gorodkin, Jan

    2005-01-01

    FOLDALIGN is a Sankoff-based algorithm for making structural alignments of RNA sequences. Here, we present a web server for making pairwise alignments between two RNA sequences, using the recently updated version of FOLDALIGN. The server can be used to scan two sequences for a common structural R...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

  16. A STUDY AND REASEARCH ON MONITORING SYSTEM AND EMBEDDED WEB SERVER BASED AUTOMATION

    OpenAIRE

    V.Sai Kishore*

    2015-01-01

    Instead of PC based servers; ARM processor based servers are becoming trend of today’s market. Cost reduction is achieved using ARM processor along with Ethernet module as Embedded Web Server. Idea is utilized for monitoring and controlling maximum no. of either home appliances or industry devices. Without using a computer, Ethernet module can communicate to the owner of the overall system, who is able to manage appliances from any location outside. This server provides a powerful...

  17. An Authentication system of Web Services Based on Web Server Log Analysis

    Directory of Open Access Journals (Sweden)

    R. Joseph Manoj

    2014-01-01

    Full Text Available Authentication is a method which validates users' identity prior to permitting them to access the web services. To enhance the security of web services, providers follow varieties of authentication methods to restrict malicious users from accessing the services. This paper proposes a new authentication method which claims user’s identity by analyzing web server log files which includes the details of requesting user’s IP address, username, password, date and time of request, status code, URL etc., and checks IP address spoofing using ingress packet filtering method. This paper also analyses the resultant data and performance of the proposed work.

  18. Using Web Server Logs to Track Users through the Electronic Forest

    Science.gov (United States)

    Coombs, Karen A.

    2005-01-01

    This article analyzes server logs, providing helpful information in making decisions about Web-based services. The author indicates, as a result of analyzing server logs, several interesting things about the users' behavior were learned. The resulting findings are discussed in this article. Certain pages of the author's Web site, for instance, are…

  19. Responsive + Server Side, a multi-device targeting web application optimization strategy

    OpenAIRE

    Lindell, Jóhann

    2015-01-01

    The purpose of this project is to investigate RESS, Responive + Server Side, a startegy for serving optimized web content to different types of end user devices. RESS is also compared to other mutli-device targeting solutions, Responisve Web Design and Server Side Adaptation, from different points of view, such as performance and workload.

  20. Web-scale Topic Models in Spark: An Asynchronous Parameter Server

    OpenAIRE

    Jagerman, Rolf; Eickhoff, Carsten

    2016-01-01

    In this paper, we train a Latent Dirichlet Allocation (LDA) topic model on the ClueWeb12 data set, a 27-terabyte Web crawl. We extend Spark, a popular framework for performing large-scale data analysis, with an asynchronous parameter server. Such a parameter server provides a distributed and concurrently accessed parameter space for the model. A Metropolis-Hastings based collapsed Gibbs sampler is implemented using this parameter server achieving an amortized O(1) sampling complexity. We comp...

  1. Analysis of Compute Vs Retrieve Intensive Web Applications and Its Impact On The Performance Of A Web Server

    Directory of Open Access Journals (Sweden)

    Syed Mutahar Aaqib

    2012-01-01

    Full Text Available The World Wide Web (WWW has undergone remarkable change over the past few years, placing substantially heavy load on Web servers. Today’s web servers host web applications that demand high computational resources. Also some applications require heavy database retrieval processing, making server load even more critical. In this paper, performance of Apache web server running compute and retrieve-intensive web workloads is analyzed. Workload files implemented in three dynamic web programming technologies: PERL, PHP and Java Servlets are used with MySQL acting as a data source. Measurements are performed with the intent to analyze the impact of application workloads on the overall performance of the web server and determine which web technology yields better performance on Windows and Linux platforms. Experimental results depict that for both compute and retrieve intensive applications, PHP exhibits better performance than PERL and Java Servlets. A multiple linear regression model was also developed to predict the web server performance and to validate the experimental results. This regression model showed that for compute and retrieve intensive web applications, PHP exhibits better performance than Perl and Java Servlets.

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

    Science.gov (United States)

    Lyapin, Sergey; Kukovyakin, Alexey

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

  3. Getting started with Oracle WebLogic Server 12c developer's guide

    CERN Document Server

    Nunes, Fabio Mazanatti

    2013-01-01

    Getting Started with Oracle WebLogic Server 12c is a fast-paced and feature-packed book, designed to get you working with Java EE 6, JDK 7 and Oracle WebLogic Server 12c straight away, so start developing your own applications.Getting Started with Oracle WebLogic Server 12c: Developer's Guide is written for developers who are just getting started, or who have some experience, with Java EE who want to learn how to develop for and use Oracle WebLogic Server. Getting Started with Oracle WebLogic Server 12c: Developer's Guide also provides a great overview of the updated features of the 12c releas

  4. Research on Scheduling Algorithms in Web Cluster Servers

    Institute of Scientific and Technical Information of China (English)

    LEI YingChun (雷迎春); GONG YiLi (龚奕利); ZHANG Song (张松); LI GuoJie (李国杰)

    2003-01-01

    This paper analyzes quantitatively the impact of the load balance scheduling algorithms and the locality scheduling algorithms on the performance of Web cluster servers, and brings forward the Adaptive_LARD algorithm. Compared with the representative LARD algorithm, the advantages of the Adaptive_LARD are that: (1) it adjusts load distribution among the back-ends through the idea of load balancing to avoid learning steps in the LARD algorithm and reinforce its adaptability; (2) by distinguishing between TCP connections accessing disks and those accessing cache memory, it can estimate the impact of different connections on the back-ends' load more precisely. Performance evaluations suggest that the proposed method outperforms the LARD algorithm by up to 14.7%.

  5. World wide web implementation of the Langley technical report server

    Science.gov (United States)

    Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.

    1994-01-01

    On January 14, 1993, NASA Langley Research Center (LaRC) made approximately 130 formal, 'unclassified, unlimited' technical reports available via the anonymous FTP Langley Technical Report Server (LTRS). LaRC was the first organization to provide a significant number of aerospace technical reports for open electronic dissemination. LTRS has been successful in its first 18 months of operation, with over 11,000 reports distributed and has helped lay the foundation for electronic document distribution for NASA. The availability of World Wide Web (WWW) technology has revolutionized the Internet-based information community. This paper describes the transition of LTRS from a centralized FTP site to a distributed data model using the WWW, and suggests how the general model for LTRS can be applied to other similar systems.

  6. The integration of web technology at ATLAS

    International Nuclear Information System (INIS)

    ATLAS (Argonne Tandem Linear Accelerator System) accelerates heavy-ion elements, and consists of 2 separate ion source injectors, 64 superconducting resonators, and 3 target areas. As with any complex accelerator facility, database management systems are used extensively to support both the archival of operational data, and the realtime control needs of the accelerator. Web technology has recently been integrated into the already existing ATLAS Oracle Rdb database system and control system documentation to enhance communication with the operators, control system engineers, and other technical support staff at ATLAS. This paper reviews the historical development of the control system database structure and user interface, and the Internet software developer tools used to create a new online interface

  7. Server Interface Descriptions for Automated Testing of JavaScript Web Applications

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Møller, Anders; Su, Zhendong

    2013-01-01

    communication patterns from sample data. By incorporating interface descriptions into the testing tool Artemis, our experimental results show that we increase the level of automation for high-coverage testing on a collection of JavaScript web applications that exchange JSON data between the clients and servers......Automated testing of JavaScript web applications is complicated by the communication with servers. Specifically, it is difficult to test the JavaScript code in isolation from the server code and database contents. We present a practical solution to this problem. First, we demonstrate that formal...... server interface descriptions are useful in automated testing of JavaScript web applications for separating the concerns of the client and the server. Second, to support the construction of server interface descriptions for existing applications, we introduce an effective inference technique that learns...

  8. New Web Server - the Java Version of Tempest - Produced

    Science.gov (United States)

    York, David W.; Ponyik, Joseph G.

    2000-01-01

    A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

  9. Web Application Security Detection of Misconfigurations in CERN servers

    CERN Document Server

    Durieux, Thomas

    2014-01-01

    CERN owns a large server farm (more than 10 000 servers). It's important to keep all servers configured and to detect vulnerabilities before malicious people. Considered the number of servers it is impossible to check them manually. So scripts are created to automatically detect vulnerabilities and misconfiguration. The final goal is to directly notify server administrator when issues are found. To achieve this goal, scripts must be extremely reliable in orther to not waste everyone's time. The reliability can only be reached by a long manually analyzis of CERN servers. The analyzis is also helping to determine the best way to detect issues and vulnerabilities.

  10. Analysis of Server Log by Web Usage Mining for Website Improvement

    OpenAIRE

    Navin Kumar Tyagi; A. K. Solanki; Manoj Wadhwa

    2010-01-01

    Web server logs stores click stream data which can be useful for mining purposes. The data is stored as a result of user's access to a website. Web usage mining an application of data mining can be used to discover user access patterns from weblog data. The obtained results are used in different applications like, site modifications, business intelligence, system improvement and personalization. In this study, we have analyzed the log files of smart sync software web server to get information...

  11. The Scalable Brain Atlas: instant web-based access to public brain atlases and related content

    OpenAIRE

    Bakker, R.; Tiesinga, P.; Kotter, R.

    2013-01-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when...

  12. Entwicklung einer lokalen Suchmaschine mit dem Web Application Server von Oracle 8

    OpenAIRE

    Weide, Jury Guido

    2003-01-01

    Die vorliegende Diplomarbeit beschäftigt sich mit dem Web Application Servers in der Version 3.0 von Oracle. Der Web Application Server ist ein Programmpaket für die Entwicklung und Implementation von serverseitigen Anwendungsprogrammen, die über das Internet benutzt werden können. Das entsprechende Anwendungsprogramm wird nur vom Webserver ausgeführt. Für die Ausführung einer mit Hilfe des Web Application Server erstellten Anwendung wird auf der Clientseite nur ein Internetbrowser benötigt. ...

  13. Upgrading the SSL protocol to TLS in the Roxen WebServer

    OpenAIRE

    Svensson, Pär

    2002-01-01

    The company Roxen Internet Software have an implementation of the secure network protocol SSL (Secure Sockets Layer) which is used in their web server product. This report describes the upgrading of that implementation to the TLS1.0 (Transport Layer Security) standard. It also describes a performance investigation of the SSL/TLS support in the Roxen WebServer and compares it with other common web servers. The initial setup time for the secure SSL/TLS connection was found to be very long in th...

  14. Analysis of Server Log by Web Usage Mining for Website Improvement

    Directory of Open Access Journals (Sweden)

    Navin Kumar Tyagi

    2010-07-01

    Full Text Available Web server logs stores click stream data which can be useful for mining purposes. The data is stored as a result of user's access to a website. Web usage mining an application of data mining can be used to discover user access patterns from weblog data. The obtained results are used in different applications like, site modifications, business intelligence, system improvement and personalization. In this study, we have analyzed the log files of smart sync software web server to get information about visitors; top errors which can be utilized by system administrator and web designer to increase the effectiveness of the web site.

  15. Design and implementation of web server soft load balancing in small and medium-sized enterprise

    Science.gov (United States)

    Yan, Liu

    2011-12-01

    With the expansion of business scale, small and medium-sized enterprises began to use information platform to improve their management and competition ability, the server becomes the core factor which restricts the enterprise's infomationization construction. This paper puts forward a suitable design scheme for small and medium-sized enterprise web server soft load balancing, and proved it effective through experiment.

  16. EnviroAtlas - Austin, TX - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas...

  17. EnviroAtlas - Des Moines, IA - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). This EnviroAtlas...

  18. C#: Connecting a Mobile Application to Oracle Server via Web Services

    Directory of Open Access Journals (Sweden)

    Daniela Ilea

    2008-01-01

    Full Text Available This article is focused on mobile development using Visual Studio 2005, web services and their connection to Oracle Server, willing to help programmers to realize simple and useful mobile applications.

  19. C# - Connecting a Mobile Application to Oracle Server via Web Services

    OpenAIRE

    Daniela Ilea

    2009-01-01

    This article is focused on mobile development using Visual Studio 2005, web services and their connection to Oracle Server, willing to help programmers to realize simple and useful mobile applications.

  20. 3Drefine: an interactive web server for efficient protein structure refinement.

    Science.gov (United States)

    Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

    2016-07-01

    3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

  1. The Web Lecture Archive Project: Archiving ATLAS Presentations and Tutorials

    CERN Multimedia

    Herr, J

    2004-01-01

    The geographical diversity of the ATLAS Collaboration presents constant challenges in the communication between and training of its members. One important example is the need for training of new collaboration members and/or current members on new developments. The Web Lecture Archive Project (WLAP), a joint project between the University of Michigan and CERN Technical Training, has addressed this challenge by recording ATLAS tutorials in the form of streamed "Web Lectures," consisting of synchronized audio, video and high-resolution slides, available on demand to anyone in the world with a Web browser. ATLAS software tutorials recorded by WLAP include ATHENA, ATLANTIS, Monte Carlo event generators, Object Oriented Analysis and Design, GEANT4, and Physics EDM and tools. All ATLAS talks, including both tutorials and meetings are available at http://www.wlap.org/browser.php?ID=atlas. Members of the University of Michigan Physics Department and Media Union, under the framework of the ATLAS Collaboratory Project ...

  2. Server Technology – Web Based Service Oriented Architecture for Mobile Augmented Reality System

    Directory of Open Access Journals (Sweden)

    Jatin Dilipkumar Shah

    2012-11-01

    Full Text Available Server Technology stands for lots of technology in mind like Microsoft, Sun Java, IBM, Open Source and many more. In mobile augmentation, server plays very important role to augment the data. Responsibility of the server is to collect the data , mixed virtual data with real data and these data sent back to client on Remote device at Remote place In this paper we briefly discuss about the server technology for web based Service oriented, also the processing software required for augmentation, it’s software technology, how they accept input from various types of devices and generated output data of various types like audio, video, 3-D graphics.

  3. A J2EE based server for muon spectrometer alignment monitoring in the ATLAS detector

    International Nuclear Information System (INIS)

    We describe the software chain for the Atlas muon optical alignment system, dedicated to the measurement of geometry corrections for the Muon Spectrometer chambers positions. The corrections are then used inside the reconstruction software. We detail in particular the architecture of the monitoring application, deployed in a J2EE server, and the monitoring tools that have been developed for the daily follow up. The system has been in production during the whole Run 1 period (2010-2013).

  4. Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology

    Science.gov (United States)

    Ritschel, Bernd; Seelus, Christoph; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; King, Todd; Hughes, John; Fung, Shing; Galkin, Ivan; Hapgood, Michael; Belehaki, Anna

    2015-04-01

    Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology European Union ESPAS, Japanese IUGONET and GFZ ISDC data server are developed for the ingestion, archiving and distributing of geo and space science domain data. Main parts of the data -managed by the mentioned data server- are related to near earth-space and geomagnetic field data. A smart mashup of the data server would allow a seamless browse and access to data and related context information. However the achievement of a high level of interoperability is a challenge because the data server are based on different data models and software frameworks. This paper is focused on the latest experiments and results for the mashup of the data server using the semantic Web approach. Besides the mashup of domain and terminological ontologies, especially the options to connect data managed by relational databases using D2R server and SPARQL technology will be addressed. A successful realization of the data server mashup will not only have a positive impact to the data users of the specific scientific domain but also to related projects, such as e.g. the development of a new interoperable version of NASA's Planetary Data System (PDS) or ICUS's World Data System alliance. ESPAS data server: https://www.espas-fp7.eu/portal/ IUGONET data server: http://search.iugonet.org/iugonet/ GFZ ISDC data server (semantic Web based prototype): http://rz-vm30.gfz-potsdam.de/drupal-7.9/ NASA PDS: http://pds.nasa.gov ICSU-WDS: https://www.icsu-wds.org

  5. ATLAS BASEMAPS IN WEB 2.0 EPOCH

    OpenAIRE

    Chabaniuk, V.; Dyshlyk, O.

    2016-01-01

    The authors have analyzed their experience of the production of various Electronic Atlases (EA) and Atlas Information Systems (AtIS) of so-called "classical type". These EA/AtIS have been implemented in the past decade in the Web 1.0 architecture (e.g., National Atlas of Ukraine, Atlas of radioactive contamination of Ukraine, and others). One of the main distinguishing features of these atlases was their static nature - the end user could not change the content of EA/AtIS. Base maps ar...

  6. Servicing the first web server - Tim Berners-Lee's NeXT

    CERN Multimedia

    unknown, Association aBCM

    2009-01-01

    In August 2009 a team from the Association aBCM in Lausanne came to CERN to give the world's first web server a health check under the watchful eye of web pioneer Robert Cailliau. They took an image of the hard drive at this time, copies of which were given to Robert Cailliau and Tim Berners-Lee.

  7. A Price-based Web Servers Desing with Load and Cache Prediction%基于价格和信息预测的Web Servers设计

    Institute of Scientific and Technical Information of China (English)

    周刚; 李天宁; 陈道蓄; 谢立

    2001-01-01

    Increasing WWW visits require efficient Web Servers architecture. In our design, Web Servers are a cluster consisting of replicated Servers. Server predicates its load ,which is used to decide the cost to visit itself. Client makes the load balancing decision ,and caches the predicated load of Cluster. Based on price theory, Client chooses the server of the lowest cost to serve itself;at the same time,Server predicates the information updating speed of Cluster,and uses it to decide the updating speed of Cache. Finally ,the system topology is given and characters are analyzed.

  8. An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

    Science.gov (United States)

    Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

    2000-01-01

    This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

  9. Remote Multimedia Monitoring System Based on Embedded Web Server for Networked Manufacturing

    Institute of Scientific and Technical Information of China (English)

    HEDeqiang; YANGYu; 等

    2002-01-01

    A new-style remote monitoring system is propsed.which is based on enterprises' embedded wed servers and can be widely used in enterprises' networked manufactureing systems.The principle and characteristics of remote monitoring system based on embedded web server are analyzed.Such a kind of system for networked manufacturing is designed ,and it proves efficient and feasible in promoting communication among enterprises,improving designing and scheduling,decreasing facility failure and reducing product cost.

  10. Design and Implementation of a Secure Web-Based File Exchange Server: Specification Design Document

    CERN Document Server

    Mokhov, Serguei A; Benssam, Ali; Benredjem, Djamel

    2011-01-01

    We report on the software engineering design and implementation of an web- and LDAP-based secure file exchange system with bi-directional authentication of all parties involved in the process that is the user's browsers and the application server mutually authenticate, and the application and database servers authenticate using certificates, credentials, etcs. with the directory service provided by LDAP using open-source technologies.

  11. A performance and installation research in web server solutions for small e-commerce systems.

    OpenAIRE

    Shirazi, Erfan; Håkansson, Mattias; Abels, Christian

    2004-01-01

    This thesis investigates two different web server solutions. One is a commercial, proprietary solution known as the Windows solution that consists of Windows Server 2003, IIS and ASP. The other is a free, open source solution consisting of FreeBSD, Apache and PHP. The both solutions had the database MySQL as a common component. The hypothesis that was used in this investigation is as follows: IIS on Windows Server is not better than Apache on FreeBSD for e-commerce systems. To answer the hypo...

  12. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    OpenAIRE

    van der Schot, Gijs; Bonvin, Alexandre M. J. J.

    2016-01-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi:10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 ...

  13. A Robust IP Packets Filtering Mechanism for Protecting Web Server from DDoS Attacks

    Institute of Scientific and Technical Information of China (English)

    WU Qingtao; SHAO Zhiqing; DING Zhiyi; LIU Gang

    2006-01-01

    Distributed denial of service (DDoS) attacks exploit the availability of Web servers, resulting in the severe loss of their connectivity. We present a robust IP packets filtering mechanism which combines the detection and filtering engine together to protect Web Servers from DDoS Attacks. The mechanism can detect DDoS attacks by inspecting inbound packets with an IP address database, and filter out lower priority IP addresses to preserve the connection for valid users by monitoring the queue's status. We use the Netfilter's technique, a framework inside the Linux 2.4.X, to implement it on a Web server. Also, we evaluate this mechanism and analyze the influence of some important parameters on system performance. The experimental results show that this mechanism is effective against DDoS attacks.

  14. Web Exhibition – ATLASES: Poetics, Politics, and Performance

    Directory of Open Access Journals (Sweden)

    Nedjeljko Frančula

    2013-12-01

    Full Text Available ATLASES: Poetics, Politics, and Performance is a web exhibition of atlases from the Special Collections and School of Geographical Sciences of the University of Bristol (http://uobatlases.net/. It includes atlases produced between 1570 to approximately 1970.The exhibition consists of four thematic parts. Renaissance Theatres contains famous and les famous atlases produced between the end of the 16th century to the middle of the 17th century, such as atlases by Ortelius (1574, Camden (1610, Speed (1611 and four atlas tomes by Blaeu (1645. Rhetoric of Truth contains geological and archaeological atlases from the 18th and the beginning of the 19th century. However, Rhetoric of Truth is not only limited to renaissance, but it also encompasses first computer generated atlases, e.g. Atlas of Breeding Birds in England and Ireland (1976 and others. The Colonial Gaze focuses on atlases applied in colonial projects and land exploitation in Africa and the Caribbean Islands, as well as in circulation of race theories in Europe and North America at the end of the 19th century. The last part, National Identities and Conflict explores the role of atlas as a powerful instrument for visualizing conflicts and shaping territorial-political ideas in the 20th century.

  15. Using Kalman Filter to Guarantee QoS Robustness of Web Server

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The exponential growth of the Internet coupled with the increasing popularity of dynamically generated content on the World Wide Web, has created the need for more and faster Web servers capable of serving the over 100 million Internet users. To converge the control method has emerged as a promising technique to solve the Web QoS problem. In this paper, a model of adaptive session is presented and a session flow self-regulating algorism based on Kalman Filter are proposed towards Web Server. And a Web QoS self-regulating scheme is advanced. To attain the goal of on-line system identification, the optimized estimation of QoS parameters is fulfilled by utilizing Kalman Filter in full domain. The simulation results shows that the proposed scheme can guarantee the QoS with both robustness and stability .

  16. AtlasDcsWebViewer: a web access to the Atlas DCS data An introduction manual to the AtlasDcsWebViewer, a web-based tool to query the PVSS Oracle database

    CERN Document Server

    Bitenc, U; The ATLAS collaboration; Ferrari, P; Luisa, L

    2009-01-01

    This note describes how to access the DCS data from a web browser. The DCS data from the various Atlas subdetectors are stored to the Oracle database using the RDB manager in PVSS. All subdetectors use either the same, or a very similar schema. The effort coordinated within the Inner Detector has produced a web-based tool to search the Atlas DCS Oracle database and to display the results. This tool has been easily extended to access the data from other Atlas subdetectors. In this note we describe the structure of the AtlasDcsWebViewer and its use.

  17. X-Switch: An Efficient , Multi-User, Multi-Language Web Application Server

    Directory of Open Access Journals (Sweden)

    Mayumbo Nyirenda

    2010-07-01

    Full Text Available Web applications are usually installed on and accessed through a Web server. For security reasons, these Web servers generally provide very few privileges to Web applications, defaulting to executing them in the realm of a guest ac- count. In addition, performance often is a problem as Web applications may need to be reinitialised with each access. Various solutions have been designed to address these security and performance issues, mostly independently of one another, but most have been language or system-specic. The X-Switch system is proposed as an alternative Web application execution environment, with more secure user-based resource management, persistent application interpreters and support for arbitrary languages/interpreters. Thus it provides a general-purpose environment for developing and deploying Web applications. The X-Switch system's experimental results demonstrated that it can achieve a high level of performance. Further- more it was shown that X-Switch can provide functionality matching that of existing Web application servers but with the added benet of multi-user support. Finally the X-Switch system showed that it is feasible to completely separate the deployment platform from the application code, thus ensuring that the developer does not need to modify his/her code to make it compatible with the deployment platform.

  18. EnviroAtlas - Durham, NC - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). This EnviroAtlas dataset is...

  19. EnviroAtlas - Portland, OR - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (http:/www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  20. EnviroAtlas - Portland, ME - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  1. EnviroAtlas -Phoenix, AZ- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Phoenix, AZ...

  2. EnviroAtlas - Milwaukee, WI - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  3. EnviroAtlas - New Bedford, MA - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  4. EnviroAtlas -- Memphis, TN (2012) -- One Meter Resolution Urban Land Cover Data Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The Memphis, TN EnviroAtlas...

  5. EnviroAtlas - Milwaukee, WI - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  6. EnviroAtlas -- Fresno, California -- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Fresno, CA EnviroAtlas...

  7. EnviroAtlas -Tampa, FL- One Meter Resolution Urban Land Cover (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Tampa, FL...

  8. EnviroAtlas -- Woodbine, IA -- One Meter Resolution Urban Land Cover Data (2011) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Woodbine, IA...

  9. EnviroAtlas -Milwaukee, WI- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Milwaukee, WI...

  10. EnviroAtlas - Fresno, CA - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  11. EnviroAtlas - Phoenix, AZ - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  12. EnviroAtlas - New Bedford, MA - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  13. EnviroAtlas - Rare Ecosystems in the Conterminous United States Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset...

  14. EnviroAtlas -- Austin, TX -- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The Austin, TX EnviroAtlas...

  15. EnviroAtlas - New York, NY - One Meter Resolution Urban Land Cover Data (2008) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The New York, NY EnviroAtlas...

  16. EnviroAtlas - Green Bay, WI - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  17. EnviroAtlas - Paterson, NJ - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  18. EnviroAtlas - Fresno, CA - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  19. EnviroAtlas - Potential Wetland Areas - Contiguous United States Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Potential...

  20. EnviroAtlas - Woodbine, IA - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  1. EnviroAtlas - Portland, OR - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (http:/www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC tree...

  2. EnviroAtlas - Potentially Restorable Wetlands on Agricultural Land - Contiguous United States Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Potentially...

  3. EnviroAtlas - Tampa, FL - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  4. EnviroAtlas - Pittsburgh, PA - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  5. EnviroAtlas -Durham, NC- One Meter Resolution Urban Area Land Cover Map (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The EnviroAtlas Durham, NC...

  6. EnviroAtlas - Woodbine, IA - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  7. EnviroAtlas -Pittsburgh, PA- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas).The EnviroAtlas Pittsburgh, PA...

  8. EnviroAtlas - Dasymetric Population in the Conterminous United States Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset...

  9. EnviroAtlas - Portland, ME - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  10. EnviroAtlas - Durham, NC - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The EnviroAtlas Durham, NC...

  11. EnviroAtlas - Pittsburgh, PA - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  12. EnviroAtlas - Tampa, FL - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  13. EnviroAtlas - Paterson, NJ - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  14. EnviroAtlas - Green Bay, WI - Tree Cover Configuration and Connectivity, Water Background Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The EnviroAtlas Durham, NC...

  15. EnviroAtlas - Potentially Restorable Wetlands in the Conterminous United States Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset...

  16. EnviroAtlas - Phoenix, AZ - Demographics by Block Group Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). This EnviroAtlas dataset is a...

  17. Modeling and analysis of software rejuvenation on dispatcher-based web server farms

    Institute of Scientific and Technical Information of China (English)

    Fan Xinyuan; Xu Guozhi; Ying Rendong; Zhang Hao

    2005-01-01

    Software rejuvenation is a recently proposed practive fault-tolerance approach to counteract software-aging phenomenon. Compared with clusters of a flat architecture, all the nodes share the same functions. The application of software rejuvenation on dispatcher-based web server farms is discussed, which employ rejuvenation both on the dispatcher and the worker pool. Stochastic reward net (SRN)models for time-based and prediction-based rejuvenation policies are constructed respectively and solved by stochastic Petri net package (SPNP). Numerical results show that appropriate rejuvenation strategies on the dispatcher and the worker pool could significantly reduce the expected downtime cost of the whole web server farm.

  18. Biological SOAP servers and web services provided by the public sequence data bank

    OpenAIRE

    Sugawara, H.; Miyazaki, S

    2003-01-01

    A number of biological data resources (i.e. databases and data analytical tools) are searchable and usable on-line thanks to the internet and the World Wide Web (WWW) servers. The output from the web server is easy for us to browse. However, it is laborious and sometimes impossible for us to write a computer program that finds a useful data resource, sends a proper query and processes the output. It is a serious obstacle to the integration of distributed heterogeneous data resources. To solve...

  19. The last ATLAS overview week now available on Web Lectures

    CERN Multimedia

    Jeremy Herr

    2006-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project, WLAP, a collaboration between the University of Michigan and CERN, has developed a synchronized system for recording and publishing educational multimedia presentations, using the Web as medium. This year, the University of Michigan team has been asked to record and publish all ATLAS Plenary sessions, as well as a large number of Physics and Computing tutorials. A significant amount of this material has already been published and can be accessed via the links below. All lectures can be viewed on any major platform with any common internet browser, either via streaming or local download (for limited bandwidth). Please enjoy the lectures and send us a note at wlap@umich.edu to tell us what you think. The newly available WLAP items relating to ATLAS is the following: ATLAS Week Plenary, CERN, 2-3 October 2006 All previous WLAP lectures are also avilable on the web.

  20. Design Architecture-Based on Web Server and Application Cluster in Cloud Environment

    Directory of Open Access Journals (Sweden)

    Gita Shah

    2014-03-01

    Full Text Available Cloud has been a computational and storage solution for many data centric organizations. The problem today those organizations are facing from t he cloud is in data searching in an efficient manner. A framework is required to distribute the w ork of searching and fetching from thousands of computers. The data in HDFS is scatter ed and needs lots of time to retrieve. The major idea is to design a web server in the map pha se using the jetty web server which will give a fast and efficient way of searching data in MapRe duce paradigm. For real time processing on Hadoop, a searchable mechanism is implemented in HD FS by creating a multilevel index in web server with multi-level index keys. The web ser ver uses to handle traffic throughput. By web clustering technology we can improve the applicatio n performance. To keep the work down, the load balancer should automatically be able to distr ibute load to the newly added nodes in the server.

  1. Modeling the Probability of Failure on LDAP Binding Operations in Iplanet Web Proxy 3.6 Server

    OpenAIRE

    De Lara, Alejandro Chinea Manrique

    2010-01-01

    This paper is devoted to the theoretical analysis of a problem derived from interaction between two Iplanet products: Web Proxy Server and the Directory Server. In particular, a probabilistic and stochastic-approximation model is proposed to minimize the occurrence of LDAP connection failures in Iplanet Web Proxy 3.6 Server. The proposed model serves not only to provide a parameterization of the aforementioned phenomena, but also to provide meaningful insights illustrating and supporting thes...

  2. fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.

    Science.gov (United States)

    Tung, Chi-Hua; Yang, Jinn-Moon

    2007-07-01

    The fastSCOP is a web server that rapidly identifies the structural domains and determines the evolutionary superfamilies of a query protein structure. This server uses 3D-BLAST to scan quickly a large structural classification database (SCOP1.71 with structural alignment tool, is adopted to align these top 10 structures to refine domain boundaries and to identify evolutionary superfamilies. Our previous works demonstrated that 3D-BLAST is as fast as BLAST, and has the characteristics of BLAST (e.g. a robust statistical basis, effective search and reliable database search capabilities) in large structural database searches based on a structural alphabet database and a structural alphabet substitution matrix. The classification accuracy of this server is approximately 98% for 586 query structures and the average execution time is approximately 5. This server was also evaluated on 8700 structures, which have no annotations in the SCOP; the server can automatically assign 7311 (84%) proteins (9420 domains) to the SCOP superfamilies in 9.6 h. These results suggest that the fastSCOP is robust and can be a useful server for recognizing the evolutionary classifications and the protein functions of novel structures. The server is accessible at http://fastSCOP.life.nctu.edu.tw. PMID:17485476

  3. HTML5实现Web服务器推送技术%Web Server Push Based on Html5

    Institute of Scientific and Technical Information of China (English)

    吴泽勋

    2014-01-01

    与HTML4及以前的版本相比,HTML5中的WebSocket具有双向通讯功能,能实现Web服务器对客户端的信息推送。要实现WebSocket需要服务器端和客户端双方的支持,客户端主要是浏览器要能实现The WebSocket API草案,而服务器端要能够解析WebSocket协议。因为支持WebSocket协议的Web服务器比较少,所以讨论使用C#语言来建构一个专用的WebSocket服务器。%Compared with HTML4 or previous versions HTML5 WebSocket has two-way communication to realize the Web server to the client information push. In order to realize the WebSocket server and client side’s support, the client browser to the WebSocket is to achieve the API draft, but the server must be able to parse the WebSocket protocol. Because the Web server which supports WebSocket protocol is rare, the construction of a dedicated WebSocket server was discussed by C#.

  4. Comparison of Web Analytics : Hosted Solutions vs Server-side Analytics

    OpenAIRE

    Mutai, Dominic

    2015-01-01

    The ratability of websites allows the aggregation of detailed data about the behavior and characteristics of website visitors. This thesis examines the value of different web metrics based on the analytics tools used and the behavior of website visitors. The objective is to test and identify key metrics and discuss how they compare between hosted solutions and server-side analytics. The value of the web metrics is evaluated by examining the relationships of the metrics to website conversions....

  5. MetaRanker 2.0: a web server for prioritization of genetic variation data

    DEFF Research Database (Denmark)

    Pers, Tune Hannes; Dworzynski, Piotr; Thomas, Cecilia Engel;

    2013-01-01

    MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein–protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, Meta...

  6. Analysis of Java Client/Server and Web Programming Tools for Development of Educational Systems.

    Science.gov (United States)

    Muldner, Tomasz

    This paper provides an analysis of old and new programming tools for development of client/server programs, particularly World Wide Web-based programs. The focus is on development of educational systems that use interactive shared workspaces to provide portable and expandable solutions. The paper begins with a short description of relevant terms.…

  7. KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

    Science.gov (United States)

    Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

    2012-07-01

    The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin. PMID:22564897

  8. Using the PL/SQL Cartridge of the Oracle Application Server to Deploy Web Applications

    Energy Technology Data Exchange (ETDEWEB)

    Begovich, C.L.

    1999-06-14

    Deploying business applications on the internal Web is a priority at Oak Ridge National Laboratory (Lockheed Martin Energy Research) and Lockheed Martin Energy Systems, Inc. as with most corporations. Three separate applications chose the Oracle Application Server (OAS), using the PL/SQL cartridge as a Web deployment method. This method was chosen primarily because the data was already stored in Oracle tables and developers knew HJSQL or at least SQL. The Database Support group had the responsibility of installing, testing, and determining standard methods for interfacing with the PL/SQL cartridge of the OAS. Note that the term Web Application Server was used for version 3, but in this discussion, OAS will be used for both version 3 and version 4.

  9. Mobile HTML5: Efficiency and Performance of WebSockets and Server-Sent Events

    OpenAIRE

    Estep, Eliot

    2013-01-01

    The advent of HTML5 (Hyper Text Markup Language revision 5) technologies are re-standardizing the web and paving the way for a new breed of real-time web applications. This has great potential for mobile browsers that are now supporting protocols such as WebSocket and Server-Sent Events (SSE). These protocols can provide ecient real-time communication in a scalable manner, especially for \\always-on" applications requiring persistent connections that are now widely used. Mobile devices are inh...

  10. Presaging critical residues in protein interfaces-web server (PCRPi-W: a web server to chart hot spots in protein interfaces.

    Directory of Open Access Journals (Sweden)

    Joan Segura Mora

    Full Text Available BACKGROUND: It is well established that only a portion of residues that mediate protein-protein interactions (PPIs, the so-called hot spot, contributes the most to the total binding energy, and thus its identification is an important and relevant question that has clear applications in drug discovery and protein design. The experimental identification of hot spots is however a lengthy and costly process, and thus there is an interest in computational tools that can complement and guide experimental efforts. PRINCIPAL FINDINGS: Here, we present Presaging Critical Residues in Protein interfaces-Web server (http://www.bioinsilico.org/PCRPi, a web server that implements a recently described and highly accurate computational tool designed to predict critical residues in protein interfaces: PCRPi. PRCPi depends on the integration of structural, energetic, and evolutionary-based measures by using Bayesian Networks (BNs. CONCLUSIONS: PCRPi-W has been designed to provide an easy and convenient access to the broad scientific community. Predictions are readily available for download or presented in a web page that includes among other information links to relevant files, sequence information, and a Jmol applet to visualize and analyze the predictions in the context of the protein structure.

  11. The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.

    Science.gov (United States)

    Bakker, Rembrandt; Tiesinga, Paul; Kötter, Rolf

    2015-07-01

    The Scalable Brain Atlas (SBA) is a collection of web services that provide unified access to a large collection of brain atlas templates for different species. Its main component is an atlas viewer that displays brain atlas data as a stack of slices in which stereotaxic coordinates and brain regions can be selected. These are subsequently used to launch web queries to resources that require coordinates or region names as input. It supports plugins which run inside the viewer and respond when a new slice, coordinate or region is selected. It contains 20 atlas templates in six species, and plugins to compute coordinate transformations, display anatomical connectivity and fiducial points, and retrieve properties, descriptions, definitions and 3d reconstructions of brain regions. The ambition of SBA is to provide a unified representation of all publicly available brain atlases directly in the web browser, while remaining a responsive and light weight resource that specializes in atlas comparisons, searches, coordinate transformations and interactive displays. PMID:25682754

  12. pKNOT: the protein KNOT web server

    OpenAIRE

    Lai, Yan-Long; Yen, Shih-Chung; Yu, Sung-Huan; Hwang, Jenn-Kang

    2007-01-01

    Knotted proteins are more commonly observed in recent years due to the enormously growing number of structures in the Protein Data Bank (PDB). Studies show that the knot regions contribute to both ligand binding and enzyme activity in proteins such as the chromophore-binding domain of phytochrome, ketol–acid reductoisomerase or SpoU methyltransferase. However, there are still many misidentified knots published in the literature due to the absence of a convenient web tool available to the gene...

  13. Improving Performance on WWW using Intelligent Predictive Caching for Web Proxy Servers

    Directory of Open Access Journals (Sweden)

    J. B. Patil

    2011-01-01

    Full Text Available Web proxy caching is used to improve the performance of the Web infrastructure. It aims to reduce network traffic, server load, and user perceived retrieval delays. The heart of a caching system is its page replacement policy, which needs to make good replacement decisions when its cache is full and a new document needs to be stored. The latest and most popular replacement policies like GDSF and GDSF# use the file size, access frequency, and age in the decision process. The effectiveness of any replacement policy can be evaluated using two metrics: hit ratio (HR and byte hit ratio (BHR. There is always a trade-off between HR and BHR. In this paper, using three different Web proxy server logs, we use trace driven analysis to evaluate the effects of different replacement policies on the performance of a Web proxy server. We propose a modification of GDSF# policy, IPGDSF#. Our simulation results show that our proposed replacement policy IPGDSF# performs better than several policies proposed in the literature in terms of hit rate as well as byte hit rate.

  14. Architecture of Embedded Web Server%嵌入式Web服务器的构建

    Institute of Scientific and Technical Information of China (English)

    位玉静; 李跃辉; 任勋益; 马晓东; 陈小星

    2011-01-01

    由于嵌入式系统自身的特点,在实际应用中需要实现人机交互的功能,而通过网页可以直观方便地对应用系统进行操作与管理,所以文中探讨了基于一种Web服务器BOA及CGI外部扩展程序构建Web Server的方法.在嵌入式uMnux系统基础之上介绍了BOA的移植配置过程及CGI程序的扩展开发.对BOA及CGI程序进行交叉编译并移植到开发板上,通过主机的浏览器访问Web Server来测试服务器的运行及CGI的执行结果.测试结果表明其运行稳定、控制方便、响应迅速,适合在嵌入式系统中做Web Server.%In practical applications, the embedded system needs to achieve the function of human-computer interaction, aa of the characteristics of itself. Proposed the way to construct the Web Server based on BOA and CGI program in order to resolve the control of the remote central office and terminal equipment. Porting BOA and CGI extension development are based on uCLinux. The BOA and CGI programs are cron-compiled and transplanted into the development board. Through the browser of the host server testing the operation of Web Server, the results of the test show that the BOA running stable,easy to control, quick to answer, reaching to the anticipated design purpose.

  15. Reducing the disk I/O of Web proxy server caches

    CERN Document Server

    Maltzahn, C G; Grunwald, D

    1999-01-01

    The dramatic increase of HTTP traffic on the Internet has resulted in widespread use of large caching proxy servers as critical Internet infrastructure components. With continued growth the demand for larger caches and higher performance proxies grows as well. The common bottleneck of large caching proxy servers is disk I/O. We evaluate ways to reduce the amount of required disk I/O. First we compare the file system interactions of two existing Web proxy servers, CERN and SQUID. Then we show how design adjustments to the current SQUID cache architecture can dramatically reduce disk I/O. Our findings suggest two that strategies can significantly reduce disk I/O: preserve locality of the HTTP reference stream while translating these references into cache references; and use virtual memory instead of the file system for objects smaller than the system page size. The evaluated techniques reduced disk I/O by 50to 70 (33 refs).

  16. CoinFold: a web server for protein contact prediction and contact-assisted protein folding.

    Science.gov (United States)

    Wang, Sheng; Li, Wei; Zhang, Renyu; Liu, Shiwang; Xu, Jinbo

    2016-07-01

    CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction. PMID:27112569

  17. 3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.

    KAUST Repository

    Le Pera, Loredana

    2015-01-22

    Protein-coding genes with multiple alternative polyadenylation sites can generate mRNA 3\\'UTR sequences of different lengths, thereby causing the loss or gain of regulatory elements, which can affect stability, localization and translation efficiency. 3USS is a web-server developed with the aim of giving experimentalists the possibility to automatically identify alternative 3 \\': UTRs (shorter or longer with respect to a reference transcriptome), an option that is not available in standard RNA-seq data analysis procedures. The tool reports as putative novel the 3 \\': UTRs not annotated in available databases. Furthermore, if data from two related samples are uploaded, common and specific alternative 3 \\': UTRs are identified and reported by the server.3USS is freely available at http://www.biocomputing.it/3uss_server.

  18. Comparing speed of Web Map Service with GeoServer on ESRI Shapefile and PostGIS

    Directory of Open Access Journals (Sweden)

    Jan Růžička

    2016-07-01

    Full Text Available There are several options how to configure Web Map Service using severalmap servers. GeoServer is one of most popular map servers nowadays.GeoServer is able to read data from several sources. Very popular datasource is ESRI Shapefile. It is well documented and most of softwarefor geodata processing is able to read and write data in this format.Another very popular data store is PostgreSQL/PostGIS object-relationaldatabase. Both data sources has advantages and disadvantages and userof GeoServer has to decide which one to use. The paper describescomparison of performance of GeoServer Web Map Service when readingdata from ESRI Shapefile or from PostgreSQL/PostGIS database.

  19. Web System for Data Quality Assessment of Tile Calorimeter During the ATLAS Operation

    International Nuclear Information System (INIS)

    TileCal, the barrel hadronic calorimeter of the ATLAS experiment, gathers almost about 10,000 electronic channels. The supervision of the detector behavior is very important in order to ensure proper operation. Collaborators perform analysis over reconstructed data of calibration runs for giving detailed considerations about the equipment status. During the commissioning period, our group has developed seven web systems to support the data quality (DQ) assessment task. Each system covers a part of the process by providing information on the latest runs, displaying the DQ status from the monitoring framework, giving details about power supplies operation, presenting the generated plots and storing the validation outcomes, assisting to write logbook entries, creating and submitting the bad channels list to the conditions database and publishing the equipment performance history. The ATLAS operation increases amount of data that are retrieved, processed and stored by the web systems. In order to accomplish the new requirements, an optimized data model was designed to reduce the number of needed queries. The web systems were reassembled in a unique system in order to provide an integrated view of the validating process. The server load was minimized by using asynchronous requests from the browser.

  20. Mining of Web Server Logs in a Distributed Cluster Using Big Data Technologies

    OpenAIRE

    Savitha K; Vijaya MS

    2014-01-01

    Big Data is an emerging growing dataset beyond the ability of a traditional database tool. Hadoop rides the big data where the massive quantity of information is processed using cluster of commodity hardware. Web server logs are semi-structured files generated by the computer in large volume usually of flat text files. It is utilized efficiently by Mapreduce as it process one line at a time. This paper performs the session identification in log files using Hadoop in a distributed cluster. Apa...

  1. CoMet—a web server for comparative functional profiling of metagenomes

    OpenAIRE

    Lingner, T.; Asshauer, K. P.; Schreiber, F.; Meinicke, P.

    2011-01-01

    Analyzing the functional potential of newly sequenced genomes and metagenomes has become a common task in biomedical and biological research. With the advent of high-throughput sequencing technologies comparative metagenomics opens the way to elucidate the genetically determined similarities and differences of complex microbial communities. We developed the web server ‘CoMet’ (http://comet.gobics.de), which provides an easy-to-use comparative metagenomics platfor...

  2. ProTox: a web server for the in silico prediction of rodent oral toxicity

    OpenAIRE

    Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert

    2014-01-01

    Animal trials are currently the major method for determining the possible toxic effects of drug candidates and cosmetics. In silico prediction methods represent an alternative approach and aim to rationalize the preclinical drug development, thus enabling the reduction of the associated time, costs and animal experiments. Here, we present ProTox, a web server for the prediction of rodent oral toxicity. The prediction method is based on the analysis of the similarity of compounds with known me...

  3. SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

    OpenAIRE

    Jiang Yi; Xie Yang; Ying Jinyong; Xie Dexuan; Yu Zeyun

    2015-01-01

    The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present an SDPBS web server in this paper that allows clients to visualize and manipulate th...

  4. Creation of a Web-Based GIS Server and Custom Geoprocessing Tools for Enhanced Hydrologic Applications

    Science.gov (United States)

    Welton, B.; Chouinard, K.; Sultan, M.; Becker, D.; Milewski, A.; Becker, R.

    2010-12-01

    Rising populations in the arid and semi arid parts of the World are increasing the demand for fresh water supplies worldwide. Many data sets needed for assessment of hydrologic applications across vast regions of the world are expensive, unpublished, difficult to obtain, or at varying scales which complicates their use. Fortunately, this situation is changing with the development of global remote sensing datasets and web-based platforms such as GIS Server. GIS provides a cost effective vehicle for comparing, analyzing, and querying a variety of spatial datasets as geographically referenced layers. We have recently constructed a web-based GIS, that incorporates all relevant geological, geochemical, geophysical, and remote sensing data sets that were readily used to identify reservoir types and potential well locations on local and regional scales in various tectonic settings including: (1) extensional environment (Red Sea rift), (2) transcurrent fault system (Najd Fault in the Arabian-Nubian Shield), and (3) compressional environments (Himalayas). The web-based GIS could also be used to detect spatial and temporal trends in precipitation, recharge, and runoff in large watersheds on local, regional, and continental scales. These applications were enabled through the construction of a web-based ArcGIS Server with Google Map’s interface and the development of customized geoprocessing tools. ArcGIS Server provides out-of-the-box setups that are generic in nature. This platform includes all of the standard web based GIS tools (e.g. pan, zoom, identify, search, data querying, and measurement). In addition to the standard suite of tools provided by ArcGIS Server an additional set of advanced data manipulation and display tools was also developed to allow for a more complete and customizable view of the area of interest. The most notable addition to the standard GIS Server tools is the custom on-demand geoprocessing tools (e.g., graph, statistical functions, custom raster

  5. DNA barcode goes two-dimensions: DNA QR code web server.

    Science.gov (United States)

    Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

  6. DNA barcode goes two-dimensions: DNA QR code web server.

    Directory of Open Access Journals (Sweden)

    Chang Liu

    Full Text Available The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  7. Detecting DDoS Attacks against Web Server Using Time Series Analysis

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Distributed Denial of Service (DDoS) attack is a major threat to the availability of Web service. The inherent presence of self-similarity in Web traffic motivates the applicability of time series analysis in the study of the burst feature of DDoS attack. This paper presents a method of detecting DDoS attacks against Web server by analyzing the abrupt change of time series data obtained from Web traffic. Time series data are specified in reference sliding window and test sliding window, and the abrupt change is modeled using Auto-Regressive (AR) process. By comparing two adjacent non-overlapping windows of the time series, the attack traffic could be detected at a time point. Combined with alarm correlation and location correlation, not only the presence of DDoS attack, but also its occurring time and location can be determined. The experimental results in a test environment are illustrated to justify our method.

  8. The use of the TWiki Web in ATLAS

    International Nuclear Information System (INIS)

    The ATLAS Experiment, with over 2000 collaborators, needs efficient and effective means of communicating information. The Collaboration has been using the TWiki Web at CERN for over three years and now has more than 7000 web pages, some of which are protected. This number greatly exceeds the number of 'static' HTML pages, and in the last year, there has been a significant migration to the TWiki. The TWiki is one example of the many different types of Wiki web which exist. In this paper, a description is given of the ATLAS TWiki at CERN. The tools used by the Collaboration to manage the TWiki are described and some of the problems encountered explained. A very useful development has been the creation of a set of Workbooks (Users' Guides) - these have benefitted from the TWiki environment and, in particular, a tool to extract pdf from the associated pages.

  9. 分布式Web服务器技术综述%A Survey on Distributed Web Server Techniques

    Institute of Scientific and Technical Information of China (English)

    马晓星; 吕建

    2002-01-01

    With the explosive growth of the World Wide Wed,many popular Web sites are faced with the challenge of the overload of tremendous requests.The best way out is using distributed Web server systems for their good scalability and low costs.In this paper,we try to give a comprehensive survey on the underlying techniques of the distributed Web server systems:request-dispatching mechanisms,load-balancing algorithms,Web content replication and distribution schemas and other important aspects.

  10. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    International Nuclear Information System (INIS)

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution

  11. A web server framework for rich interactive access to geologic and water quality data.

    Science.gov (United States)

    Scharling, Peter; Hinsby, Klaus; Brennan, Kelsy

    2014-05-01

    Geodata visualization and analysis is founded on proper access to all available data. Throughout several research projects Earthfx and GEUS managed to gather relevant data from both national and local databases into one platform. The web server platform which is easy accessible on the internet displays all types of spatially distributed geodata ranging from geochemistry, geological and geophysical well logs, surface- and airborne geophysics to any type of temporal measurements like water levels and trends in groundwater chemistry. Geological cross sections are an essential tool for the geoscientist. Moving beyond plan-view web mapping, GEUS and Earthfx have developed a webserver technology that provides the user with the ability to dynamically interact with geologic models developed for various projects in Denmark and in transboundary aquifers across the Danish-German border. The web map interface allows the user to interactively define the location of a multi-point profile, and the selected profile will be quickly drawn and illustrated as a slice through the 3D geologic model. Including all borehole logs within a user defined offset from the profile. A key aspect of the webserver technology is that the profiles are presented through a fully dynamic interface. Web users can select and interact with borehole logs contained in the underlying database, adjust vertical exaggeration, and add or remove off-section boreholes by dynamically adjusting the offset projection distance. In a similar manner to the profile tool, an interactive water level and water chemistry graphing tool has been integrated into the web service interface. Again, the focus is on providing a level of functionality beyond simple data display. Future extensions to the web interface and functionality are possible, as the web server utilizes the same code engine that is used for desktop geologic model construction and water quality data management. In summary, the GEUS/Earthfx web server tools

  12. EnviroAtlas -- Green Bay, Wisconsin -- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Green Bay, WI one...

  13. EnviroAtlas - New Bedford, MA - One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The New Bedford, MA land...

  14. EnviroAtlas -Portland, ME- One Meter Resolution Urban Land Cover (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Portland, ME land cover...

  15. EnviroAtlas -- New Bedford, Massachusetts -- One Meter Resolution Urban Land Cover Data (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The New Bedford, MA land...

  16. Modeling the Probability of Failure on LDAP Binding Operations in Iplanet Web Proxy 3.6 Server

    CERN Document Server

    de Lara, Alejandro Chinea Manrique

    2010-01-01

    This paper is devoted to the theoretical analysis of a problem derived from interaction between two Iplanet products: Web Proxy Server and the Directory Server. In particular, a probabilistic and stochastic-approximation model is proposed to minimize the occurrence of LDAP connection failures in Iplanet Web Proxy 3.6 Server. The proposed model serves not only to provide a parameterization of the aforementioned phenomena, but also to provide meaningful insights illustrating and supporting these theoretical results. In addition, we shall also address practical considerations when estimating the parameters of the proposed model from experimental data. Finally, we shall provide some interesting results from real-world data collected from our customers.

  17. The Waveform Server: A Web-based Interactive Seismic Waveform Interface

    Science.gov (United States)

    Newman, R. L.; Clemesha, A.; Lindquist, K. G.; Reyes, J.; Steidl, J. H.; Vernon, F. L.

    2009-12-01

    Seismic waveform data has traditionally been displayed on machines that are either local area networked to, or directly host, a seismic networks waveform database(s). Typical seismic data warehouses allow online users to query and download data collected from regional networks passively, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. The system is used to display data from the USArray experiment, a US continent-wide migratory transportable seismic array. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running Boulder Real Time Technology's (BRTT) Antelope Real Time System (ARTS). The software is freely available from the Antelope contributed code Git repository. Screenshot of the web-based waveform server interface

  18. RaptorX-Property: a web server for protein structure property prediction.

    Science.gov (United States)

    Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

    2016-07-01

    RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. PMID:27112573

  19. An integrated medical image database and retrieval system using a web application server.

    Science.gov (United States)

    Cao, Pengyu; Hashiba, Masao; Akazawa, Kouhei; Yamakawa, Tomoko; Matsuto, Takayuki

    2003-08-01

    We developed an Integrated Medical Image Database and Retrieval System (INIS) for easy access by medical staff. The INIS mainly consisted of four parts: specific servers to save medical images from multi-vendor modalities of CT, MRI, CR, ECG and endoscopy; an integrated image database (DB) server to save various kinds of images in a DICOM format; a Web application server to connect clients to the integrated image DB and the Web browser terminals connected to an HIS system. The INIS provided a common screen design to retrieve CT, MRI, CR, endoscopic and ECG images, and radiological reports, which would allow doctors to retrieve radiological images and corresponding reports, or ECG images of a patient simultaneously on a screen. Doctors working in internal medicine on average accessed information 492 times a month. Doctors working in cardiological and gastroenterological accessed information 308 times a month. Using the INIS, medical staff could browse all or parts of a patient's medical images and reports. PMID:12909158

  20. ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

    Science.gov (United States)

    Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G.; Gelly, Jean-Christophe

    2016-01-01

    Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/. PMID:27319297

  1. Atlas Basemaps in Web 2.0 Epoch

    Science.gov (United States)

    Chabaniuk, V.; Dyshlyk, O.

    2016-06-01

    The authors have analyzed their experience of the production of various Electronic Atlases (EA) and Atlas Information Systems (AtIS) of so-called "classical type". These EA/AtIS have been implemented in the past decade in the Web 1.0 architecture (e.g., National Atlas of Ukraine, Atlas of radioactive contamination of Ukraine, and others). One of the main distinguishing features of these atlases was their static nature - the end user could not change the content of EA/AtIS. Base maps are very important element of any EA/AtIS. In classical type EA/AtIS they were static datasets, which consisted of two parts: the topographic data of a fixed scale and data of the administrative-territorial division of Ukraine. It is important to note that the technique of topographic data production was based on the use of direct channels of topographic entity observation (such as aerial photography) for the selected scale. Changes in the information technology of the past half-decade are characterized by the advent of the "Web 2.0 epoch". Due to this, in cartography appeared such phenomena as, for example, "neo-cartography" and various mapping platforms like OpenStreetMap. These changes have forced developers of EA/AtIS to use new atlas basemaps. Our approach is described in the article. The phenomenon of neo-cartography and/or Web 2.0 cartography are analysed by authors using previously developed Conceptual framework of EA/AtIS. This framework logically explains the cartographic phenomena relations of three formations: Web 1.0, Web 1.0x1.0 and Web 2.0. Atlas basemaps of the Web 2.0 epoch are integrated information systems. We use several ways to integrate separate atlas basemaps into the information system - by building: weak integrated information system, structured system and meta-system. This integrated information system consists of several basemaps and falls under the definition of "big data". In real projects it is already used the basemaps of three strata: Conceptual

  2. The ATLAS tile calorimeter web systems for data quality

    International Nuclear Information System (INIS)

    The ATLAS detector consists of four major components: inner tracker, calorimeter, muon spectrometer and magnet system. In the Tile Calorimeter (TileCal), there are 4 partitions, each partition has 64 modules and each module has up to 48 channels. During the ATLAS pre-operation phase, a group of physicists need to analyze the Tile Calorimeter data quality, generate reports and update the official database, when necessary. The Tile Commissioning Web System (TCWS) retrieves information from different directories and databases, executes programs that generate results, stores comments and verifies the calorimeter status. TCWS integrates different applications, each one presenting a unique data view. The Web Interface for Shifters (WIS) supports monitoring tasks by managing test parameters and all the calorimeter status. The TileComm Analysis stores plots, automatic analyses results and comments concerning the tests. With the necessity of increasing granularity, a new application was created: the Monitoring and Calibration Web System (MCWS). This application supports data quality analyses at the channel level by presenting the automatic analyses results, the problematic known channels and the channels masked by the shifters. Through the web system, it is possible to generate plots and reports, related to the channels, identify new bad channels and update the Bad Channels List at the ATLAS official database (COOL DB). The Data Quality Monitoring Viewer (DQM Viewer) displays the data quality automatic results through an oriented visualization.

  3. From the CERN web: LHCb, ATLAS, ILC and more

    CERN Multimedia

    2015-01-01

    This new section highlights articles, blog posts and press releases published in the CERN web environment over the past weeks. This way, you won’t miss a thing...     LHCb sees small deviations from the lepton universality 1 September – LHCb collaboration The LHCb experiment at CERN has made the first measurement at a hadron collider of B meson decays that have already shown small deviations from the predictions of the Standard Model in earlier studies at an electron-positron collider. Continue to read…     The figure shows the density of allowed supersymmetric models before and after the ATLAS Run 1 searches. The missing points have been ruled out by the LHC data. The x-axis shows the mass of the supersymmetric dark matter particle, while the y-axis shows the predicted density of those particles in the universe.     ATLAS is narrowing down the theoretical candidates for dark matter 25 August – ATLAS collab...

  4. FAST REAL TIME ANALYSIS OF WEB SERVER MASSIVE LOG FILES USING AN IMPROVED WEB MINING ARCHITECTURE

    OpenAIRE

    Hussain Mohammad Abu-Dalbouh

    2013-01-01

    The web has played a vital role to detect the information and finding the reasons to organize a system. As the web sites were increased, the web log files also increased based on the web searching. Our challenge and the task are to reduce the log files and classify the best results to reach the task which we used. Aimed to overcome the deficiency of abundant data to web mining, the study proposed a path extraction using Euclidean Distance based algorithm with a sequential pattern clustering m...

  5. MetaRanker 2.0: a web server for prioritization of genetic variation data

    OpenAIRE

    Pers, Tune Hannes; Dworzynski, Piotr; Thomas, Cecilia Engel; Hansen, Kasper Lage; Brunak, Søren

    2013-01-01

    MetaRanker 2.0 is a web server for prioritization of common and rare frequency genetic variation data. Based on heterogeneous data sets including genetic association data, protein–protein interactions, large-scale text-mining data, copy number variation data and gene expression experiments, MetaRanker 2.0 prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 is made freely available at www.cbs.dtu.dk/services/MetaRa...

  6. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES).

    Science.gov (United States)

    Kolekar, Pandurang; Pataskar, Abhijeet; Kulkarni-Kale, Urmila; Pal, Jayanta; Kulkarni, Abhijeet

    2016-01-01

    Cellular mRNAs are predominantly translated in a cap-dependent manner. However, some viral and a subset of cellular mRNAs initiate their translation in a cap-independent manner. This requires presence of a structured RNA element, known as, Internal Ribosome Entry Site (IRES) in their 5' untranslated regions (UTRs). Experimental demonstration of IRES in UTR remains a challenging task. Computational prediction of IRES merely based on sequence and structure conservation is also difficult, particularly for cellular IRES. A web server, IRESPred is developed for prediction of both viral and cellular IRES using Support Vector Machine (SVM). The predictive model was built using 35 features that are based on sequence and structural properties of UTRs and the probabilities of interactions between UTR and small subunit ribosomal proteins (SSRPs). The model was found to have 75.51% accuracy, 75.75% sensitivity, 75.25% specificity, 75.75% precision and Matthews Correlation Coefficient (MCC) of 0.51 in blind testing. IRESPred was found to perform better than the only available viral IRES prediction server, VIPS. The IRESPred server is freely available at http://bioinfo.net.in/IRESPred/. PMID:27264539

  7. How to secure web servers by the intrusion prevention system (IPS?

    Directory of Open Access Journals (Sweden)

    Yousef Farhaoui

    2016-03-01

    Full Text Available Information technology and especially the Internet are playing an increasing role in our society. Approaches by signature show limits on intrusion detection / attacks by the fact that most web vulnerabilities are specifically for specific applications may be developed in-house by companies. Behavioral methods are therefore an interesting approach in this area. An IPS (Intrusion Prevention System is a tool that is used to enhance the security level. We present here the secure IPS architecture web server. We will also discuss measures that define the effectiveness of our IPS and very recent work of standardization and homogenization of our IPS platform. The approach relies on preventive mechanisms: it is then to develop devices capable of preventing any action that would result in a violation of the security policy. However, experienceand results shows that it is impossible to build a fully secure system for technical or practical reasons.

  8. DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines

    OpenAIRE

    Lin, Hsuan-Hung; Tseng, Lin-Yu

    2010-01-01

    The proper prediction of the location of disulfide bridges is efficient in helping to solve the protein folding problem. Most of the previous works on the prediction of disulfide connectivity pattern use the prior knowledge of the bonding state of cysteines. The DBCP web server provides prediction of disulfide bonding connectivity pattern without the prior knowledge of the bonding state of cysteines. The method used in this server improves the accuracy of disulfide connectivity pattern predic...

  9. MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence

    OpenAIRE

    Lippi, Marco; Passerini, Andrea; Punta, Marco; Rost, Burkhard; Frasconi, Paolo

    2008-01-01

    Summary: The web server MetalDetector classifies histidine residues in proteins into one of two states (free or metal bound) and cysteines into one of three states (free, metal bound or disulfide bridged). A decision tree integrates predictions from two previously developed methods (DISULFIND and Metal Ligand Predictor). Cross-validated performance assessment indicates that our server predicts disulfide bonding state at 88.6% precision and 85.1% recall, while it identifies cysteines and histi...

  10. deepTools2: a next generation web server for deep-sequencing data analysis.

    Science.gov (United States)

    Ramírez, Fidel; Ryan, Devon P; Grüning, Björn; Bhardwaj, Vivek; Kilpert, Fabian; Richter, Andreas S; Heyne, Steffen; Dündar, Friederike; Manke, Thomas

    2016-07-01

    We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available. PMID:27079975

  11. Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

    Science.gov (United States)

    Lavezzo, Enrico; Falda, Marco; Fontana, Paolo; Bianco, Luca; Toppo, Stefano

    2016-01-15

    Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/. PMID:26318087

  12. DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.

    Science.gov (United States)

    Liu, Chun-Chi; Tseng, Yu-Ting; Li, Wenyuan; Wu, Chia-Yu; Mayzus, Ilya; Rzhetsky, Andrey; Sun, Fengzhu; Waterman, Michael; Chen, Jeremy J W; Chaudhary, Preet M; Loscalzo, Joseph; Crandall, Edward; Zhou, Xianghong Jasmine

    2014-07-01

    The DiseaseConnect (http://disease-connect.org) is a web server for analysis and visualization of a comprehensive knowledge on mechanism-based disease connectivity. The traditional disease classification system groups diseases with similar clinical symptoms and phenotypic traits. Thus, diseases with entirely different pathologies could be grouped together, leading to a similar treatment design. Such problems could be avoided if diseases were classified based on their molecular mechanisms. Connecting diseases with similar pathological mechanisms could inspire novel strategies on the effective repositioning of existing drugs and therapies. Although there have been several studies attempting to generate disease connectivity networks, they have not yet utilized the enormous and rapidly growing public repositories of disease-related omics data and literature, two primary resources capable of providing insights into disease connections at an unprecedented level of detail. Our DiseaseConnect, the first public web server, integrates comprehensive omics and literature data, including a large amount of gene expression data, Genome-Wide Association Studies catalog, and text-mined knowledge, to discover disease-disease connectivity via common molecular mechanisms. Moreover, the clinical comorbidity data and a comprehensive compilation of known drug-disease relationships are additionally utilized for advancing the understanding of the disease landscape and for facilitating the mechanism-based development of new drug treatments. PMID:24895436

  13. incaRNAfbinv: a web server for the fragment-based design of RNA sequences.

    Science.gov (United States)

    Drory Retwitzer, Matan; Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme; Barash, Danny

    2016-07-01

    In recent years, new methods for computational RNA design have been developed and applied to various problems in synthetic biology and nanotechnology. Lately, there is considerable interest in incorporating essential biological information when solving the inverse RNA folding problem. Correspondingly, RNAfbinv aims at including biologically meaningful constraints and is the only program to-date that performs a fragment-based design of RNA sequences. In doing so it allows the design of sequences that do not necessarily exactly fold into the target, as long as the overall coarse-grained tree graph shape is preserved. Augmented by the weighted sampling algorithm of incaRNAtion, our web server called incaRNAfbinv implements the method devised in RNAfbinv and offers an interactive environment for the inverse folding of RNA using a fragment-based design approach. It takes as input: a target RNA secondary structure; optional sequence and motif constraints; optional target minimum free energy, neutrality and GC content. In addition to the design of synthetic regulatory sequences, it can be used as a pre-processing step for the detection of novel natural occurring RNAs. The two complementary methodologies RNAfbinv and incaRNAtion are merged together and fully implemented in our web server incaRNAfbinv, available at http://www.cs.bgu.ac.il/incaRNAfbinv. PMID:27185893

  14. RV-Typer: A Web Server for Typing of Rhinoviruses Using Alignment-Free Approach.

    Directory of Open Access Journals (Sweden)

    Pandurang S Kolekar

    Full Text Available Rhinoviruses (RV are increasingly being reported to cause mild to severe infections of respiratory tract in humans. RV are antigenically the most diverse species of the genus Enterovirus and family Picornaviridae. There are three species of RV (RV-A, -B and -C, with 80, 32 and 55 serotypes/types, respectively. Antigenic variation is the main limiting factor for development of a cross-protective vaccine against RV.Serotyping of Rhinoviruses is carried out using cross-neutralization assays in cell culture. However, these assays become laborious and time-consuming for the large number of strains. Alternatively, serotyping of RV is carried out by alignment-based phylogeny of both protein and nucleotide sequences of VP1. However, serotyping of RV based on alignment-based phylogeny is a multi-step process, which needs to be repeated every time a new isolate is sequenced. In view of the growing need for serotyping of RV, an alignment-free method based on "return time distribution" (RTD of amino acid residues in VP1 protein has been developed and implemented in the form of a web server titled RV-Typer. RV-Typer accepts nucleotide or protein sequences as an input and computes return times of di-peptides (k = 2 to assign serotypes. The RV-Typer performs with 100% sensitivity and specificity. It is significantly faster than alignment-based methods. The web server is available at http://bioinfo.net.in/RV-Typer/home.html.

  15. SSDL personel dosimetry system: migration from a client - server system into a web-based system

    International Nuclear Information System (INIS)

    Personnel Dosimetry System has been used by the Secondary Standard Dosimetry Laboratory (SSDL), Nuclear Malaysia since ten years ago. The system is a computerized database system with a client-server concept. This system has been used by Film Badge Laboratory, SSDL to record details of clients, calculation of Film Badge dosage, management of radiation workers data's, generating of dosage report, retrieval of statistical reports regarding film badge usage for the purpose of reporting to monitoring bodies such as Atomic Energy Licensing Board (AELB), Ministry of Health and others. But, due to technical problems that frequently occurs, the system is going to be replaced by a newly developed web- based system called e-SSDL. This paper describe the problems that regularly occurs in the previous system, explains how the process of replacing the client-server system with a web-based system is done and the differences between the previous and current system. This paper will also present details architecture of the new system and the new process introduced in processing film badges. (Author)

  16. Epitopia: a web-server for predicting B-cell epitopes

    Directory of Open Access Journals (Sweden)

    Martz Eric

    2009-09-01

    Full Text Available Abstract Background Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire protein, a computational tool that predicts the most probable epitope regions is desirable. Results The Epitopia server is a web-based tool that aims to predict immunogenic regions in either a protein three-dimensional structure or a linear sequence. Epitopia implements a machine-learning algorithm that was trained to discern antigenic features within a given protein. The Epitopia algorithm has been compared to other available epitope prediction tools and was found to have higher predictive power. A special emphasis was put on the development of a user-friendly graphical interface for displaying the results. Conclusion Epitopia is a user-friendly web-server that predicts immunogenic regions for both a protein structure and a protein sequence. Its accuracy and functionality make it a highly useful tool. Epitopia is available at http://epitopia.tau.ac.il and includes extensive explanations and example predictions.

  17. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

    Science.gov (United States)

    Cottret, Ludovic; Wildridge, David; Vinson, Florence; Barrett, Michael P; Charles, Hubert; Sagot, Marie-France; Jourdan, Fabien

    2010-07-01

    High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr. PMID:20444866

  18. NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints.

    Science.gov (United States)

    Heller, Davide Martin; Giorgetti, Alejandro

    2010-07-01

    Nuclear magnetic resonance (NMR) spectroscopy together with X-ray crystallography, are the main techniques used for the determination of high-resolution 3D structures of biological molecules. The output of an NMR experiment includes a set of lower and upper limits for the distances (constraints) between pairs of atoms. If the number of constraints is high enough, there will be a finite number of possible conformations (models) of the macromolecule satisfying the data. Thus, the more constraints are measured, the better defined these structures will be. The availability of a user-friendly tool able to help in the analysis and interpretation of the number of experimental constraints per residue, is thus of valuable importance when assessing the levels of structure definition of NMR solved biological macromolecules, in particular, when high-quality structures are needed in techniques such as, computational biology approaches, site-directed mutagenesis experiments and/or drug design. Here, we present a free publicly available web-server, i.e. NMR Constraints Analyser, which is aimed at providing an automatic graphical analysis of the NMR experimental constraints atom by atom. The NMR Constraints Analyser server is available from the web-page http://molsim.sci.univr.it/constraint. PMID:20513646

  19. VLDP web server: a powerful geometric tool for analysing protein structures in their environment.

    Science.gov (United States)

    Esque, Jérémy; Léonard, Sylvain; de Brevern, Alexandre G; Oguey, Christophe

    2013-07-01

    Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. We propose a set of accurate tools, for analysing protein structures, based on the reliable method of Voronoi-Laguerre tessellations. The Voronoi Laguerre Delaunay Protein web server (VLDPws) computes the Laguerre tessellation on a whole given system first embedded in solvent. Through this fine description, VLDPws gives the following data: (i) Amino acid volumes evaluated with high precision, as confirmed by good correlations with experimental data. (ii) A novel definition of inter-residue contacts within the given protein. (iii) A measure of the residue exposure to solvent that significantly improves the standard notion of accessibility in some cases. At present, no equivalent web server is available. VLDPws provides output in two complementary forms: direct visualization of the Laguerre tessellation, mostly its polygonal molecular surfaces; files of volumes; and areas, contacts and similar data for each residue and each atom. These files are available for download for further analysis. VLDPws can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/vldp. PMID:23761450

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

    Science.gov (United States)

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

    2016-07-01

    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. PMID:27198219

  1. A Web Server and Mobile App for Computing Hemolytic Potency of Peptides

    Science.gov (United States)

    Chaudhary, Kumardeep; Kumar, Ritesh; Singh, Sandeep; Tuknait, Abhishek; Gautam, Ankur; Mathur, Deepika; Anand, Priya; Varshney, Grish C.; Raghava, Gajendra P. S.

    2016-03-01

    Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present study describes a web server and mobile app developed for predicting, and screening of peptides having hemolytic potency. Firstly, we generated a dataset HemoPI-1 that contains 552 hemolytic peptides extracted from Hemolytik database and 552 random non-hemolytic peptides (from Swiss-Prot). The sequence analysis of these peptides revealed that certain residues (e.g., L, K, F, W) and motifs (e.g., “FKK”, “LKL”, “KKLL”, “KWK”, “VLK”, “CYCR”, “CRR”, “RFC”, “RRR”, “LKKL”) are more abundant in hemolytic peptides. Therefore, we developed models for discriminating hemolytic and non-hemolytic peptides using various machine learning techniques and achieved more than 95% accuracy. We also developed models for discriminating peptides having high and low hemolytic potential on different datasets called HemoPI-2 and HemoPI-3. In order to serve the scientific community, we developed a web server, mobile app and JAVA-based standalone software (http://crdd.osdd.net/raghava/hemopi/).

  2. A Web Server and Mobile App for Computing Hemolytic Potency of Peptides

    Science.gov (United States)

    Chaudhary, Kumardeep; Kumar, Ritesh; Singh, Sandeep; Tuknait, Abhishek; Gautam, Ankur; Mathur, Deepika; Anand, Priya; Varshney, Grish C.; Raghava, Gajendra P. S.

    2016-01-01

    Numerous therapeutic peptides do not enter the clinical trials just because of their high hemolytic activity. Recently, we developed a database, Hemolytik, for maintaining experimentally validated hemolytic and non-hemolytic peptides. The present study describes a web server and mobile app developed for predicting, and screening of peptides having hemolytic potency. Firstly, we generated a dataset HemoPI-1 that contains 552 hemolytic peptides extracted from Hemolytik database and 552 random non-hemolytic peptides (from Swiss-Prot). The sequence analysis of these peptides revealed that certain residues (e.g., L, K, F, W) and motifs (e.g., “FKK”, “LKL”, “KKLL”, “KWK”, “VLK”, “CYCR”, “CRR”, “RFC”, “RRR”, “LKKL”) are more abundant in hemolytic peptides. Therefore, we developed models for discriminating hemolytic and non-hemolytic peptides using various machine learning techniques and achieved more than 95% accuracy. We also developed models for discriminating peptides having high and low hemolytic potential on different datasets called HemoPI-2 and HemoPI-3. In order to serve the scientific community, we developed a web server, mobile app and JAVA-based standalone software (http://crdd.osdd.net/raghava/hemopi/). PMID:26953092

  3. PredPlantPTS1: a web server for the prediction of plant peroxisomal proteins

    Directory of Open Access Journals (Sweden)

    Sigrun eReumann

    2012-08-01

    Full Text Available Prediction of subcellular protein localization is essential to correctly assign unknown proteins to cell organelle-specific protein networks and to ultimately determine protein function. For metazoa, several computational approaches have been developed in the past decade to predict peroxisomal proteins carrying the peroxisome targeting signal type 1 (PTS1. However, plant-specific PTS1 protein prediction methods have been lacking up to now, and pre-existing methods generally were incapable of correctly predicting low-abundance plant proteins possessing non-canonical PTS1 patterns. Recently, we presented a machine learning approach that is able to predict PTS1 proteins for higher plants (spermatophytes with high accuracy and which can correctly identify unknown targeting patterns, i.e. novel PTS1 tripeptides and tripeptide residues. Here we describe the first plant-specific web server PredPlantPTS1 for the prediction of plant PTS1 proteins using the above-mentioned underlying models. The server allows the submission of protein sequences from diverse spermatophytes and also performs well for mosses and algae. The easy-to-use web interface provides detailed output in terms of (i the peroxisomal targeting probability of the given sequence, (ii information whether a particular non-canonical PTS1 tripeptide has already been experimentally verified, and (iii the prediction scores for the single C-terminal 14 amino acid residues. The latter allows identification of predicted residues that inhibit peroxisome targeting and which can be optimized using site-directed mutagenesis to raise the peroxisome targeting efficiency. The prediction server will be instrumental in identifying low-abundance and stress-inducible peroxisomal proteins and defining the entire peroxisomal proteome of Arabidopsis and agronomically important crop plants. PredPlantPTS1 is freely accessible at ppp.gobics.de.

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

    Science.gov (United States)

    Wolfe, Christopher R; Reyna, Valerie F

    2002-05-01

    Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own. PMID:12109013

  5. Web servers and services for electrostatics calculations with APBS and PDB2PQR.

    Science.gov (United States)

    Unni, Samir; Huang, Yong; Hanson, Robert M; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W; Nielsen, Jens E; Baker, Nathan A

    2011-05-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization of electrostatic potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  6. LigSearch: a knowledge-based web server to identify likely ligands for a protein target

    International Nuclear Information System (INIS)

    LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch

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

    Directory of Open Access Journals (Sweden)

    Asa Thibodeau

    2016-06-01

    Full Text Available 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/.

  8. SEWS : an web-based server for evaluating syntactic annotation tools SEWS : un serveur d’évaluation orienté Web pour la syntaxe

    Directory of Open Access Journals (Sweden)

    Olivier Hamon

    2009-06-01

    Full Text Available Examples of Automated Evaluation platforms deployed as Web server are currently very rare and often underestimated. Time and, effort savings, faster system improvement, com- mon paradigm of evaluation for a community, the benefits offered by such services are plentiful. In this paper, we present a platform for evaluating automatically parsers and we comment on its deployment during an evaluation campaign. First, we draw up a state-of-the-art for plat- forms used in evaluation of NLP systems, then we present the tools available for Web server deployment. Next, we describe our platform and its deployment in the PASSAGE project as a Web server. Finally we show the interest of generalizing such service to other NLP domains.

  9. Prolog Server Pages

    OpenAIRE

    Suciu, Alin; Pusztai, Kalman; Vancea, Andrei

    2006-01-01

    Prolog Server Pages (PSP) is a scripting language, based on Prolog, than can be embedded in HTML documents. To run PSP applications one needs a web server, a web browser and a PSP interpreter. The code is executed, by the interpreter, on the server-side (web server) and the output (together with the html code in witch the PSP code is embedded) is sent to the client-side (browser). The current implementation supports Apache Web Server. We implemented an Apache web server module that handles PS...

  10. FAF-Drugs3: a web server for compound property calculation and chemical library design.

    Science.gov (United States)

    Lagorce, David; Sperandio, Olivier; Baell, Jonathan B; Miteva, Maria A; Villoutreix, Bruno O

    2015-07-01

    Drug attrition late in preclinical or clinical development is a serious economic problem in the field of drug discovery. These problems can be linked, in part, to the quality of the compound collections used during the hit generation stage and to the selection of compounds undergoing optimization. Here, we present FAF-Drugs3, a web server that can be used for drug discovery and chemical biology projects to help in preparing compound libraries and to assist decision-making during the hit selection/lead optimization phase. Since it was first described in 2006, FAF-Drugs has been significantly modified. The tool now applies an enhanced structure curation procedure, can filter or analyze molecules with user-defined or eight predefined physicochemical filters as well as with several simple ADMET (absorption, distribution, metabolism, excretion and toxicity) rules. In addition, compounds can be filtered using an updated list of 154 hand-curated structural alerts while Pan Assay Interference compounds (PAINS) and other, generally unwanted groups are also investigated. FAF-Drugs3 offers access to user-friendly html result pages and the possibility to download all computed data. The server requires as input an SDF file of the compounds; it is open to all users and can be accessed without registration at http://fafdrugs3.mti.univ-paris-diderot.fr. PMID:25883137

  11. Performance of Web-based image distribution: server-oriented measurements

    International Nuclear Information System (INIS)

    The aim of this study was to assess the performance of Web-based image distribution when multiple personal computers (PCs) are downloading images simultaneously for different server hardware configurations. Using specially developed software, the time-to-display (TTD) of different image types was measured with up to 16 concurrent PCs for various combinations of processor, random access memory (RAM), network connection and image compression. The TTD increased linearly with the number of concurrent PCs but remained under 5 s in most of the cases, even with 16 concurrent PCs. Only with a 10-Mbit/s network connection or with lossy compression were TTDs above 5 s obtained. Two processors instead of one led to a slight and constant improvement of the TTD. Reducing the amount of RAM increased the TTD mainly for computed radiography (CR) images. There was no difference between a 200- and 100-Mbit/s network, but 10 Mbit/s proved significantly worse. When increasing the number of clients lossless compression performed substantially better than lossy. A standard off-the-shelf server provides an appropriate download performance even with 16 concurrent clients. Processor speed and RAM amount are of minor importance, but it is highly recommended to use a 100-Mbit/s network connection and to avoid the application of on-demand lossy compression in a local area network. (orig.)

  12. Modeling and Performance Analysis of Dispatching Policies in Dispatcher- Based Web Server Cluster

    Institute of Scientific and Technical Information of China (English)

    XIONG Zhi; YAN Puliu; GUO Chengcheng

    2006-01-01

    There are two kinds of dispatching policies in content-aware web server cluster: segregation dispatching policy and mixture dispatching policy. Traditional scheduling algorithms all adopt mixture dispatching policy. They do not consider that dynamic requests' serving has the tendency to slow down static requests' serving, and that different requests have different resource demands, so they can not use cluster's resource reasonably and effectively. This paper uses stochastic reward net (SRN) to model and analyze the two dispatching policies, and uses stochastic Petri net package (SPNP) to simulate the models. The simulation results and practical tests both show that segregation dispatching policy is better than mixture dispatching policy. The principle of segregation dispatching policy can guide us to design efficient scheduling algorithm.

  13. MATLAB WEB SERVER AND ITS APPLICATION IN REMOTE COLLABORATIVE DESIGN OF MAGNETIC BEARING SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Acclimatizing itself to the development of network,Math Works Inc constructed a MATLAB Web Server environment by dint of which one can browse the calculation and plots of MATLAB through Internet directly.The installation and use of the environment is introduced.A code established on the platform of MATLAB,which deals with the modal analysis of magnetic bearing system(MBS) supporting rotors of five degrees of freedom and considering the coupling of thrust bearing with radical bearings is modified to work in the environment.The purpose is to realize a remote call of the code by users through Internet for the performance analysis of the system.Such an application is very important to the concurrent design of MBS and for the utilization of distributive knowledge acquisition resources in collaborative design.The work on modification and realization is described and the results are discussed.

  14. PROTOTIPE PEMESANAN BAHAN PUSTAKA MELALUI WEB MENGGUNAKAN ACTIVE SERVER PAGE (ASP

    Directory of Open Access Journals (Sweden)

    Djoni Haryadi Setiabudi

    2002-01-01

    Full Text Available Electronic commerce is one of the components in the internet that growing fast in the world. In this research, it is developed the prototype for library service that offers library collection ordering especially books and articles through World Wide Web. In order to get an interaction between seller and buyer, there is an urgency to develop a dynamic web, which needs the technology and software. One of the programming languages is called Active Server Pages (ASP and it is combining with database system to store data. The other component as an interface between application and database is ActiveX Data Objects (ADO. ASP has an advantage in the scripting method and it is easy to make the configuration with database. This application consists of two major parts those are administrator and user. This prototype has the facilities for editing, searching and looking through ordering information online. Users can also do downloading process for searching and ordering articles. Paying method in this e-commerce system is quite essential because in Indonesia not everybody has a credit card. As a solution to this situation, this prototype has a form for user who does not have credit card. If the bill has been paid, he can do the transaction online. In this case, one of the ASP advantages will be used. This is called "session" when data in process would not be lost as long as the user still in that "session". This will be used in user area and admin area where the users and the admin can do various processes. Abstract in Bahasa Indonesia : Electronic commerce adalah satu bagian dari internet yang berkembang pesat di dunia saat ini. Pada penelitian ini dibuat suatu prototipe program aplikasi untuk pengembangan jasa layanan perpustakaan khususnya pemesanan artikel dan buku melalui World Wide Web. Untuk membangun aplikasi berbasis web diperlukan teknologi dan software yang mendukung pembuatan situs web dinamis sehingga ada interaksi antara pembeli dan penjual

  15. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences

    Directory of Open Access Journals (Sweden)

    Meinicke Peter

    2009-09-01

    Full Text Available Abstract Background Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Description Based on machine learning techniques for Pfam domain detection, the UFO web server for ultra-fast functional profiling allows researchers to process large protein sequence collections instantaneously. Besides the frequencies of Pfam and GO categories, the user also obtains the sequence specific assignments to Pfam domain families. In addition, a comparison with existing genomes provides dissimilarity scores with respect to 821 reference proteomes. Considering the underlying UFO domain detection, the results on 206 test genomes indicate a high sensitivity of the approach. In comparison with current state-of-the-art HMMs, the runtime measurements show a considerable speed up in the range of four orders of magnitude. For an average size prokaryotic genome, the computation of a functional profile together with its comparison typically requires about 10 seconds of processing time. Conclusion For the first time the UFO web server makes it possible to get a quick overview on the functional inventory of newly sequenced organisms. The genome scale comparison with a large number of precomputed profiles allows a first guess about functionally related organisms. The service is freely available and does not require user registration or specification of a valid email address.

  16. 基于Java的Web服务器性能测试工具研究%Java-based Web server performance testing tools to study

    Institute of Scientific and Technical Information of China (English)

    贺蕴彬

    2013-01-01

    国民经济的不断增长,推动了计算机技术的普及,我国计算机用户的数量急剧增多,大大增加了 Web服务器的承载压力,导致 Web 服务器在使用的过程中出现响应延时的现象,因此需要对 Web 服务器的性能测试工具进行研究,以完善 Web 服务器的使用。首先阐述了 Web 服务器的分析和设计,其次分析介绍了 Web 服务器的性能测试工具。%The growing national economy,promote the popularization of computer technology,China’s sharp increase in the number of computer users,greatly increasing the Web server hosting the pressure,leading to a Web server in use occurred during latency and,therefore,the need for Web server performance testing tool for research to improve the use of the Web server.This paper first gives an overview on Java,but also elaborates the Web server analysis and design,the final analysis describes the Web server performance testing tools.

  17. Mining of Web Server Logs in a Distributed Cluster Using Big Data Technologies

    Directory of Open Access Journals (Sweden)

    Savitha K

    2014-01-01

    Full Text Available Big Data is an emerging growing dataset beyond the ability of a traditional database tool. Hadoop rides the big data where the massive quantity of information is processed using cluster of commodity hardware. Web server logs are semi-structured files generated by the computer in large volume usually of flat text files. It is utilized efficiently by Mapreduce as it process one line at a time. This paper performs the session identification in log files using Hadoop in a distributed cluster. Apache Hadoop Mapreduce a data processing platform is used in pseudo distributed mode and in fully distributed mode. The framework effectively identifies the session utilized by the web surfer to recognize the unique users and pages accessed by the users. The identified session is analyzed in R to produce a statistical report based on total count of visit per day. The results are compared with non-hadoop approach a java environment, and it results in a better time efficiency, storage and processing speed of the proposed work.

  18. A Robust Mechanism for Defending Distributed Denial OF Service Attacks on Web Servers

    CERN Document Server

    Sen, Jaydip

    2011-01-01

    Distributed Denial of Service (DDoS) attacks have emerged as a popular means of causing mass targeted service disruptions, often for extended periods of time. The relative ease and low costs of launching such attacks, supplemented by the current inadequate sate of any viable defense mechanism, have made them one of the top threats to the Internet community today. Since the increasing popularity of web-based applications has led to several critical services being provided over the Internet, it is imperative to monitor the network traffic so as to prevent malicious attackers from depleting the resources of the network and denying services to legitimate users. This paper first presents a brief discussion on some of the important types of DDoS attacks that currently exist and some existing mechanisms to combat these attacks. It then points out the major drawbacks of the currently existing defense mechanisms and proposes a new mechanism for protecting a web-server against a DDoS attack. In the proposed mechanism, ...

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

    Science.gov (United States)

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

    2016-07-01

    Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene function related terms. Translation of hundreds of gene identifiers is another core feature of g:Profiler. Since its first publication in 2007, our web server has become a popular tool of choice among basic and translational researchers. Timeliness is a major advantage of g:Profiler as genome and pathway information is synchronized with the Ensembl database in quarterly updates. g:Profiler supports 213 species including mammals and other vertebrates, plants, insects and fungi. The 2016 update of g:Profiler introduces several novel features. We have added further functional datasets to interpret gene lists, including transcription factor binding site predictions, Mendelian disease annotations, information about protein expression and complexes and gene mappings of human genetic polymorphisms. Besides the interactive web interface, g:Profiler can be accessed in computational pipelines using our R package, Python interface and BioJS component. g:Profiler is freely available at http://biit.cs.ut.ee/gprofiler/. PMID:27098042

  20. EMBEDDED WEB SERVER & GPRS BASED ADVANCED INDUSTRIAL AUTOMATION USING LINUX RTOS

    Directory of Open Access Journals (Sweden)

    MANIVANNAN M,

    2010-11-01

    Full Text Available Design of Data Acquisition and Control System (DACS is the challenging part of any measurement, automation and control system applications. These applications widely use the single chip data acquisition method. But this method leads to the problem of poor real time and reliability. And it doesn’t able to process with embedded webdocuments and networked embedded devices. The main objective of this work is to overcome these drawbacks and to design a system for remote I/O data acquisition and control by Linux portable Advanced RISC Machine (ARM processor and in-build web server application with General Packet Radio Service (GPRS technology. Real time Linux operating system is the better choice for any Embedded Real Time applications with minimal real time constraints. GPRS module eliminates the need of internet software suite in ARM processor and mass storage for web applications and allows the user to interface with many real time embedded applications like remote DACS and embedded processors like ARM Core.

  1. miRQuest: integration of tools on a Web server for microRNA research.

    Science.gov (United States)

    Aguiar, R R; Ambrosio, L A; Sepúlveda-Hermosilla, G; Maracaja-Coutinho, V; Paschoal, A R

    2016-01-01

    This report describes the miRQuest - a novel middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification that use different programming languages and methods to realize this task. It is difficult to understand each tool and apply it to diverse datasets and organisms available for miRNA analysis. miRQuest can easily be used by biologists and researchers with limited experience with bioinformatics. We built it using the middleware architecture on a Web platform for miRNA research that performs two main functions: i) integration of different miRNA prediction tools for miRNA identification in a user-friendly environment; and ii) comparison of these prediction tools. In both cases, the user provides sequences (in FASTA format) as an input set for the analysis and comparisons. All the tools were selected on the basis of a survey of the literature on the available tools for miRNA prediction. As results, three different cases of use of the tools are also described, where one is the miRNA identification analysis in 30 different species. Finally, miRQuest seems to be a novel and useful tool; and it is freely available for both benchmarking and miRNA identification at http://mirquest.integrativebioinformatics.me/. PMID:27050998

  2. Web server for the administrative and technical documentation of the radiodiagnostic facilities

    Energy Technology Data Exchange (ETDEWEB)

    Soto, M; Campayo, J. M; Guardia, V. [Logistica y Acondicionamientos Industriales SAU, Sorolla Center, Local 10, Av. de las Cortes Valencianas No. 58, 46015 Valencia (Spain); Mayo, P., E-mail: m.soto@lainsa.co [TITANIA Servicios Tecnologicos SL, Sorolla Center, Local 10, Av. de las Cortes Valencianas No. 58, 46015 Valencia (Spain)

    2010-10-15

    Nowadays Radiological Protection Technical Unit of LAINSA as part of Grupo Dominguis, has assigned radiological security tasks in a high number of medical X-ray facilities. It is recognised by the Nuclear Security Council as a specialist in the assessment of protection against the radiological risks associated with medical, industrial and nuclear activities. It is also authorised as an external personal dosimetry centre. Concretely medical X-ray facilities generate big amount of information because of national regulatory authority to assure the good functioning of it. This information is formed by administrative procedures for the regulatory authority in industrial and public health area, periodic quality controls of the radiographic equipment s, radiological verification in different locations to measure the radioactivity levels, certificates of employees training to work with radioactivity, dosimetric registrations of professional exposure employees and medical aptitude documents for their job, etc. In this paper it is presented a net server application to manage this information in an effective way by web. In this server each facility has an online net space with private key access and where there are all the administrative documents and nuclear security reports of the facility. Moreover, the client who is responsible of the radiological security of the centre, can have at any moment all this information, minimizing delay times and optimizing the information store support in electronic format. The objective is that this information can be updated for consulting, modifying or checking at anytime quickly and safety. All this information has to be accessible for the interested medical facility, for the Radiological Protection Technical Unit which has been contracted by the facility to do the assessment in radiological protection and for the regulatory authority in nuclear security to guarantee well-practice in medical and nuclear activities. (Author)

  3. Web server for the administrative and technical documentation of the radiodiagnostic facilities

    International Nuclear Information System (INIS)

    Nowadays Radiological Protection Technical Unit of LAINSA as part of Grupo Dominguis, has assigned radiological security tasks in a high number of medical X-ray facilities. It is recognised by the Nuclear Security Council as a specialist in the assessment of protection against the radiological risks associated with medical, industrial and nuclear activities. It is also authorised as an external personal dosimetry centre. Concretely medical X-ray facilities generate big amount of information because of national regulatory authority to assure the good functioning of it. This information is formed by administrative procedures for the regulatory authority in industrial and public health area, periodic quality controls of the radiographic equipment s, radiological verification in different locations to measure the radioactivity levels, certificates of employees training to work with radioactivity, dosimetric registrations of professional exposure employees and medical aptitude documents for their job, etc. In this paper it is presented a net server application to manage this information in an effective way by web. In this server each facility has an online net space with private key access and where there are all the administrative documents and nuclear security reports of the facility. Moreover, the client who is responsible of the radiological security of the centre, can have at any moment all this information, minimizing delay times and optimizing the information store support in electronic format. The objective is that this information can be updated for consulting, modifying or checking at anytime quickly and safety. All this information has to be accessible for the interested medical facility, for the Radiological Protection Technical Unit which has been contracted by the facility to do the assessment in radiological protection and for the regulatory authority in nuclear security to guarantee well-practice in medical and nuclear activities. (Author)

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

    Science.gov (United States)

    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…

  5. An object-oriented approach to deploying highly configurable Web interfaces for the ATLAS experiment

    Science.gov (United States)

    Lange, Bruno; Maidantchik, Carmen; Pommes, Kathy; Pavani, Varlen; Arosa, Breno; Abreu, Igor

    2015-12-01

    The ATLAS Technical Coordination disposes of 17 Web systems to support its operation. These applications, whilst ranging from managing the process of publishing scientific papers to monitoring radiation levels in the equipment in the experimental cavern, are constantly prone to changes in requirements due to the collaborative nature of the experiment and its management. In this context, a Web framework is proposed to unify the generation of the supporting interfaces. FENCE assembles classes to build applications by making extensive use of JSON configuration files. It relies heavily on Glance, a technology that was set forth in 2003 to create an abstraction layer on top of the heterogeneous sources that store the technical coordination data. Once Glance maps out the database modeling, records can be referenced in the configuration files by wrapping unique identifiers around double enclosing brackets. The deployed content can be individually secured by attaching clearance attributes to their description thus ensuring that view/edit privileges are granted to eligible users only. The framework also provides tools for securely writing into a database. Fully HTML5-compliant multi-step forms can be generated from their JSON description to assure that the submitted data comply with a series of constraints. Input validation is carried out primarily on the server- side but, following progressive enhancement guidelines, verification might also be performed on the client-side by enabling specific markup data attributes which are then handed over to the jQuery validation plug-in. User monitoring is accomplished by thoroughly logging user requests along with any POST data. Documentation is built from the source code using the phpDocumentor tool and made readily available for developers online. Fence, therefore, speeds up the implementation of Web interfaces and reduces the response time to requirement changes by minimizing maintenance overhead.

  6. The digital anatomist information system and its use in the generation and delivery of Web-based anatomy atlases.

    Science.gov (United States)

    Brinkley, J F; Bradley, S W; Sundsten, J W; Rosse, C

    1997-12-01

    Advances in network and imaging technology, coupled with the availability of 3-D datasets such as the Visible Human, provide a unique opportunity for developing information systems in anatomy that can deliver relevant knowledge directly to the clinician, researcher or educator. A software framework is described for developing such a system within a distributed architecture that includes spatial and symbolic anatomy information resources, Web and custom servers, and authoring and end-user client programs. The authoring tools have been used to create 3-D atlases of the brain, knee and thorax that are used both locally and throughout the world. For the one and a half year period from June 1995-January 1997, the on-line atlases were accessed by over 33,000 sites from 94 countries, with an average of over 4000 "hits" per day, and 25,000 hits per day during peak exam periods. The atlases have been linked to by over 500 sites, and have received at least six unsolicited awards by outside rating institutions. The flexibility of the software framework has allowed the information system to evolve with advances in technology and representation methods. Possible new features include knowledge-based image retrieval and tutoring, dynamic generation of 3-D scenes, and eventually, real-time virtual reality navigation through the body. Such features, when coupled with other on-line biomedical information resources, should lead to interesting new ways for managing and accessing structural information in medicine. PMID:9466836

  7. Report of International Coastal Atlas Network Workshop 6: Expanding Participation in Coastal Web Atlas Development and Use

    OpenAIRE

    Dwyer, Ned; Kopke, Kathrin

    2014-01-01

    From June 16th to 17th, 2013, the International Coastal Atlas Network (ICAN) held a workshop on “Expanding Participation in Coastal Web Atlas Development and Use”, at the University of Victoria, British Columbia, Canada. The workshop (aka “ICAN 6”) engaged 29 participants from 9 countries, representing 22 organizations and multiple areas of scientific and technical expertise. This meeting was a follow-up to the successful 2011 workshop on “Coastal Atlases as Engines for Coastal & Marine Spati...

  8. EnviroAtlas - Paterson, New Jersey - One Meter Resolution Urban Land Cover (2010) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Paterson, New Jersey EnviroAtlas One Meter-scale Urban Land Cover Web Service comprises approximately 66 km2 around the city of Paterson. The land cover data...

  9. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers.

    Science.gov (United States)

    Busato, Mirko; Giorgetti, Alejandro

    2016-08-01

    Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well. PMID:27102413

  10. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. PMID:26410586

  11. New nuclear data service at CNEA: retrieval of the update libraries from a local Web-Server

    International Nuclear Information System (INIS)

    A new On-line Nuclear Data Service was implemented at National Atomic Energy Commission (CNEA) Web-Site. The information usually issued by the Nuclear Data Section of IAEA (NDS-IAEA) on CD-ROM, as well as complementary libraries periodically downloaded from the a mirror server of NDS-IAEA Service located at IPEN, Brazil are available on the new CNEA Web page. In the site, users can find numerical data on neutron, charged-particle, and photonuclear reactions, nuclear structure, and decay data, with related bibliographic information. This data server is permanently maintained and updated by CNEA staff members. This crew also offers assistance on the use and retrieval of nuclear data to local users. (author)

  12. Design and Implementation of Embedded Web Server Security Based on SSL%基于SSL的嵌入式Web服务器安全设计与实现

    Institute of Scientific and Technical Information of China (English)

    沈勇; 朱超

    2012-01-01

    Embedded Web servers face the same problem of network security as traditional Web servers. The architecture and characteristics of embedded Web technologies are introduced, and its security requirements are analyzed. On this basis, a security enhancing scheme based on SSL protocol for embedded Web server is given. Analyzing and selecting the SSL protocol and Web server software package, a security embedded Web server system is constructed. Its security is analyzed and tested. Experiments show that, the security scheme can ensure the confidentiality, integrality and non-repudiation of information services of embedded Web server, and achieve the effect of enhancing security.%嵌入式Web服务器与传统Web服务器一样,面临网络安全问题.介绍嵌入式Web技术的体系结构和特点,给出一种基于SSL协议的嵌入式Web服务器安全增强方案设计.分析并选择适合的SSL协议和Web服务器软件包,构建一个安全的嵌入式Web服务器系统,测试并分析该系统的安全性.实验表明,该安全方案可以保障嵌入式Web服务器信息服务的机密性、完整性和不可否认性,达到了安全增强的效果.

  13. The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties

    OpenAIRE

    Jensen, Jan H.; Kromann, Jimmy C.

    2013-01-01

    A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or P...

  14. PRISM: a web server and repository for prediction of protein–protein interactions and modeling their 3D complexes

    OpenAIRE

    Baspinar, Alper; Cukuroglu, Engin; Nussinov, Ruth; Keskin, Ozlem; Gursoy, Attila

    2014-01-01

    The PRISM web server enables fast and accurate prediction of protein–protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein structures, PRISM will provide a structural model of their complex if a matching template interface is available. Users can download the complex structure, retrieve the interface r...

  15. Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering

    OpenAIRE

    Rajni Verma; Ulrich Schwaneberg; Danilo Roccatano

    2012-01-01

    The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE) and the review summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this review is to provide concise ...

  16. catRAPID omics: a web server for large-scale prediction of protein–RNA interactions

    Science.gov (United States)

    Agostini, Federico; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica; Cirillo, Davide; Tartaglia, Gian Gaetano

    2013-01-01

    Summary: Here we introduce catRAPID omics, a server for large-scale calculations of protein–RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences without size restriction; (iii) analysis of nucleic acid binding regions in proteins; and (iv) detection of RNA motifs involved in protein recognition. Results: We developed a web server to allow fast calculation of ribonucleoprotein associations in Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae and Xenopus tropicalis (custom libraries can be also generated). The catRAPID omics was benchmarked on the recently published RNA interactomes of Serine/arginine-rich splicing factor 1 (SRSF1), Histone-lysine N-methyltransferase EZH2 (EZH2), TAR DNA-binding protein 43 (TDP43) and RNA-binding protein FUS (FUS) as well as on the protein interactomes of U1/U2 small nucleolar RNAs, X inactive specific transcript (Xist) repeat A region (RepA) and Crumbs homolog 3 (CRB3) 3′-untranslated region RNAs. Our predictions are highly significant (P < 0.05) and will help the experimentalist to identify candidates for further validation. Availability: catRAPID omics can be freely accessed on the Web at http://s.tartaglialab.com/catrapid/omics. Documentation, tutorial and FAQs are available at http://s.tartaglialab.com/page/catrapid_group. Contact: gian.tartaglia@crg.eu PMID:23975767

  17. Getting to the Source: a Survey of Quantitative Data Sources Available to the Everyday Librarian: Part 1: Web Server Log Analysis

    OpenAIRE

    Lisa Goddard

    2007-01-01

    This is the first part of a two‐part article that provides a survey of data sources which are likely to be immediately available to the typical practitioner who wishes to engage instatistical analysis of collections and services within his or her own library. Part I outlines the data elements which can be extracted from web server logs, and discusses web log analysis tools. Part II looks at logs, reports, and data sources from proxy servers, resource vendors, link resolvers, federated search ...

  18. Interoperability Between Coastal Web Atlases Using Semantic Mediation: A Case Study of the International Coastal Atlas Network (ICAN)

    Science.gov (United States)

    Wright, D. J.; Lassoued, Y.; Dwyer, N.; Haddad, T.; Bermudez, L. E.; Dunne, D.

    2009-12-01

    Coastal mapping plays an important role in informing marine spatial planning, resource management, maritime safety, hazard assessment and even national sovereignty. As such, there is now a plethora of data/metadata catalogs, pre-made maps, tabular and text information on resource availability and exploitation, and decision-making tools. A recent trend has been to encapsulate these in a special class of web-enabled geographic information systems called a coastal web atlas (CWA). While multiple benefits are derived from tailor-made atlases, there is great value added from the integration of disparate CWAs. CWAs linked to one another can query more successfully to optimize planning and decision-making. If a dataset is missing in one atlas, it may be immediately located in another. Similar datasets in two atlases may be combined to enhance study in either region. *But how best to achieve semantic interoperability to mitigate vague data queries, concepts or natural language semantics when retrieving and integrating data and information?* We report on the development of a new prototype seeking to interoperate between two initial CWAs: the Marine Irish Digital Atlas (MIDA) and the Oregon Coastal Atlas (OCA). These two mature atlases are used as a testbed for more regional connections, with the intent for the OCA to use lessons learned to develop a regional network of CWAs along the west coast, and for MIDA to do the same in building and strengthening atlas networks with the UK, Belgium, and other parts of Europe. Our prototype uses semantic interoperability via services harmonization and ontology mediation, allowing local atlases to use their own data structures, and vocabularies (ontologies). We use standard technologies such as OGC Web Map Services (WMS) for delivering maps, and OGC Catalogue Service for the Web (CSW) for delivering and querying ISO-19139 metadata. The metadata records of a given CWA use a given ontology of terms called local ontology. Human or machine

  19. A Secure Web-Based File Exchange Server: Software Requirements Specification Document

    OpenAIRE

    Mokhov, Serguei A.; Laverdière, Marc-André; Benssam, Ali; Benredjem, Djamel

    2011-01-01

    This document presents brief software specification of a secure file exchange system prototype involving mutual authentication of the users via their browser and the application server with PKI-based certificates as credentials, the use of LDAP for credential management, and authentication between the application and database servers to maintain a high level of trust between all parties.

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

    Science.gov (United States)

    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,…

  1. myPhyloDB: a local web server for the storage and analysis of metagenomic data.

    Science.gov (United States)

    Manter, Daniel K; Korsa, Matthew; Tebbe, Caleb; Delgado, Jorge A

    2016-01-01

    myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org. PMID:27022159

  2. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-01

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. PMID:27106060

  3. Database and a worldwide web-application server as a tool for remote participation at TEXTOR-94

    International Nuclear Information System (INIS)

    This paper describes the use of a central database for storing the TEXTOR-94 machine parameters as defined by the engineer in charge. Furthermore, the possibility of writing an online experiment logbook is given to the physicist in charge. An online display of the comments for a discharge, given by the physicist, is installed. In addition the plasma quantities, necessary for the characterization of a discharge, are evaluated and stored within the database. An overview picture is created from the stored data with important time traces as plasma current, density and temperature and stored as a graphic interchangeable format file in the database. With a central worldwide web (WEB)-application server and a commercial WEB-browser the stored information can be accessed from different locations, specially from the home base of the three Trilateral Euregio Cluster partners

  4. Web-based Quality Control Tool used to validate CERES products on a cluster of Linux servers

    Science.gov (United States)

    Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Mlynczak, P.; Mitrescu, C.; Doelling, D.

    2014-12-01

    There have been a few popular desktop tools used in the Earth Science community to validate science data. Because of the limitation on the capacity of desktop hardware such as disk space and CPUs, those softwares are not able to display large amount of data from files.This poster will talk about an in-house developed web-based software built on a cluster of Linux servers. That allows users to take advantage of a few Linux servers working in parallel to generate hundreds images in a short period of time. The poster will demonstrate:(1) The hardware and software architecture is used to provide high throughput of images. (2) The software structure that can incorporate new products and new requirement quickly. (3) The user interface about how users can manipulate the data and users can control how the images are displayed.

  5. Controlling and accessing vehicle functions by mobile from remote place by sending GPS Co-ordinates to the Web server

    Directory of Open Access Journals (Sweden)

    Dr. Khanna SamratVivekanand Omprakash

    2012-01-01

    Full Text Available This paper represents how the co-ordinates from the Google map stored into database . It stored into the central web server . This co-ordinates then transfer to client program for searching the locations of particular location for electronic device . Client can access the data from internet and use into program by using API . Development of software for a particular device for putting into the vehicle has been develop. In the inbuilt circuit assigning sim card and transferring the signal to the network. Supplying a single text of co-ordinates of locations using google map in terms of latitudes and longitudes. The information in terms of string separated by comma can be extracted and stored into the database of web server . Different mobile number with locations can be stored into the database simultaneously into the server of different clients . The concept of 3 Tier Client /Server architecture is used. The sim card can access information of GPRS system with the network provider of card . Setting of electronic device signal for receiving and sending message done. Different operations can be performed on the device as it can be attached with other electronic circuit of vehicle. Windows Mobile application developed for client slide. User can take different decision of vehicle from mobile by sending sms to the device . Device receives the operation and send to the electronic circuit of vehicle for certain operations. From remote place using mobile you can get the information of your vehicle and also you can control vehicle it by providing password to the electronic circuit for authorization and authentication. The concept of vehicle security and location of vehicle can be identified. The functions of vehicle can be accessed and control like speed , brakes and lights etc as per the software application interface with electronic circuit of vehicle.

  6. The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers

    OpenAIRE

    Fox, Joanne A.; Butland, Stefanie L.; McMillan, Scott; Campbell, Graeme; Ouellette, B. F. Francis

    2005-01-01

    The Bioinformatics Links Directory is an online community resource that contains a directory of freely available tools, databases, and resources for bioinformatics and molecular biology research. The listing of the servers published in this and previous issues of Nucleic Acids Research together with other useful tools and websites represents a rich repository of resources that are openly provided to the research community using internet technologies. The 166 servers highlighted in the 2005 We...

  7. TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

    Directory of Open Access Journals (Sweden)

    Menossi Marcelo

    2007-05-01

    Full Text Available Abstract Background The nucleotide sequence flanking the translation initiation codon (start codon context affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this paper we present a web server that performs computations to investigate the usage of alternative translation initiation sites for the synthesis of new protein variants that might have different functions. Results An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at http://ipe.cbmeg.unicamp.br/pub/TISs-ST. Conclusion The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.

  8. iGPCR-drug: a web server for predicting interaction between GPCRs and drugs in cellular networking.

    Directory of Open Access Journals (Sweden)

    Xuan Xiao

    Full Text Available Involved in many diseases such as cancer, diabetes, neurodegenerative, inflammatory and respiratory disorders, G-protein-coupled receptors (GPCRs are among the most frequent targets of therapeutic drugs. It is time-consuming and expensive to determine whether a drug and a GPCR are to interact with each other in a cellular network purely by means of experimental techniques. Although some computational methods were developed in this regard based on the knowledge of the 3D (dimensional structure of protein, unfortunately their usage is quite limited because the 3D structures for most GPCRs are still unknown. To overcome the situation, a sequence-based classifier, called "iGPCR-drug", was developed to predict the interactions between GPCRs and drugs in cellular networking. In the predictor, the drug compound is formulated by a 2D (dimensional fingerprint via a 256D vector, GPCR by the PseAAC (pseudo amino acid composition generated with the grey model theory, and the prediction engine is operated by the fuzzy K-nearest neighbour algorithm. Moreover, a user-friendly web-server for iGPCR-drug was established at http://www.jci-bioinfo.cn/iGPCR-Drug/. For the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated math equations presented in this paper just for its integrity. The overall success rate achieved by iGPCR-drug via the jackknife test was 85.5%, which is remarkably higher than the rate by the existing peer method developed in 2010 although no web server was ever established for it. It is anticipated that iGPCR-Drug may become a useful high throughput tool for both basic research and drug development, and that the approach presented here can also be extended to study other drug - target interaction networks.

  9. Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences.

    Science.gov (United States)

    Liu, Bin; Liu, Fule; Wang, Xiaolong; Chen, Junjie; Fang, Longyun; Chou, Kuo-Chen

    2015-07-01

    With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems in computational biology is how to effectively formulate the sequence of a biological sample (such as DNA, RNA or protein) with a discrete model or a vector that can effectively reflect its sequence pattern information or capture its key features concerned. Although several web servers and stand-alone tools were developed to address this problem, all these tools, however, can only handle one type of samples. Furthermore, the number of their built-in properties is limited, and hence it is often difficult for users to formulate the biological sequences according to their desired features or properties. In this article, with a much larger number of built-in properties, we are to propose a much more flexible web server called Pse-in-One (http://bioinformatics.hitsz.edu.cn/Pse-in-One/), which can, through its 28 different modes, generate nearly all the possible feature vectors for DNA, RNA and protein sequences. Particularly, it can also generate those feature vectors with the properties defined by users themselves. These feature vectors can be easily combined with machine-learning algorithms to develop computational predictors and analysis methods for various tasks in bioinformatics and system biology. It is anticipated that the Pse-in-One web server will become a very useful tool in computational proteomics, genomics, as well as biological sequence analysis. Moreover, to maximize users' convenience, its stand-alone version can also be downloaded from http://bioinformatics.hitsz.edu.cn/Pse-in-One/download/, and directly run on Windows, Linux, Unix and Mac OS. PMID:25958395

  10. Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering

    Directory of Open Access Journals (Sweden)

    Rajni Verma

    2012-09-01

    Full Text Available The combination of computational and directed evolution methods has proven a winning strategy for protein engineering. We refer to this approach as computer-aided protein directed evolution (CAPDE and the review summarizes the recent developments in this rapidly growing field. We will restrict ourselves to overview the availability, usability and limitations of web servers, databases and other computational tools proposed in the last five years. The goal of this review is to provide concise information about currently available computational resources to assist the design of directed evolution based protein engineering experiment.

  11. Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

    OpenAIRE

    Honda Kiyoshi; Boulos Maged

    2006-01-01

    Abstract Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article w...

  12. CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy

    Institute of Scientific and Technical Information of China (English)

    Guanghong Zuo; Bailin Hao

    2015-01-01

    A faithful phylogeny and an objective taxonomy for prokaryotes should agree with each other and ultimately follow the genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference and detailed comparison with taxonomy are great challenges. We now provide one solution in the latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3. The server resides in a cluster of 64 cores and is equipped with an interactive, collapsible, and expandable tree display. It is capable of comparing the tree branching order with prokaryotic classification at all taxonomic ranks from domains down to species and strains. CVTree3 allows for inquiry by taxon names and trial on lineage modifications. In addition, it reports a summary of monophyletic and non-monophyletic taxa at all ranks as well as produces print-quality subtree figures. After giving an overview of retrospective verification of the CVTree approach, the power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes. A few discrepancies between CVTree and 16S rRNA analyses are also summarized with regard to possible taxonomic revisions. CVTree3 is freely accessible to all users at http://tlife.fudan.edu.cn/cvtree3/without login requirements.

  13. The State of the Art in Locally Distributed Web-Server Systems

    Directory of Open Access Journals (Sweden)

    M. Ezhilvendan

    2013-01-01

    Full Text Available The paper describes a novel algorithms for a load balancer, allocates the work to the clusters of SIP server. The several load balancing algorithms for distributing Session Initiation Protocol (SIP request to a cluster of SIP servers. This algorithm also supports the following three techniques such as CJSQ, TJSQ and TLWL. It is combine knowledge of the SIP, recognizing variability in call length, dynamic estimates of back-end server load for different SIP transactions. In this paper load balancer improves both throughput and response time. The SIP is a protocol of growing importance, with uses for VOIP, IPTV, audio conferencing, instant messaging. We present a detailed analysis of occupancy to show how our algorithms significantly reduce response time.

  14. Microsoft TerraServer

    OpenAIRE

    Barclay, Tom; Eberl, Robert; Gray, Jim; Nordlinger, John; Raghavendran, Guru; Slutz, Don; Smith, Greg; Smoot, Phil; Hoffman, John; Robb III, Natt; Rossmeissl, Hedy; Duff, Beth; Lee, George; Mathesmier, Theresa; Sunne, Randall

    1998-01-01

    The Microsoft TerraServer stores aerial and satellite images of the earth in a SQL Server Database served to the public via the Internet. It is the world's largest atlas, combining five terabytes of image data from the United States Geodetic Survey, Sovinformsputnik, and Encarta Virtual Globe. Internet browsers provide intuitive spatial and gazetteer interfaces to the data. The TerraServer is also an E-Commerce application. Users can buy the right to use the imagery using Microsoft Site Serve...

  15. Justifying the need for forensically ready protocols: A case study of identifying malicious web servers using client honeypots

    Energy Technology Data Exchange (ETDEWEB)

    Seifert, Christian; Endicott-Popovsky, Barbara E.; Frincke, Deborah A.; Komisarczuk, Peter; Muschevici, Radu; Welch, Ian D.

    2008-01-03

    Abstract: Client honeypot technology can find malicious web servers that attack web browsers and push malware, so called drive-by-downloads, to the client machine. Merely recording the network traffic is insufficient to perform an efficient forensic analysis of the attack. Custom tools need to be developed to access and examine the embedded data of the network protocols. Once the information is extracted from the network data, it cannot be used to perform a behavioral analysis on the attack, therefore limiting the ability to answer what exactly happened on the attacked system. Implementation of a record/ replay mechanism is proposed that allows the forensic examiner to easily extract application data from recorded network streams and allows applications to interact with such data for behavioral analysis purposes. A concrete implementation of such a setup for HTTP and DNS protocols using the HTTP proxy Squid and DNS proxy pdnsd is presented and its effect on digital forensic analysis demonstrated.

  16. EarthServer - Opportunities and challenges of serving ECMWF's peta-sized archive through OGC web-services

    Science.gov (United States)

    Wagemann, Julia; Siemen, Stephan; Lamy-Thepaut, Sylvie

    2016-04-01

    ECMWF is partner of the EU-funded (Horizon2020) EarthServer-2 project and is setting up a web service that facilitates climate data access, exploration, analysis and visualisation based on Open Geospatial Consortium (OGC) standards. By doing this, ECMWF data shall become easier accessible to researchers and decision-makers of the MetOcean and GIS community. MARS is ECMWF's Meteorological Archive and Retrieval System, the world's largest archive of meteorological data. In November 2015, the MARS archive held ~87 PB of data and grew by additional ~3 PB every month. In order for users to fully benefit from the potential of a data volume beyond the PB, it is in the interest of ECMWF as a data provider to minimize the necessary data transport and yet, to provide access to the full range of data and information. The aim of the three-year project is to establish a connection between the rasdaman server technology and ECMWF's MARS archive and thus, provide access to more than 1 PB of global reanalysis served by the OGC-based standard data access protocols Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS). By presenting first results of serving meteorological data, the presentation will show opportunities for data users using OGC web services. A further focus will be set on current challenges of serving climate data from ECMWF's archive and specific requirements of the MetOcean community, e.g. related to the support of GRIB and netCDF data, in order to collectively work on mature Big Data standards across all Earth Science disciplines.

  17. A Server-Side Feature Detection System for an Enterprise Web CMS

    OpenAIRE

    2013-01-01

    Mobile devices have in later years become increasingly popular to use for browsing the Web. With this increased popularity, the limitations of the devices, along with the complexity of modern Web pages, have become apparent. Several methods have been introduced to alleviate the issues encountered on the “Mobile Web”, including Responsive Web Design (RWD) and Device Experiences (DE). In this thesis, I present the Web technologies and concepts involved historically, along with their perceived p...

  18. E-Learning Technologies: Employing Matlab Web Server to Facilitate the Education of Mathematical Programming

    Science.gov (United States)

    Karagiannis, P.; Markelis, I.; Paparrizos, K.; Samaras, N.; Sifaleras, A.

    2006-01-01

    This paper presents new web-based educational software (webNetPro) for "Linear Network Programming." It includes many algorithms for "Network Optimization" problems, such as shortest path problems, minimum spanning tree problems, maximum flow problems and other search algorithms. Therefore, webNetPro can assist the teaching process of courses such…

  19. The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification.

    Science.gov (United States)

    Afrasiabi, Cyrus; Samad, Bushra; Dineen, David; Meacham, Christopher; Sjölander, Kimmen

    2013-07-01

    The PhyloFacts 'Fast Approximate Tree Classification' (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT's high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts' broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/. PMID:23685612

  20. SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data.

    Science.gov (United States)

    Li, Jun; Roebuck, Paul; Grünewald, Stefan; Liang, Han

    2012-07-01

    An important task in biomedical research is identifying biomarkers that correlate with patient clinical data, and these biomarkers then provide a critical foundation for the diagnosis and treatment of disease. Conventionally, such an analysis is based on individual genes, but the results are often noisy and difficult to interpret. Using a biological network as the searching platform, network-based biomarkers are expected to be more robust and provide deep insights into the molecular mechanisms of disease. We have developed a novel bioinformatics web server for identifying network-based biomarkers that most correlate with patient survival data, SurvNet. The web server takes three input files: one biological network file, representing a gene regulatory or protein interaction network; one molecular profiling file, containing any type of gene- or protein-centred high-throughput biological data (e.g. microarray expression data or DNA methylation data); and one patient survival data file (e.g. patients' progression-free survival data). Given user-defined parameters, SurvNet will automatically search for subnetworks that most correlate with the observed patient survival data. As the output, SurvNet will generate a list of network biomarkers and display them through a user-friendly interface. SurvNet can be accessed at http://bioinformatics.mdanderson.org/main/SurvNet. PMID:22570412

  1. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

    DEFF Research Database (Denmark)

    Amico, M.; Finelli, M.; Rossi, I.; Zauli, A.; Elofsson, A.; Viklund, H.; Heijne, G. von; Joes, D.; Krogh, A.; Fariselli, P.; Luigi, Martelli P.; Casadio, R.

    2006-01-01

    The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes ( http://www.biosapiens.info/ ). In this context, the PONGO DAS server ( http://...

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

    CERN Document Server

    Odier, Jerome; The ATLAS collaboration; Fulachier, Jerome; Lambert, Fabian

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  4. Getting to the Source: a Survey of Quantitative Data Sources Available to the Everyday Librarian: Part 1: Web Server Log Analysis

    Directory of Open Access Journals (Sweden)

    Lisa Goddard

    2007-03-01

    Full Text Available This is the first part of a two‐part article that provides a survey of data sources which are likely to be immediately available to the typical practitioner who wishes to engage instatistical analysis of collections and services within his or her own library. Part I outlines the data elements which can be extracted from web server logs, and discusses web log analysis tools. Part II looks at logs, reports, and data sources from proxy servers, resource vendors, link resolvers, federated search engines, institutional repositories, electronic reference services, and the integrated library system.

  5. The library without walls: images, medical dictionaries, atlases, medical encyclopedias free on web.

    Science.gov (United States)

    Giglia, E

    2008-09-01

    The aim of this article was to present the ''reference room'' of the Internet, a real library without walls. The reader will find medical encyclopedias, dictionaries, atlases, e-books, images, and will also learn something useful about the use and reuse of images in a text and in a web site, according to the copyright law. PMID:18762749

  6. PINTA: a web server for network-based gene prioritization from expression data

    DEFF Research Database (Denmark)

    Nitsch, Daniela; Tranchevent, Léon-Charles; Goncalves, Joana P.; Vogt, Josef Korbinian; Madeira, Sara C.; Moreau, Yves

    PINTA (available at http://www.esat.kuleuven.be/ pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein–protein interaction...

  7. Analyzing Web Server Logs to Improve a Site's Usage. The Systems Librarian

    Science.gov (United States)

    Breeding, Marshall

    2005-01-01

    This column describes ways to streamline and optimize how a Web site works in order to improve both its usability and its visibility. The author explains how to analyze logs and other system data to measure the effectiveness of the Web site design and search engine.

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

    CERN Document Server

    Odier, Jerome; The ATLAS collaboration; Fulachier, Jerome; Lambert, Fabian

    2015-01-01

    The ATLAS Metadata Interface (AMI) can be considered to be a mature application because it has existed for at least 10 years. Over the last year, we have been adapting the application to some recently available technologies. The web interface, which previously manipulated XML documents using XSL transformations, has been migrated to Asynchronous Java Script (AJAX). Web development has been considerably simplified by the development of a framework for AMI based on JQuery and Twitter Bootstrap. Finally there has been a major upgrade of the python web service client.

  9. The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties

    CERN Document Server

    Jensen, Jan H

    2013-01-01

    A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or PM3 level of theory (all other properties) in a matter of seconds or minutes depending on the size of the molecule. The results, though approximate, can help students develop a "chemical intuition" about how molecular structure affects molecular properties, without performing the underlying calculations by hand, a near impossible task for all but the simplest chemical systems.

  10. The Web-based Application Server: Combining earth observation with in-situ data and modelling. ISECA Final Report D3.1

    OpenAIRE

    de Kok, J.-L.; DeCorte, L; Peelaerts, W.

    2014-01-01

    The report describes the purpose, architecture and functionalities of the ISECA Web-based Application Server (WAS). This web-based information system combines earth observation and in-situ data with examples of model simulations related to eutrophication for the 2Seas Territorial Waters of the Southern North Sea. Step-by-step instructions on how to use the WAS are included in this report. More background information on the problem of eutrophication and eutrophication modelling is found in IS...

  11. Enhanced Service-Oriented Open Sensor Web Architecture with Application Server Based Mashup

    OpenAIRE

    Muhammad Sohail Khan; DoHyeun Kim

    2014-01-01

    Connecting the sensing devices present in the physical world to detect and measure various physical phenomenon such as temperature, humidity, and pollution into a network and presenting them as web resources to the end users have become the goal of a variety of research activities. As the physical network of these devices inherently possesses a heterogeneous nature thus most of the sensor web studies are based on providing domain specific solutions. Service-oriented architecture (SOA) has pro...

  12. Web server of the Centre for Photonuclear Experiments Data of the Scientific Research Institute for Nuclear Physics, Moscow State University: Hypertext version of the nuclear physics database

    International Nuclear Information System (INIS)

    The nuclear databases which have been developed at the Centre for Photonuclear Experiments Data of the D.V. Skobel'tsyn Scientific Research Institute for Nuclear Physics, M.V. Lomonosov Moscow State University, and put on the Centre's web server, are presented. The possibilities for working with these databases on the Internet are described. (author)

  13. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet.

    Science.gov (United States)

    Tyagi, M; Sharma, P; Swamy, C S; Cadet, F; Srinivasan, N; de Brevern, A G; Offmann, B

    2006-07-01

    Encoding protein 3D structures into 1D string using short structural prototypes or structural alphabets opens a new front for structure comparison and analysis. Using the well-documented 16 motifs of Protein Blocks (PBs) as structural alphabet, we have developed a methodology to compare protein structures that are encoded as sequences of PBs by aligning them using dynamic programming which uses a substitution matrix for PBs. This methodology is implemented in the applications available in Protein Block Expert (PBE) server. PBE addresses common issues in the field of protein structure analysis such as comparison of proteins structures and identification of protein structures in structural databanks that resemble a given structure. PBE-T provides facility to transform any PDB file into sequences of PBs. PBE-ALIGNc performs comparison of two protein structures based on the alignment of their corresponding PB sequences. PBE-ALIGNm is a facility for mining SCOP database for similar structures based on the alignment of PBs. Besides, PBE provides an interface to a database (PBE-SAdb) of preprocessed PB sequences from SCOP culled at 95% and of all-against-all pairwise PB alignments at family and superfamily levels. PBE server is freely available at http://bioinformatics.univ-reunion.fr/PBE/. PMID:16844973

  14. Digital content sewed together within a library catalogue WebLib - The CERN Document Server

    CERN Document Server

    Vigen, Jens

    2002-01-01

    Aggregation, harvesting, personalization techniques, portals, service provision, etc. have all become buzzwords. Most of them simply describing what librarians have been doing for hundreds of years. Prior to the Web few people outside the libraries were concerned about these issues, a situation which today it is completely turned upside down. Hopefully the new actors on the arena of knowledge management will take full advantage of all the available "savoir faire". At CERN, the European Organization for Nuclear Research, librarians and informaticians have set up a complete system, WebLib, actually based on the traditional library catalogue. Digital content is, within this framework, being integrated to the highest possible level in order to meet the strong requirements of the particle physics community. The paper gives an overview of the steps CERN has made towards the digital library from the day the laboratory conceived the World Wide Web to present.

  15. Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

    Directory of Open Access Journals (Sweden)

    Honda Kiyoshi

    2006-01-01

    Full Text Available Abstract Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium standards, including WMS (Web Map Service. WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described.

  16. New data access with HTTP/WebDAV in the ATLAS experiment

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration; Serfon, Cedric; Garonne, Vincent; Blunier, Sylvain; Lavorini, Vincenzo; Nilsson, Paul

    2015-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in the years 2010-2012, distributed computing has become the established way to analyse collider data. The ATLAS experiment Grid infrastructure includes more than 130 sites worldwide, ranging from large national computing centres to smaller university clusters. So far the storage technologies and access protocols to the clusters that host this tremendous amount of data vary from site to site. HTTP/WebDAV offers the possibility to use a unified industry standard to access the storage. We present the deployment and testing of HTTP/WebDAV for local and remote data access in the ATLAS experiment for the new data management system Rucio and the PanDA workload management system. Deployment and large scale tests have been performed using the Grid testing system HammerCloud and the ROOT HTTP plugin Davix.

  17. New data access with HTTP/WebDAV in the ATLAS experiment

    Science.gov (United States)

    Elmsheuser, J.; Walker, R.; Serfon, C.; Garonne, V.; Blunier, S.; Lavorini, V.; Nilsson, P.

    2015-12-01

    With the exponential growth of LHC (Large Hadron Collider) data in the years 2010-2012, distributed computing has become the established way to analyse collider data. The ATLAS experiment Grid infrastructure includes more than 130 sites worldwide, ranging from large national computing centres to smaller university clusters. So far the storage technologies and access protocols to the clusters that host this tremendous amount of data vary from site to site. HTTP/WebDAV offers the possibility to use a unified industry standard to access the storage. We present the deployment and testing of HTTP/WebDAV for local and remote data access in the ATLAS experiment for the new data management system Rucio and the PanDA workload management system. Deployment and large scale tests have been performed using the Grid testing system HammerCloud and the ROOT HTTP plugin Davix.

  18. New data access with HTTP/WebDAV in the ATLAS experiment

    CERN Document Server

    Elmsheuser, Johannes; The ATLAS collaboration; Serfon, Cedric; Garonne, Vincent; Blunier, Sylvain; Lavorini, Vincenzo; Nilsson, Paul

    2015-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in the years 2010-2012, distributed computing has become the established way to analyze collider data. The ATLAS experiment Grid infrastructure includes more than 130 sites worldwide, ranging from large national computing centres to smaller university clusters. So far the storage technologies and access protocols to the clusters that host this tremendous amount of data vary from site to site. HTTP/WebDAV offers the possibility to use a unified industry standard to access the storage. We present the deployment and testing of HTTP/WebDAV for local and remote data access in the ATLAS experiment for the new data management system Rucio and the PanDA workload management system. Deployment and large scale tests have been performed using the Grid testing system HammerCloud and the ROOT HTTP plugin Davix.

  19. PIMA: Protein-Protein interactions in Macromolecular Assembly - a web server for its Analysis and Visualization

    OpenAIRE

    Kaleeckal Mathew, Oommen; Sowdhamini, Ramanathan

    2016-01-01

    Protein-protein interactions are essential for the basic biological machinery of the cell. This is important for processes like protein synthesis, enzyme kinetics, molecular assembly and signal transduction. A high number of macromolecular structural complexes are known due to recent advances in structure determination techniques. Therefore, it is of interest to develop an interactive tool to objectively analyze large protein complexes. Hence, we describe the development and utility of a web ...

  20. UFO: a web server for ultra-fast functional profiling of whole genome protein sequences

    OpenAIRE

    Meinicke Peter

    2009-01-01

    Abstract Background Functional profiling is a key technique to characterize and compare the functional potential of entire genomes. The estimation of profiles according to an assignment of sequences to functional categories is a computationally expensive task because it requires the comparison of all protein sequences from a genome with a usually large database of annotated sequences or sequence families. Description Based on machine learning techniques for Pfam domain detection, the UFO web ...

  1. Update on XplorMed: a web server for exploring scientific literature

    OpenAIRE

    Perez-Iratxeta, C.; Perez, A. J.; Bork, P.; Andrade-Navarro, M A

    2003-01-01

    As scientific literature databases like MEDLINE increase in size, so does the time required to search them. Scientists must frequently inspect long lists of references manually, often just reading the titles. XplorMed is a web tool that aids MEDLINE searching by summarizing the subjects contained in the results, thus allowing users to focus on subjects of interest. Here we describe new features added to XplorMed during the last 2 years (http://www.bork.embl-heidelberg.de/xplormed/).

  2. Creating the Semantic Web: the Role of an agricultural Ontology Server (AOS)

    OpenAIRE

    Fisseha, Frehiwot; Hagedorn, Kat; Keizer, Johannes

    2002-01-01

    "Knowledge management is vital for effective decision-making.....It is therefore essential to maintain and improve the coverage, quantity, utility, timeliness and accessibility of the information collected and disseminated." (citation from the Strategic Framework for FAO). FAO is a huge content provider for the World Wide Web. The FAO website has more than 6 gigabytes of information that contains knowledge created by more than 4000 FAO staff working in the world to combat hunger and to help p...

  3. Radiology CME on the Web using secure document transfer and internationally distributed image servers.

    OpenAIRE

    McEnery, K. W.; Roth, S. M.; Walkup, R. V.

    1996-01-01

    We describe the implementation of a World Wide Web-based Continuing Medical Educational (CME) program in Diagnostic Radiology which allows accumulation of Category I credit. The program implements an unknown case presentation format which includes multiple choice questions, didactic information, and literature references with links to abstracts. Physician participation is anticipated to occur in brief sessions during which the program automatically tracks CME credit accumulation. To allow an ...

  4. Web servers and services for electrostatics calculations with APBS and PDB2PQR

    OpenAIRE

    Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrosta...

  5. 校园网Web服务器安全策略研究%Research of Secure Policy for Campus Web Server

    Institute of Scientific and Technical Information of China (English)

    王建强

    2011-01-01

    随着基于Web的应用系统越来越多,应用越来越广泛,其安全性也越来越受到人们的重视。分析了当前Web服务器面临的安全威胁,讨论了几种加强校园网Web服务器安全性的几种策略。将这些策略应用到榆林学院校园网Web服务器上后,可以有效地提高校园网Web服务器的安全性。%More and more applicatieus of the Web,more and more attention is being paid to their safety.In this paper,we firstly analyzed the current security threats facing Web server,and then some strategy were discussed to enhance the campus Web server security.With these policies,the campus Web server security could be effectively improved.

  6. Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server

    Directory of Open Access Journals (Sweden)

    Unrau Peter J

    2006-04-01

    interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN9 comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects231011.

  7. Implementation of a World Wide Web server for the oil and gas industry

    International Nuclear Information System (INIS)

    The Gas and Oil Technology Exchange and Communication Highway (GO-TECH) provides an electronic information system for the petroleum community for exchanging ideas, data, and technology. The PC-based system fosters communication and discussion by linking the oil and gas producers with resource centers, government agencies, consulting firms, service companies, national laboratories, academic research groups, and universities throughout the world. The oil and gas producers can access the GO-TECH World Wide Web (WWW) home page through modem links, as well as through the Internet. Future GO-TECH applications will include the establishment of virtual corporations consisting of consortia of small companies, consultants, and service companies linked by electronic information systems. These virtual corporations will have the resources and expertise previously found only in major corporations

  8. RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

    Directory of Open Access Journals (Sweden)

    Ogurtsov Aleksey Y

    2008-10-01

    Full Text Available Abstract Background Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. Description We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. Conclusion We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.

  9. USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques.

    Science.gov (United States)

    Li, Hongjian; Leung, Kwong-S; Wong, Man-H; Ballester, Pedro J

    2016-07-01

    Ligand-based Virtual Screening (VS) methods aim at identifying molecules with a similar activity profile across phenotypic and macromolecular targets to that of a query molecule used as search template. VS using 3D similarity methods have the advantage of biasing this search toward active molecules with innovative chemical scaffolds, which are highly sought after in drug design to provide novel leads with improved properties over the query molecule (e.g. patentable, of lower toxicity or increased potency). Ultrafast Shape Recognition (USR) has demonstrated excellent performance in the discovery of molecules with previously-unknown phenotypic or target activity, with retrospective studies suggesting that its pharmacophoric extension (USRCAT) should obtain even better hit rates once it is used prospectively. Here we present USR-VS (http://usr.marseille.inserm.fr/), the first web server using these two validated ligand-based 3D methods for large-scale prospective VS. In about 2 s, 93.9 million 3D conformers, expanded from 23.1 million purchasable molecules, are screened and the 100 most similar molecules among them in terms of 3D shape and pharmacophoric properties are shown. USR-VS functionality also provides interactive visualization of the similarity of the query molecule against the hit molecules as well as vendor information to purchase selected hits in order to be experimentally tested. PMID:27106057

  10. dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions.

    Science.gov (United States)

    Wu, Jiaxin; Wu, Mengmeng; Li, Lianshuo; Liu, Zhuo; Zeng, Wanwen; Jiang, Rui

    2016-01-01

    The recent advancement of the next generation sequencing technology has enabled the fast and low-cost detection of all genetic variants spreading across the entire human genome, making the application of whole-genome sequencing a tendency in the study of disease-causing genetic variants. Nevertheless, there still lacks a repository that collects predictions of functionally damaging effects of human genetic variants, though it has been well recognized that such predictions play a central role in the analysis of whole-genome sequencing data. To fill this gap, we developed a database named dbWGFP (a database and web server of human whole-genome single nucleotide variants and their functional predictions) that contains functional predictions and annotations of nearly 8.58 billion possible human whole-genome single nucleotide variants. Specifically, this database integrates 48 functional predictions calculated by 17 popular computational methods and 44 valuable annotations obtained from various data sources. Standalone software, user-friendly query services and free downloads of this database are available at http://bioinfo.au.tsinghua.edu.cn/dbwgfp. dbWGFP provides a valuable resource for the analysis of whole-genome sequencing, exome sequencing and SNP array data, thereby complementing existing data sources and computational resources in deciphering genetic bases of human inherited diseases. PMID:26989155

  11. TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.

    Science.gov (United States)

    Hamed, Mohamed; Spaniol, Christian; Nazarieh, Maryam; Helms, Volkhard

    2015-07-01

    TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir. PMID:25943543

  12. Interactive atlas using web browser: CT and MRI of the temporal bone

    International Nuclear Information System (INIS)

    The purposes of this study were to construct an interactive atlas of the temporal bone using a web-browser and to provide a template for web-based teaching files, using free and shared applets and scripts on the internet. HRCT and MR images of the temporal bone including its normal anatomy, tumors, trauma, inflammation, anomalies and vascular diseases were used in this study. Acquired radiologic images were transformed to GIF/JPG formats and to achieve appropriate image quality, were retouched. Text and image files of normal anatomy and diseases were written by HTML. JavaScript and applets were inserted in the HTML files for the interactive display of images and texts. In order to review anatomic features and diseases, a search index was also attached to the last part of the file. Using interactive images and text, temporal bone anatomy and disorders were displayed. Scripts and applets were also useful for indicating specific points of interest when a mouse was placed over the anatomic sites. The atlas may be viewed in the form of a CD-ROM, or via the internet using any computer platform or web-browser. This web-based teaching file of the temporal bone offers dynamic and interactive education. It can be usefully employed as a template for the production of interactive educational materials, offering JavaScript and providing suitable input for classes. It can replace texts and imaging contents. (author)

  13. The Monitoring and Calibration Web Systems for the ATLAS Tile Calorimeter Data Quality Analysis

    Science.gov (United States)

    Sivolella, A.; Maidantchik, C.; Ferreira, F.

    2012-12-01

    The Tile Calorimeter (TileCal) is one of the ATLAS sub-detectors. The read-out is performed by about 10,000 PhotoMultiplier Tubes (PMTs). The signal of each PMT is digitized by an electronic channel. The Monitoring and Calibration Web System (MCWS) supports the data quality analysis of the electronic channels. This application was developed to assess the detector status and verify its performance. It can provide to the user the list of TileCal known problematic channels, that is stored in the ATLAS condition database (COOL DB). The bad channels list guides the data quality validator in identifying new problematic channels and is used in data reconstruction and the system allows to update the channels list directly in the COOL database. MCWS can generate summary results, such as eta-phi plots and comparative tables of the masked channels percentage. Regularly, during the LHC (Large Hadron Collider) shutdown a maintenance of the detector equipments is performed. When a channel is repaired, its calibration constants stored in the COOL database have to be updated. Additionally MCWS system manages the update of these calibration constants values in the COOL database. The MCWS has been used by the Tile community since 2008, during the commissioning phase, and was upgraded to comply with ATLAS operation specifications. Among its future developments, it is foreseen an integration of MCWS with the TileCal control Web system (DCS) in order to identify high voltage problems automatically.

  14. The research and implementation of coalfield spontaneous combustion of carbon emission WebGIS based on Silverlight and ArcGIS server

    International Nuclear Information System (INIS)

    As an important sub-topic of the natural process of carbon emission data public information platform construction, coalfield spontaneous combustion of carbon emission WebGIS system has become an important study object. In connection with data features of coalfield spontaneous combustion carbon emissions (i.e. a wide range of data, which is rich and complex) and the geospatial characteristics, data is divided into attribute data and spatial data. Based on full analysis of the data, completed the detailed design of the Oracle database and stored on the Oracle database. Through Silverlight rich client technology and the expansion of WCF services, achieved the attribute data of web dynamic query, retrieval, statistical, analysis and other functions. For spatial data, we take advantage of ArcGIS Server and Silverlight-based API to invoke GIS server background published map services, GP services, Image services and other services, implemented coalfield spontaneous combustion of remote sensing image data and web map data display, data analysis, thematic map production. The study found that the Silverlight technology, based on rich client and object-oriented framework for WCF service, can efficiently constructed a WebGIS system. And then, combined with ArcGIS Silverlight API to achieve interactive query attribute data and spatial data of coalfield spontaneous emmission, can greatly improve the performance of WebGIS system. At the same time, it provided a strong guarantee for the construction of public information on China's carbon emission data

  15. The research and implementation of coalfield spontaneous combustion of carbon emission WebGIS based on Silverlight and ArcGIS server

    Science.gov (United States)

    Zhu, Z.; Bi, J.; Wang, X.; Zhu, W.

    2014-02-01

    As an important sub-topic of the natural process of carbon emission data public information platform construction, coalfield spontaneous combustion of carbon emission WebGIS system has become an important study object. In connection with data features of coalfield spontaneous combustion carbon emissions (i.e. a wide range of data, which is rich and complex) and the geospatial characteristics, data is divided into attribute data and spatial data. Based on full analysis of the data, completed the detailed design of the Oracle database and stored on the Oracle database. Through Silverlight rich client technology and the expansion of WCF services, achieved the attribute data of web dynamic query, retrieval, statistical, analysis and other functions. For spatial data, we take advantage of ArcGIS Server and Silverlight-based API to invoke GIS server background published map services, GP services, Image services and other services, implemented coalfield spontaneous combustion of remote sensing image data and web map data display, data analysis, thematic map production. The study found that the Silverlight technology, based on rich client and object-oriented framework for WCF service, can efficiently constructed a WebGIS system. And then, combined with ArcGIS Silverlight API to achieve interactive query attribute data and spatial data of coalfield spontaneous emmission, can greatly improve the performance of WebGIS system. At the same time, it provided a strong guarantee for the construction of public information on China's carbon emission data.

  16. The TDAQ Analytics Dashboard: a real-time web application for the ATLAS TDAQ control infrastructure

    Science.gov (United States)

    Lehmann Miotto, Giovanna; Magnoni, Luca; Sloper, John Erik

    2011-12-01

    The ATLAS Trigger and Data Acquisition (TDAQ) infrastructure is responsible for filtering and transferring ATLAS experimental data from detectors to mass storage systems. It relies on a large, distributed computing system composed of thousands of software applications running concurrently. In such a complex environment, information sharing is fundamental for controlling applications behavior, error reporting and operational monitoring. During data taking, the streams of messages sent by applications and data published via information services are constantly monitored by experts to verify the correctness of running operations and to understand problematic situations. To simplify and improve system analysis and errors detection tasks, we developed the TDAQ Analytics Dashboard, a web application that aims to collect, correlate and visualize effectively this real time flow of information. The TDAQ Analytics Dashboard is composed of two main entities that reflect the twofold scope of the application. The first is the engine, a Java service that performs aggregation, processing and filtering of real time data stream and computes statistical correlation on sliding windows of time. The results are made available to clients via a simple web interface supporting SQL-like query syntax. The second is the visualization, provided by an Ajax-based web application that runs on client's browser. The dashboard approach allows to present information in a clear and customizable structure. Several types of interactive graphs are proposed as widgets that can be dynamically added and removed from visualization panels. Each widget acts as a client for the engine, querying the web interface to retrieve data with desired criteria. In this paper we present the design, development and evolution of the TDAQ Analytics Dashboard. We also present the statistical analysis computed by the application in this first period of high energy data taking operations for the ATLAS experiment.

  17. The TDAQ Analytics Dashboard: a real-time web application for the ATLAS TDAQ control infrastructure

    International Nuclear Information System (INIS)

    The ATLAS Trigger and Data Acquisition (TDAQ) infrastructure is responsible for filtering and transferring ATLAS experimental data from detectors to mass storage systems. It relies on a large, distributed computing system composed of thousands of software applications running concurrently. In such a complex environment, information sharing is fundamental for controlling applications behavior, error reporting and operational monitoring. During data taking, the streams of messages sent by applications and data published via information services are constantly monitored by experts to verify the correctness of running operations and to understand problematic situations. To simplify and improve system analysis and errors detection tasks, we developed the TDAQ Analytics Dashboard, a web application that aims to collect, correlate and visualize effectively this real time flow of information. The TDAQ Analytics Dashboard is composed of two main entities that reflect the twofold scope of the application. The first is the engine, a Java service that performs aggregation, processing and filtering of real time data stream and computes statistical correlation on sliding windows of time. The results are made available to clients via a simple web interface supporting SQL-like query syntax. The second is the visualization, provided by an Ajax-based web application that runs on client's browser. The dashboard approach allows to present information in a clear and customizable structure. Several types of interactive graphs are proposed as widgets that can be dynamically added and removed from visualization panels. Each widget acts as a client for the engine, querying the web interface to retrieve data with desired criteria. In this paper we present the design, development and evolution of the TDAQ Analytics Dashboard. We also present the statistical analysis computed by the application in this first period of high energy data taking operations for the ATLAS experiment.

  18. The ATLAS Public Web Pages: Online Management of HEP External Communication Content

    CERN Document Server

    Goldfarb, Steven; Phoboo, Abha Eli; Shaw, Kate

    2015-01-01

    The ATLAS Education and Outreach Group is in the process of migrating its public online content to a professionally designed set of web pages built on the Drupal content management system. Development of the front-end design passed through several key stages, including audience surveys, stakeholder interviews, usage analytics, and a series of fast design iterations, called sprints. Implementation of the web site involves application of the html design using Drupal templates, refined development iterations, and the overall population of the site with content. We present the design and development processes and share the lessons learned along the way, including the results of the data-driven discovery studies. We also demonstrate the advantages of selecting a back-end supported by content management, with a focus on workflow. Finally, we discuss usage of the new public web pages to implement outreach strategy through implementation of clearly presented themes, consistent audience targeting and messaging, and th...

  19. SpectroWeb: An Interactive Graphical Database of Digital Stellar Spectral Atlases

    CERN Document Server

    Lobel, A

    2007-01-01

    SpectroWeb is an online maintained interactive graphical database of digital spectral atlases of spectral standard stars at http://spectra.freeshell.org . It is an efficient and user-friendly research tool for accurate analyses of stellar spectra observed with large spectral resolution, including the solar spectrum. The web-interface displays observed and theoretical stellar spectra, and comprehensively provides detailed atomic and molecular line information via user interaction. It fully integrates interactive spectrum visualization tools for the analysis, management, and maintenance of large volumes of spectral line-identification, -transition, and -property data. SpectroWeb 1.0 currently offers optical (3300-6800 A) flux normalized high-resolution spectra of Betelgeuse (M2), Arcturus (K1), The Sun (G2), Beta Aqr (G0), Procyon (F5), and Canopus (F0). The provided line identifications are based on state of the art spectrum synthesis calculations. The graphical database is under permanent development as an on...

  20. OPC UA IPbus server

    CERN Document Server

    Cristian-Valeriu, Soare

    2015-01-01

    The OPC UA IPbus server is a software tool which intends to connect IPbus-compatible devices such as data acquisition FPGAs to industry standard Unified Architecture clients (e.g. WinCC OA UA client, UA expert). It has been the missing link between IPbus devices and the ATLAS DCS.

  1. Low-cost Embedded Web Server Based on W5500%用 W5500构成的低成本嵌入式 Web服务器

    Institute of Scientific and Technical Information of China (English)

    茅胜荣; 肖家文; 乔东海

    2016-01-01

    In the era of HTML5 ,the B/S(Browser/Server) model has been applied in many applications with the number of Web server increasing .In the embedded field ,if the client wants to realize the function of the remote monitoring server ,the Web server not only need to parse the user requests ,but also need to make a quick and accurate response to the commands .Based on the OSI reference model and the HTTP communication ,a Web server is established ,which can run in a microcontroller ,without any complex web server framework . It can give a real‐time response to the traditional requests like HTML ,JavaScript and CSS ,and has the characteristics such as low re‐source consumption ,high efficiency ,good security ,low power consumption and low cost .%在HTML5的时代下,随着Web服务器的数量与日俱增,B/S(Browser/Server)模型得到了更加广泛的应用。在嵌入式领域,客户端可以实现远程监控服务器的功能,这不仅需要服务器解析用户请求,而且需要对用户指令作出快速准确的响应。本文在OSI互联参考模型的基础上,深入研究HTTP通信机制,抛弃了现有复杂的Web服务器框架,自主搭建了一个在单片机上运行的Web服务器,它能即时响应HTML网页、JavaScript脚本和CSS样式的请求,且具有占用资源少、运行效率高、安全性好、低功耗、低成本的特点。

  2. The Monitoring and Calibration Web Systems for the ATLAS Tile Calorimeter Data Quality Analysis

    CERN Document Server

    Sivolella, A; The ATLAS collaboration; Ferreira, F

    2012-01-01

    The Tile Calorimeter (TileCal), one of the ATLAS detectors, has four partitions, where each one contains 64 modules and each module has up to 48 PhotoMulTipliers (PMTs), totalizing more than 10,000 electronic channels. The Monitoring and Calibration Web System (MCWS) supports data quality analyses at channels level. This application was developed to assess the detector status and verify its performance, presenting the problematic known channels list from the official database that stores the detector conditions data (COOL). The bad channels list guides the data quality validator during analyses in order to identify new problematic channels. Through the system, it is also possible to update the channels list directly in the COOL database. MCWS generates results, as eta-phi plots and comparative tables with masked channels percentage, which concerns TileCal status, and it is accessible by all ATLAS collaboration. Annually, there is an intervention on LHC (Large Hadronic Collider) when the detector equipments (P...

  3. ADAM Project – A generic web interface for retrieval and display of ATLAS TDAQ information.

    CERN Document Server

    Harwood, A; The ATLAS collaboration; Lehmann Miotto, G

    2011-01-01

    This paper describes a new approach to the visualization of stored information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers, to the network utilization are stored in several databases for a posterior analysis. Although the ability to view these data-sets individually is already in place, there currently is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple diversely structured providers. It is capable of aggregating and correlating the data according to user defined criteria. Finally it v...

  4. The ADAM project: a generic web interface for retrieval and display of ATLAS TDAQ information.

    CERN Document Server

    Harwood, A; The ATLAS collaboration; Magnoni, L; Vandelli, W; Savu, D

    2011-01-01

    This paper describes a new approach to the visualization of stored information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers to the network utilization are stored in several databases for later analysis. Although the ability to view these data-sets individually is already in place, currently there is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple providers that have different structures. It is capable of aggregating and correlating the data according to user defined criteria. Finally, ...

  5. The ADAM project: a generic web interface for retrieval and display of ATLAS TDAQ information

    International Nuclear Information System (INIS)

    This paper describes a new approach to the visualization of information about the operation of the ATLAS Trigger and Data Acquisition system. ATLAS is one of the two general purpose detectors positioned along the Large Hadron Collider at CERN. Its data acquisition system consists of several thousand computers interconnected via multiple gigabit Ethernet networks, that are constantly monitored via different tools. Operational parameters ranging from the temperature of the computers to the network utilization are stored in several databases for later analysis. Although the ability to view these data-sets individually is already in place, currently there is no way to view this data together, in a uniform format, from one location. The ADAM project has been launched in order to overcome this limitation. It defines a uniform web interface to collect data from multiple providers that have different structures. It is capable of aggregating and correlating the data according to user defined criteria. Finally, it visualizes the collected data using a flexible and interactive front-end web system. Structurally, the project comprises of 3 main levels of the data collection cycle: The Level 0 represents the information sources within ATLAS. These providers do not store information in a uniform fashion. The first step of the project was to define a common interface with which to expose stored data. The interface designed for the project originates from the Google Data Protocol API. The idea is to allow read-only access to data providers, through HTTP requests similar in format to the SQL query structure. This provides a standardized way to access this different information sources within ATLAS. The Level 1 can be considered the engine of the system. The primary task of the Level 1 is to gather data from multiple data sources via the common interface, to correlate this data together, or over a defined time series, and expose the combined data as a whole to the Level 2 web

  6. The Next Generation ATLAS Production System

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration; Golubkov, Dmitry; Klimentov, Alexei; Maeno, Tadashi; Mashinistov, Ruslan; Vaniachine, Alexandre

    2015-01-01

    The ATLAS experiment at LHC data processing and simulation grows continuously, as more data and more use cases emerge. For data processing the ATLAS experiment adopted the data transformation approach, where software applications transform the input data into outputs. In the ATLAS production system, each data transformation is represented by a task, a collection of many jobs, dynamically submitted by the ATLAS workload management system (PanDA/JEDI) and executed on the Grid, clouds and supercomputers. Patterns in ATLAS data transformation workflows composed of many tasks provided a scalable production system framework for template definitions of the many-tasks workflows. User interface and system logic of these workflows are being implemented in the Database Engine for Tasks (DEFT). Such development required using modern computing technologies and approaches. We report technical details of this development: database implementation, server logic and Web user interface technologies.

  7. Web tools for large-scale 3D biological images and atlases

    Directory of Open Access Journals (Sweden)

    Husz Zsolt L

    2012-06-01

    Full Text Available Abstract Background Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. Results The standard Internet Imaging Protocol (IIP has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Conclusions Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.

  8. BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases

    DEFF Research Database (Denmark)

    Bimpikis, Konstantinos; Budd, Aidan; Linding, Rune;

    2003-01-01

    SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public...... web servers available. However, with the increasingly large datasets available it is now quite common that a user is interested in some subset of homologous sequences but has no efficient way to restrict retrieval to that set. By allowing the user to control SRS from the BLAST output, BLAST2SRS (http......://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword....

  9. An object-oriented approach to deploying highly configurable Web interfaces for the ATLAS experiment

    CERN Document Server

    Lange Ramos, Bruno; The ATLAS collaboration; Pommes, Kathy; Pavani Neto, Varlen; Vieira Arosa, Breno; Abreu Da Silva, Igor

    2015-01-01

    The ATLAS Technical Coordination disposes of 17 Web systems to support its operation. These applications, whilst ranging from supporting the process of publishing scientific papers to monitoring radiation levels in the equipment at the cave, are constantly prone to changes in requirements due to the collaborative nature of the experiment and its management. In this context, a Web framework is proposed to unify the generation of the supporting interfaces. Fence assembles classes to build applications by making extensive use of JSON configuration files. It relies vastly on Glance, a technology that was set forth in 2003 to create an abstraction layer on top of the heterogeneous sources that store the technical coordination data. Once Glance maps out the database modeling, records can be referenced in the configuration files by wrapping unique identifiers around double enclosing brackets. The deployed content can be individually secured by attaching clearance attributes to their description thus ensuring that vi...

  10. An object-oriented approach to deploying highly configurable web interfaces for the ATLAS experiment

    CERN Document Server

    Lange Ramos, Bruno; The ATLAS collaboration; Pommes, Kathy; Pavani Neto, Varlen; Vieira Arosa, Breno

    2015-01-01

    In order to manage a heterogeneous and worldwide collaboration, the ATLAS experiment develops web systems that range from supporting the process of publishing scientific papers to monitoring equipment radiation levels. These systems are vastly supported by Glance, a technology that was set forward in 2004 to create an abstraction layer on top of varied databases that automatically recognizes their modeling and generate web search interfaces. Fence (Front ENd ENgine for glaNCE) assembles classes to build applications by making extensive use of configuration files. It produces templates of the core JSON files on top of which it is possible to create Glance-compliant search interfaces. Once the database, its schemas and tables are defined using Glance, its records can be incorporated into the templates by escaping the returned values with a reference to the column identifier wrapped around double enclosing brackets. The developer may also expand on available configuration files to create HTML forms and securely ...

  11. Performance Enhancement of a Web-Based Picture Archiving and Communication System Using Commercial Off-the-Shelf Server Clusters

    Directory of Open Access Journals (Sweden)

    Yan-Lin Liu

    2014-01-01

    Full Text Available The rapid development of picture archiving and communication systems (PACSs thoroughly changes the way of medical informatics communication and management. However, as the scale of a hospital’s operations increases, the large amount of digital images transferred in the network inevitably decreases system efficiency. In this study, a server cluster consisting of two server nodes was constructed. Network load balancing (NLB, distributed file system (DFS, and structured query language (SQL duplication services were installed. A total of 1 to 16 workstations were used to transfer computed radiography (CR, computed tomography (CT, and magnetic resonance (MR images simultaneously to simulate the clinical situation. The average transmission rate (ATR was analyzed between the cluster and noncluster servers. In the download scenario, the ATRs of CR, CT, and MR images increased by 44.3%, 56.6%, and 100.9%, respectively, when using the server cluster, whereas the ATRs increased by 23.0%, 39.2%, and 24.9% in the upload scenario. In the mix scenario, the transmission performance increased by 45.2% when using eight computer units. The fault tolerance mechanisms of the server cluster maintained the system availability and image integrity. The server cluster can improve the transmission efficiency while maintaining high reliability and continuous availability in a healthcare environment.

  12. Ajax, XSLT and SVG: Displaying ATLAS conditions data with new web technologies

    International Nuclear Information System (INIS)

    The combination of three relatively recent technologies is described which allows an easy path from database retrieval to interactive web display. SQL queries on an Oracle database can be performed in a manner which directly return an XML description of the result, and Ajax techniques (Asynchronous JavaScript And XML) are used to dynamically inject the data into a web display accompanied by an XSLT transform template which determines how the data will be formatted. By tuning the transform to generate SVG (Scalable Vector Graphics) a direct graphical representation can be produced in the web page while retaining the database data as the XML source, allowing dynamic links to be generated in the web representation, but programmatic use of the data when used from a user application. With the release of the SVG 1.2 Tiny draft specification, the display can also be tailored for display on mobile devices. The technologies are described and a sample application demonstrated, showing conditions data from the ATLAS Semiconductor Tracker.

  13. Ajax, XSLT and SVG: Displaying ATLAS conditions data with new web technologies

    Science.gov (United States)

    Roe, S. A.; ATLAS Collaboration

    2010-04-01

    The combination of three relatively recent technologies is described which allows an easy path from database retrieval to interactive web display. SQL queries on an Oracle database can be performed in a manner which directly return an XML description of the result, and Ajax techniques (Asynchronous JavaScript And XML) are used to dynamically inject the data into a web display accompanied by an XSLT transform template which determines how the data will be formatted. By tuning the transform to generate SVG (Scalable Vector Graphics) a direct graphical representation can be produced in the web page while retaining the database data as the XML source, allowing dynamic links to be generated in the web representation, but programmatic use of the data when used from a user application. With the release of the SVG 1.2 Tiny draft specification, the display can also be tailored for display on mobile devices. The technologies are described and a sample application demonstrated, showing conditions data from the ATLAS Semiconductor Tracker.

  14. Building a web-based CAD server for clinical use, evaluation, and incremental learning. Implementation of analysis function based on execution result and clinical feedback

    International Nuclear Information System (INIS)

    Development of clinical image analysis software such as computer-assisted detection/diagnosis (CAD) involves a cycle of algorithm development, software implementation, clinical use, refinement of algorithm and software based on feedback. This cycle is expected to accelerate development of CAD software. We have been building a web-based CAD server that enables radiologists to use CAD software and to give feedback in clinical environment. The platform has been utilized in our hospital for 16 months, and more than 2,000 cases of feedback data have been accumulated. In this report, we introduce additional functions for performance evaluation based on executed results of CAD software and clinical feedback. (author)

  15. Application of LabVIEW Web Server in Non-sinusoidal Electric Power Remote Measure and Control System%LabVIEW Web Server在非正弦电能远程测控系统中的应用

    Institute of Scientific and Technical Information of China (English)

    陈馨; 付志超; 张聪

    2011-01-01

    View of the current power system voltage and current distortion, the current status of power quality detection technology and the traditional test instrument system problems, to develop a virtual instrument based on the non-sinusoidal electric power detection system; The remote control of detecting non-sinusoidal electric power system, by adopting LabVIEW Web Server, remote measure and control system based on network communication technology. The system structure and its software structure of detecting non-sinusoidal electric power system are given in this paper, also described the LabVIEW Web Server network communication. Distributed large-scale detecting non-sinusoidal electric power system,LabVIEW Web Server network communication has been employed in the remote control system.%针对目前电力系统电压、电流畸变,当前电能质量检测技术的现状及传统仪器测试系统存在的问题,开发一种基于虚拟仪器技术的非正弦电能检测系统;非正弦电能检测系统的远程控制,设计采用了基于网络通信的IabVIEW Web Server远程监控技术.介绍了非正弦电能检测系统的总体结构和软件结构、LabVIEWWeb Server通信技术,叙述了分布式大型非正弦电能测控系统及LabVIEW Web Server通信技术在远程测控系统中的应用.

  16. Linux Server Security

    CERN Document Server

    Bauer, Michael D

    2005-01-01

    Linux consistently appears high up in the list of popular Internet servers, whether it's for the Web, anonymous FTP, or general services such as DNS and delivering mail. But security is the foremost concern of anyone providing such a service. Any server experiences casual probe attempts dozens of time a day, and serious break-in attempts with some frequency as well. This highly regarded book, originally titled Building Secure Servers with Linux, combines practical advice with a firm knowledge of the technical tools needed to ensure security. The book focuses on the most common use of Linux--

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

    CERN Document Server

    Pineda, A S

    2015-01-01

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

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

    CERN Document Server

    Sanchez, Arturo; The ATLAS collaboration

    2015-01-01

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

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

    Science.gov (United States)

    Sánchez Pineda, A.

    2015-12-01

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

  20. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    Science.gov (United States)

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense. PMID:22234525

  1. The ATLAS Public Web Pages: Online Management of HEP External Communication Content

    Science.gov (United States)

    Goldfarb, S.; Marcelloni, C.; Eli Phoboo, A.; Shaw, K.

    2015-12-01

    The ATLAS Education and Outreach Group is in the process of migrating its public online content to a professionally designed set of web pages built on the Drupal [1] content management system. Development of the front-end design passed through several key stages, including audience surveys, stakeholder interviews, usage analytics, and a series of fast design iterations, called sprints. Implementation of the web site involves application of the html design using Drupal templates, refined development iterations, and the overall population of the site with content. We present the design and development processes and share the lessons learned along the way, including the results of the data-driven discovery studies. We also demonstrate the advantages of selecting a back-end supported by content management, with a focus on workflow. Finally, we discuss usage of the new public web pages to implement outreach strategy through implementation of clearly presented themes, consistent audience targeting and messaging, and the enforcement of a well-defined visual identity.

  2. The Monitoring and Calibration Web Systems for the ATLAS Tile Calorimeter Data Quality Analysis

    CERN Document Server

    Sivolella, A; Ferreira, F

    2012-01-01

    The Tile Calorimeter (TileCal) is one of the ATLAS sub-detectors. The read-out is performed by about 10,000 PhotoMultiplier Tubes (PMTs). The signal of each PMT is digitized by an electronic channel. The Monitoring and Calibration Web System (MCWS) supports the data quality analysis of the electronic channels. This application was developed to assess the detector status and verify its performance. It can provide to the user the list of TileCal known problematic channels, that is stored in the ATLAS condition database (COOL DB). The bad channels list guides the data quality validator in identifying new problematic channels and is used in data reconstruction and the system allows to update the channels list directly in the COOL database. MCWS can generate summary results, such as eta-phi plots and comparative tables of the masked channels percentage. Regularly, during the LHC (Large Hadron Collider) shutdown a maintenance of the detector equipments is performed. When a channel is repaired, its calibration const...

  3. Web System for Data Quality Assessment of Tile Calorimeter During the ATLAS Operation

    CERN Document Server

    Guimaraes Ferreira, F; The ATLAS collaboration; Fink Grael, F; Sivolella Gomes, A; Balabram Filho, L

    2010-01-01

    TileCal is the barrel hadronic calorimeter of the ATLAS experiment and has ~10 000 electronic channels. Supervising the detector behavior is a very important task to ensure proper operation. Collaborators perform analyzes over reconstructed data of calibration runs in order to give detailed considerations about failures and to assert the equipment status. Then, the data quality responsible provides the list of problematic channels that should not be considered for physics analysis. Since the commissioning period, our group has developed seven web systems that guide the collaborators through the data quality assessment task. Each system covers a part of the job, providing information on the latest runs, displaying status from the automatic monitoring framework, giving details about power supplies operation, presenting the generated plots and storing the validation outcomes, assisting to write logbook entries, creating and submitting the bad channels list to the conditions database and publishing the equipment ...

  4. Web System for Data Quality Assessment of Tile Calorimeter During the ATLAS Operation

    CERN Document Server

    Maidantchik1, C; The ATLAS collaboration; Grael, F; Sivolella, A; Balabram, L

    2011-01-01

    TileCal is the barrel hadronic calorimeter of the ATLAS experiment and has about 10 000 electronic channels. Supervising the detector behavior is a very important task to ensure proper operation. Collaborators perform analyzes over reconstructed data of calibration runs in order to give detailed considerations about failures and to assert the equipment status. Since the commissioning period, our group has developed seven web systems that guide the collaborators through the data quality assessment task. Each system covers a part of the job, providing information on the latest runs, displaying status from the automatic monitoring framework, giving details about power supplies operation, presenting the generated plots and storing the validation outcomes, assisting to write logbook entries, creating and submitting the bad channels list to the conditions database and publishing the equipment performance history. Due to the beginning of the operation, runs are acquired more often. The increasing amount of data repr...

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

    CERN Document Server

    Lassnig, Mario; The ATLAS collaboration; Barisits, Martin-Stefan; Serfon, Cedric; Vigne, Ralph; Garonne, Vincent

    2015-01-01

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

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

    CERN Document Server

    Lassnig, Mario; The ATLAS collaboration; Vigne, Ralph; Barisits, Martin-Stefan; Garonne, Vincent; Serfon, Cedric

    2015-01-01

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

  7. Hipax Cluster PACS Server

    Directory of Open Access Journals (Sweden)

    Ramin Payrovi

    2007-08-01

    Full Text Available Best Performace: With our Hipax Cluster PACS Server solution we are introducing the parallel computing concept as an extremely fast software system to the PACS world. In contrast to the common PACS servers, the Hipax Cluster PACS software is not only restricted to one or two computers, but can be used on a couple of servers controlling each other."nThus, the same services can be run simultaneously on different computers. The scalable system can also be expanded subsequently without lost of per-formance by adding further processors or Hipax server units, for example, if new clients or modalities are to be connected."nMaximum Failure Security: The Cluster Server concept offers high failure security. If one of the server PCs breaks down, the services can be assumed by another Hipax server unit, temporarily. If the overload of one of the server PCs is imminent, the services will be carried out by another Hipax unit (load balancing. To increase the security, e.g. against fire, the single Hipax servers can also be located separately. This concept offers maximum security, flexibility, performance, redundancy and scalability."nThe Hipax Cluster PACS Server is easy to be administrated using a web interface. In the case of a system failure (e.g. overloading, breakdown of a server PC the system administrator receives a mes-sage via Email and is so enabled to solve the problem."nFeatures"n• Based on SQL database"n• Different services running on separate PCs"n• The Hipax Server unis are coordinated and able to control each other"n• Exponentiates the power of a cluster server to the whole PACS (more processors"n• Scalable to the demands"n• Maximum performance"n• Load balancing for optimum efficiency"n• Maximum failure security because of expo-nentiated redundancy"n• Warning Email automatically sent to the system administrator in the case of failure"n• Web interface for system configuration"n• Maintenance without shut down the system

  8. 自然过程碳排放数据信息WebGIS%Natural Process of Carbon Emissions Data Information WebGIS Based on ArcGIS Server and Silverlight

    Institute of Scientific and Technical Information of China (English)

    祝作佳; 毕建涛; 王星星; 龚跃健; 欧阳文森

    2014-01-01

    As the focus of the natural process of carbon emissions data content information management system construction, the natural process of carbon emissions research data WebGIS system construction has become the object of study. The WebGIS system uses Silverlight as the client platform and uses the ArcGIS Server as the system GIS Server. It is combined with WCF RIA Service, ArcGIS API for Silverlight and other WebGIS technologies. We designed the system frame structure and the spatial database and gave out the spatial data and non-spatial data organization and its web access strategy. It achieved the non-spatial data network dynamic query, retrieval, statistics and analysis. It has functions of displaying the spatial data web maps, analyzing spatial data and making the matic map, etc. In the process of system building, we focused on the analysis of key technologies, involved WebGIS and the specific implementation of solutions. Studies had shown that building a WebGIS system based on the Silverlight technology and ArcGIS Server platform, not only can solve the release and management of geospatial data, develop the system function fast and efficiently, but also can meet the requirements of high interactivity and response time, and improve the performance of WebGIS system.%作为自然过程碳排放数据信息管理系统建设的重点内容,自然过程碳排放研究数据WebGIS系统的构建成为了本文的研究对象。该系统以Silverlight为客户端平台,以ArcGIS Server作为系统GIS服务器,结合WCF RIA Service、ArcGIS API for Silverlight等WebGIS技术进行了系统的框架结构和空间数据库的设计,给出了系统属性数据和空间数据的组织和 Web 访问策略,实现属性数据的网络动态查询、检索、统计和分析与空间数据的网络地图展示、空间分析和专题图制作等功能。在系统构建过程中,重点分析了其涉及的WebGIS关键技术和解决方案的具体实施。研究

  9. Multi-tiered Client/Server Database Application Based on Web%基于Web的多层客户/服务器数据库应用程序

    Institute of Scientific and Technical Information of China (English)

    李文生; 潘世兵

    2001-01-01

    讨论基于Web的多层客户/服务器数据库应用计算模型,并提出采用Delphi建立基于Web的多层客户/服务器数据库应用程序的方法和步骤。%This Paper discusses the computing model of multie-tieredclient/server database application based on Web and proposes method and steps for constructing multie-tiered client/server database application based on Web with Delphi.

  10. THttpServer class in ROOT

    Science.gov (United States)

    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.

  11. ATLAS Live: Collaborative Information Streams

    Science.gov (United States)

    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.

  12. ATLAS Live: Collaborative Information Streams

    International Nuclear Information System (INIS)

    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.

  13. ATLAS

    Data.gov (United States)

    Federal Laboratory Consortium — ATLAS is a particle physics experiment at the Large Hadron Collider at CERN, the European Organization for Nuclear Research. Scientists from Brookhaven have played...

  14. PmiRExAt: plant miRNA expression atlas database and web applications.

    Science.gov (United States)

    Gurjar, Anoop Kishor Singh; Panwar, Abhijeet Singh; Gupta, Rajinder; Mantri, Shrikant S

    2016-01-01

    High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in. PMID:27081157

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

    Science.gov (United States)

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

    2015-12-01

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

  16. Qualitative Web Analytics: New Insights into Navigation Analysis and User Behavior - A Case Study of the German Education Server.

    OpenAIRE

    Keil, Stefan; Böhm, Peter; Rittberger, Marc

    2015-01-01

    Web analytics is a common approach to monitoring and analyzing user behavior on websites. We investigated three different research aspects which can be addressed using web analytics data. Our main concern was the dana quality, followed by general findings on user behavior as well as potential usability issues. We chose an iterative, qualitative approach in order to address all three aspects. Further, we annotated usage data in detail to achieve a deeper understanding of possible user intentio...

  17. Plan de migración de un servidor web basado en Windows Server 2008 e IIS

    OpenAIRE

    SERRANO LÓPEZ, FRANCISCO RUBÉN

    2011-01-01

    El presente proyecto final de carrera plantea la migración de todas las páginas web de un servidor antiguo a otro moderno. Se realizo con una única máquina, con la cual se realizaban dos conexiones remotas, una de ellas para acceder al servidor antiguo y la restante para conectar con el servidor moderno. Por medio de conexiones FTP se migraron los ficheros de las páginas Web y las bases de datos desde el antiguo servidor al nuevo. Una Vez allí se configuraba para que todo funci...

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

    DEFF Research Database (Denmark)

    Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund;

    2012-01-01

    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. Results 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...

  19. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  20. Development of the Health Atlas of Jalisco: A New Web-Based Service for the Ministry of Health and the Community in Mexico

    Science.gov (United States)

    Robles, Juan; Fonseca León, Joel

    2016-01-01

    Background Maps have been widely used to provide a visual representation of information of a geographic area. Health atlases are collections of maps related to conditions, infrastructure or services provided. Various countries have put resources towards producing health atlases that support health decision makers to enhance their services to the communities. Latin America, as well as Spain, have produced several atlases of importance such as the interactive mortality atlas of Andalucía, which is very similar to the one that is presented in this paper. In Mexico, the National Institute of Public Health produced the only health atlas found that is of relevance. It was published online in 2003 and is currently still active. Objective The objective of this work is to describe the methods used to develop the Health Atlas of Jalisco (HAJ), and show its characteristics and how it interactively works with the user as a Web-based service. Methods This work has an ecological design in which the analysis units are the 125 municipalities (counties) of the state of Jalisco, Mexico. We created and published online a geographic health atlas displaying a system based on input from official health database of the Health Ministry of Jalisco (HMJ), and some databases from the National Institute of Statistics and Geography (NISGI). The atlas displays 256 different variables as health-direct or health-related indicators. Instant Atlas software was used to generate the online application. The atlas was developed using these procedures: (1) datasheet processing and base maps generation, (2) software arrangements, and (3) website creation. Results The HAJ is a Web-based service that allows users to interact with health and general data, regions, and categories according to their information needs and generates thematic maps (eg, the total population of the state or of a single municipality grouped by age or sex). The atlas is capable of displaying more than 32,000 different maps by

  1. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

    Directory of Open Access Journals (Sweden)

    Liu Chang

    2012-12-01

    Full Text Available Abstract Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.

  2. ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

    OpenAIRE

    Sushko, Iurii; Salmina, Elena; Potemkin, Vladimir A.; Poda, Gennadiy; Igor V Tetko

    2012-01-01

    The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, a...

  3. Scientific LogAnalyzer: a web-based tool for analyses of server log files in psychological research.

    Science.gov (United States)

    Reips, Ulf-Dietrich; Stieger, Stefan

    2004-05-01

    Scientific LogAnalyzer is a platform-independent interactive Web service for the analysis of log files. Scientific LogAnalyzer offers several features not available in other log file analysis tools--for example, organizational criteria and computational algorithms suited to aid behavioral and social scientists. Scientific LogAnalyzer is highly flexible on the input side (unlimited types of log file formats), while strictly keeping a scientific output format. Features include (1) free definition of log file format, (2) searching and marking dependent on any combination of strings (necessary for identifying conditions in experiment data), (3) computation of response times, (4) detection of multiple sessions, (5) speedy analysis of large log files, (6) output in HTML and/or tab-delimited form, suitable for import into statistics software, and (7) a module for analyzing and visualizing drop-out. Several methodological features specifically needed in the analysis of data collected in Internet-based experiments have been implemented in the Web-based tool and are described in this article. A regression analysis with data from 44 log file analyses shows that the size of the log file and the domain name lookup are the two main factors determining the duration of an analysis. It is less than a minute for a standard experimental study with a 2 x 2 design, a dozen Web pages, and 48 participants (ca. 800 lines, including data from drop-outs). The current version of Scientific LogAnalyzer is freely available for small log files. Its Web address is http://genpsylab-logcrunsh.unizh.ch/. PMID:15354696

  4. Integration of ROOT Notebooks as an ATLAS analysis web-based tool in outreach and public data release

    CERN Document Server

    Sanchez, Arturo; The ATLAS collaboration

    2016-01-01

    The integration of the ROOT data analysis framework with the Jupyter Notebook technology presents an incredible potential in the enhance and expansion of educational and training programs: starting from university students in their early years, passing to new ATLAS PhD students and post doctoral researchers, to those senior analysers and professors that want to restart their contact with the analysis of data or to include a more friendly but yet very powerful open source tool in the classroom. Such tools have been already tested in several environments and a fully web-based integration together with Open Access Data repositories brings the possibility to go a step forward in the search of ATLAS for integration between several CERN projects in the field of the education and training, developing new computing solutions on the way.

  5. 一种基于ARM的嵌入式Web服务器的研究与实现%Research and Realization of an Embedded Web Server Based on ARM

    Institute of Scientific and Technical Information of China (English)

    李波; 关沫

    2013-01-01

    为了实现将嵌入式设备接入Internet,并可通过Web浏览器对其进行远程访问、管理等操作的目的,文中以Samsung公司的S3C2440AL ARM9处理器作为硬件核心,以Linux操作系统下的Boa服务器作为软件平台,研究并实现了一个嵌入式Web服务器.给出了系统硬件平台结构的设计及组成,详细讨论了Linux操作系统和CGIC库的移植过程,对Boa服务器的建立以及运用CGI实现浏览器与嵌入式Web服务器之间的动态交互技术进行了研究.对该嵌入式Web服务器的实验测试结果表明其响应迅速,运行稳定,满足应用设计需求.%To realize the online remote access and management to the embedded devices using the Web browser over Intemet,an embedded Web server,which takes Samsung corporation's S3C2440AL ARM9 processor as hardware core and Boa server of Linux operating system as software platform,is designed and realized in the paper.The system hardware architecture is presented.The process of the Linux operating system and CGIC library being transplanted to ARM platform is discussed in detail.The realization of Boa and dynamic interaction between Web browser and the embedded Web server by using CGI are especially analyzed.The experimental result of the embedded Web server shows that it responds rapidly and runs steadily,achieves the application purpose.

  6. Essential Mac OS X panther server administration integrating Mac OS X server into heterogeneous networks

    CERN Document Server

    Bartosh, Michael

    2004-01-01

    If you've ever wondered how to safely manipulate Mac OS X Panther Server's many underlying configuration files or needed to explain AFP permission mapping--this book's for you. From the command line to Apple's graphical tools, the book provides insight into this powerful server software. Topics covered include installation, deployment, server management, web application services, data gathering, and more

  7. ATLAS Live: Collaborative Information Streams

    CERN Document Server

    Goldfarb, S; The ATLAS collaboration

    2011-01-01

    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 th...

  8. ATLAS Live: Collaborative Information Streams

    CERN Document Server

    Goldfarb, S; The ATLAS collaboration

    2010-01-01

    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 the SCALA digital signage software system. The system is robust and flexible, allowing for the usage of 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 intrascreen divisibility. The video is made available to the collaboration or public through the encoding and webcasting of standard video streams, viewable on all common platforms, using a web browser or other common video t...

  9. Study on Server Push Technology of WebSocket%基于WebSocket的服务器推送技术研究

    Institute of Scientific and Technical Information of China (English)

    李锡辉; 杨丽

    2014-01-01

    服务器推送技术的出现较好的解决了人们在海量信息中寻求有用信息的方式.分析传统服务器推送技术存在的缺陷,阐释了HTML5中WebSocket的通信机制及信息推送的实现方式.

  10. ATLAS

    CERN Multimedia

    Akhnazarov, V; Canepa, A; Bremer, J; Burckhart, H; Cattai, A; Voss, R; Hervas, L; Kaplon, J; Nessi, M; Werner, P; Ten kate, H; Tyrvainen, H; Vandelli, W; Krasznahorkay, A; Gray, H; Alvarez gonzalez, B; Eifert, T F; Rolando, G; Oide, H; Barak, L; Glatzer, J; Backhaus, M; Schaefer, D M; Maciejewski, J P; Milic, A; Jin, S; Von torne, E; Limbach, C; Medinnis, M J; Gregor, I; Levonian, S; Schmitt, S; Waananen, A; Monnier, E; Muanza, S G; Pralavorio, P; Talby, M; Tiouchichine, E; Tocut, V M; Rybkin, G; Wang, S; Lacour, D; Laforge, B; Ocariz, J H; Bertoli, W; Malaescu, B; Sbarra, C; Yamamoto, A; Sasaki, O; Koriki, T; Hara, K; Da silva gomes, A; Carvalho maneira, J; Marcalo da palma, A; Chekulaev, S; Tikhomirov, V; Snesarev, A; Buzykaev, A; Maslennikov, A; Peleganchuk, S; Sukharev, A; Kaplan, B E; Swiatlowski, M J; Nef, P D; Schnoor, U; Oakham, G F; Ueno, R; Orr, R S; Abouzeid, O; Haug, S; Peng, H; Kus, V; Vitek, M; Temming, K K; Dang, N P; Meier, K; Schultz-coulon, H; Geisler, M P; Sander, H; Schaefer, U; Ellinghaus, F; Rieke, S; Nussbaumer, A; Liu, Y; Richter, R; Kortner, S; Fernandez-bosman, M; Ullan comes, M; Espinal curull, J; Chiriotti alvarez, S; Caubet serrabou, M; Valladolid gallego, E; Kaci, M; Carrasco vela, N; Lancon, E C; Besson, N E; Gautard, V; Bracinik, J; Bartsch, V C; Potter, C J; Lester, C G; Moeller, V A; Rosten, J; Crooks, D; Mathieson, K; Houston, S C; Wright, M; Jones, T W; Harris, O B; Byatt, T J; Dobson, E; Hodgson, P; Hodgkinson, M C; Dris, M; Karakostas, K; Ntekas, K; Oren, D; Duchovni, E; Etzion, E; Oren, Y; Ferrer, L M; Testa, M; Doria, A; Merola, L; Sekhniaidze, G; Giordano, R; Ricciardi, S; Milazzo, A; Falciano, S; De pedis, D; Dionisi, C; Veneziano, S; Cardarelli, R; Verzegnassi, C; Soualah, R; Ochi, A; Ohshima, T; Kishiki, S; Linde, F L; Vreeswijk, M; Werneke, P; Muijs, A; Vankov, P H; Jansweijer, P P M; Dale, O; Lund, E; Bruckman de renstrom, P; Dabrowski, W; Adamek, J D; Wolters, H; Micu, L; Pantea, D; Tudorache, V; Mjoernmark, J; Klimek, P J; Ferrari, A; Abdinov, O; Akhoundov, A; Hashimov, R; Shelkov, G; Khubua, J; Ladygin, E; Lazarev, A; Glagolev, V; Dedovich, D; Lykasov, G; Zhemchugov, A; Zolnikov, Y; Ryabenko, M; Sivoklokov, S; Vasilyev, I; Shalimov, A; Lobanov, M; Paramoshkina, E; Mosidze, M; Bingul, A; Nodulman, L J; Guarino, V J; Yoshida, R; Drake, G R; Calafiura, P; Haber, C; Quarrie, D R; Alonso, J R; Anderson, C; Evans, H; Lammers, S W; Baubock, M; Anderson, K; Petti, R; Suhr, C A; Linnemann, J T; Richards, R A; Tollefson, K A; Holzbauer, J L; Stoker, D P; Pier, S; Nelson, A J; Isakov, V; Martin, A J; Adelman, J A; Paganini, M; Gutierrez, P; Snow, J M; Pearson, B L; Cleland, W E; Savinov, V; Wong, W; Goodson, J J; Li, H; Lacey, R A; Gordeev, A; Gordon, H; Lanni, F; Nevski, P; Rescia, S; Kierstead, J A; Liu, Z; Yu, W W H; Bensinger, J; Hashemi, K S; Bogavac, D; Cindro, V; Hoeferkamp, M R; Coelli, S; Iodice, M; Piegaia, R N; Alonso, F; Wahlberg, H P; Barberio, E L; Limosani, A; Rodd, N L; Jennens, D T; Hill, E C; Pospisil, S; Smolek, K; Schaile, D A; Rauscher, F G; Adomeit, S; Mattig, P M; Wahlen, H; Volkmer, F; Calvente lopez, S; Sanchis peris, E J; Pallin, D; Podlyski, F; Says, L; Boumediene, D E; Scott, W; Phillips, P W; Greenall, A; Turner, P; Gwilliam, C B; Kluge, T; Wrona, B; Sellers, G J; Millward, G; Adragna, P; Hartin, A; Alpigiani, C; Piccaro, E; Bret cano, M; Hughes jones, R E; Mercer, D; Oh, A; Chavda, V S; Carminati, L; Cavasinni, V; Fedin, O; Patrichev, S; Ryabov, Y; Nesterov, S; Grebenyuk, O; Sasso, J; Mahmood, H; Polsdofer, E; Dai, T; Ferretti, C; Liu, H; Hegazy, K H; Benjamin, D P; Zobernig, G; Ban, J; Brooijmans, G H; Keener, P; Williams, H H; Le geyt, B C; Hines, E J; Fadeyev, V; Schumm, B A; Law, A T; Kuhl, A D; Neubauer, M S; Shang, R; Gagliardi, G; Calabro, D; Conta, C; Zinna, M; Jones, G; Li, J; Stradling, A R; Hadavand, H K; Mcguigan, P; Chiu, P; Baldelomar, E; Stroynowski, R A; Kehoe, R L; De groot, N; Timmermans, C; Lach-heb, F; Addy, T N; Nakano, I; Moreno lopez, D; Grosse-knetter, J; Tyson, B; Rude, G D; Tafirout, R; Benoit, P; Danielsson, H O; Elsing, M; Fassnacht, P; Froidevaux, D; Ganis, G; Gorini, B; Lasseur, C; Lehmann miotto, G; Kollar, D; Aleksa, M; Sfyrla, A; Duehrssen-debling, K; Fressard-batraneanu, S; Van der ster, D C; Bortolin, C; Schumacher, J; Mentink, M; Geich-gimbel, C; Yau wong, K H; Lafaye, R; Crepe-renaudin, S; Albrand, S; Hoffmann, D; Pangaud, P; Meessen, C; Hrivnac, J; Vernay, E; Perus, A; Henrot versille, S L; Le dortz, O; Derue, F; Piccinini, M; Polini, A; Terada, S; Arai, Y; Ikeno, M; Fujii, H; Nagano, K; Ukegawa, F; Aguilar saavedra, J A; Conde muino, P; Castro, N F; Eremin, V; Kopytine, M; Sulin, V; Tsukerman, I; Korol, A; Nemethy, P; Bartoldus, R; Glatte, A; Chelsky, S; Van nieuwkoop, J; Bellerive, A; Sinervo, J K; Battaglia, A; Barbier, G J; Pohl, M; Rosselet, L; Alexandre, G B; Prokoshin, F; Pezoa rivera, R A; Batkova, L; Kladiva, E; Stastny, J; Kubes, T; Vidlakova, Z; Esch, H; Homann, M; Herten, L G; Zimmermann, S U; Pfeifer, B; Stenzel, H; Andrei, G V; Wessels, M; Buescher, V; Kleinknecht, K; Fiedler, F M; Schroeder, C D; Fernandez, E; Mir martinez, L; Vorwerk, V; Bernabeu verdu, J; Salt, J; Civera navarrete, J V; Bernard, R; Berriaud, C P; Chevalier, L P; Hubbard, R; Schune, P; Nikolopoulos, K; Batley, J R; Brochu, F M; Phillips, A W; Teixeira-dias, P J; Rose, M B D; Buttar, C; Buckley, A G; Nurse, E L; Larner, A B; Boddy, C; Henderson, J; Costanzo, D; Tarem, S; Maccarrone, G; Laurelli, P F; Alviggi, M; Chiaramonte, R; Izzo, V; Palumbo, V; Fraternali, M; Crosetti, G; Marchese, F; Yamaguchi, Y; Hessey, N P; Mechnich, J M; Liebig, W; Kastanas, K A; Sjursen, T B; Zalieckas, J; Cameron, D G; Banka, P; Kowalewska, A B; Dwuznik, M; Mindur, B; Boldea, V; Hedberg, V; Smirnova, O; Sellden, B; Allahverdiyev, T; Gornushkin, Y; Koultchitski, I; Tokmenin, V; Chizhov, M; Gongadze, A; Khramov, E; Sadykov, R; Krasnoslobodtsev, I; Smirnova, L; Kramarenko, V; Minaenko, A; Zenin, O; Beddall, A J; Ozcan, E V; Hou, S; Wang, S; Moyse, E; Willocq, S; Chekanov, S; Le compte, T J; Love, J R; Ciocio, A; Hinchliffe, I; Tsulaia, V; Gomez, A; Luehring, F; Zieminska, D; Huth, J E; Gonski, J L; Oreglia, M; Tang, F; Shochet, M J; Costin, T; Mcleod, A; Uzunyan, S; Martin, S P; Pope, B G; Schwienhorst, R H; Brau, J E; Ptacek, E S; Milburn, R H; Sabancilar, E; Lauer, R; Saleem, M; Mohamed meera lebbai, M R; Lou, X; Reeves, K B; Rijssenbeek, M; Novakova, P N; Rahm, D; Steinberg, P A; Wenaus, T J; Paige, F; Ye, S; Kotcher, J R; Assamagan, K A; Oliveira damazio, D; Maeno, T; Henry, A; Dushkin, A; Costa, G; Meroni, C; Resconi, S; Lari, T; Biglietti, M; Lohse, T; Gonzalez silva, M L; Monticelli, F G; Saavedra, A F; Patel, N D; Ciodaro xavier, T; Asevedo nepomuceno, A; Lefebvre, M; Albert, J E; Kubik, P; Faltova, J; Turecek, D; Solc, J; Schaile, O; Ebke, J; Losel, P J; Zeitnitz, C; Sturm, P D; Barreiro alonso, F; Modesto alapont, P; Soret medel, J; Garzon alama, E J; Gee, C N; Mccubbin, N A; Sankey, D; Emeliyanov, D; Dewhurst, A L; Houlden, M A; Klein, M; Burdin, S; Lehan, A K; Eisenhandler, E; Lloyd, S; Traynor, D P; Ibbotson, M; Marshall, R; Pater, J; Freestone, J; Masik, J; Haughton, I; Manousakis katsikakis, A; Sampsonidis, D; Krepouri, A; Roda, C; Sarri, F; Fukunaga, C; Nadtochiy, A; Kara, S O; Timm, S; Alam, S M; Rashid, T; Goldfarb, S; Espahbodi, S; Marley, D E; Rau, A W; Dos anjos, A R; Haque, S; Grau, N C; Havener, L B; Thomson, E J; Newcomer, F M; Hansl-kozanecki, G; Deberg, H A; Takeshita, T; Goggi, V; Ennis, J S; Olness, F I; Kama, S; Ordonez sanz, G; Koetsveld, F; Elamri, M; Mansoor-ul-islam, S; Lemmer, B; Kawamura, G; Bindi, M; Schulte, S; Kugel, A; Kretz, M P; Kurchaninov, L; Blanchot, G; Chromek-burckhart, D; Di girolamo, B; Francis, D; Gianotti, F; Nordberg, M Y; Pernegger, H; Roe, S; Boyd, J; Wilkens, H G; Pauly, T; Fabre, C; Tricoli, A; Bertet, D; Ruiz martinez, M A; Arnaez, O L; Lenzi, B; Boveia, A J; Gillberg, D I; Davies, J M; Zimmermann, R; Uhlenbrock, M; Kraus, J K; Narayan, R T; John, A; Dam, M; Padilla aranda, C; Bellachia, F; Le flour chollet, F M; Jezequel, S; Dumont dayot, N; Fede, E; Mathieu, M; Gensolen, F D; Alio, L; Arnault, C; Bouchel, M; Ducorps, A; Kado, M M; Lounis, A; Zhang, Z P; De vivie de regie, J; Beau, T; Bruni, A; Bruni, G; Grafstrom, P; Romano, M; Lasagni manghi, F; Massa, L; Shaw, K; Ikegami, Y; Tsuno, S; Kawanishi, Y; Benincasa, G; Blagov, M; Fedorchuk, R; Shatalov, P; Romaniouk, A; Belotskiy, K; Timoshenko, S; Hooft van huysduynen, L; Lewis, G H; Wittgen, M M; Mader, W F; Rudolph, C J; Gumpert, C; Mamuzic, J; Rudolph, G; Schmid, P; Corriveau, F; Belanger-champagne, C; Yarkoni, S; Leroy, C; Koffas, T; Harack, B D; Weber, M S; Beck, H; Leger, A; Gonzalez sevilla, S; Zhu, Y; Gao, J; Zhang, X; Blazek, T; Rames, J; Sicho, P; Kouba, T; Sluka, T; Lysak, R; Ristic, B; Kompatscher, A E; Von radziewski, H; Groll, M; Meyer, C P; Oberlack, H; Stonjek, S M; Cortiana, G; Werthenbach, U; Ibragimov, I; Czirr, H S; Cavalli-sforza, M; Puigdengoles olive, C; Tallada crespi, P; Marti i garcia, S; Gonzalez de la hoz, S; Guyot, C; Meyer, J; Schoeffel, L O; Garvey, J; Hawkes, C; Hillier, S J; Staley, R J; Salvatore, P F; Santoyo castillo, I; Carter, J; Yusuff, I B; Barlow, N R; Berry, T S; Savage, G; Wraight, K G; Steele, G E; Hughes, G; Walder, J W; Love, P A; Crone, G J; Waugh, B M; Boeser, S; Sarkar, A M; Holmes, A; Massey, R; Pinder, A; Nicholson, R; Korolkova, E; Katsoufis, I; Maltezos, S; Tsipolitis, G; Leontsinis, S; Levinson, L J; Shoa, M; Abramowicz, H E; Bella, G; Gershon, A; Urkovsky, E; Taiblum, N; Gatti, C; Della pietra, M; Lanza, A; Negri, A; Flaminio, V; Lacava, F; Petrolo, E; Pontecorvo, L; Rosati, S; Zanello, L; Pasqualucci, E; Di ciaccio, A; Giordani, M; Yamazaki, Y; Jinno, T; Nomachi, M; De jong, P J; Ferrari, P; Homma, J; Van der graaf, H; Igonkina, O B; Stugu, B S; Buanes, T; Pedersen, M; Turala, M; Olszewski, A J; Koperny, S Z; Onofre, A; Castro nunes fiolhais, M; Alexa, C; Cuciuc, C M; Akesson, T P A; Hellman, S L; Milstead, D A; Bondyakov, A; Pushnova, V; Budagov, Y; 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Kiesling, C; Macchiolo, A; Nisius, R; Schacht, P; Von der schmitt, J G; Kortner, O; Atlay, N B; Segura sole, E; Grinstein, S; Neissner, C; Bruckner, D M; Oliver garcia, E; Boonekamp, M; Perrin, P; Gaillot, F M; Wilson, J A; Thomas, J P; Thompson, P D; Palmer, J D; Falk, I E; Chavez barajas, C A; Sutton, M R; Robinson, D; Kaneti, S A; Wu, T; Robson, A; Shaw, C; Buzatu, A; Qin, G; Jones, R; Bouhova-thacker, E V; Viehhauser, G; Weidberg, A R; Gilbert, L; Johansson, P D C; Orphanides, M; Vlachos, S; Behar harpaz, S; Papish, O; Lellouch, D J H; Turgeman, D; Benary, O; La rotonda, L; Vena, R; Tarasio, A; Marzano, F; Gabrielli, A; Di stante, L; Liberti, B; Aielli, G; Oda, S; Nozaki, M; Takeda, H; Hayakawa, T; Miyazaki, K; Maeda, J; Sugimoto, T; Pettersson, N E; Bentvelsen, S; Groenstege, H L; Lipniacka, A; Vahabi, M; Ould-saada, F; Chwastowski, J J; Hajduk, Z; Kaczmarska, A; Olszowska, J B; Trzupek, A; Staszewski, R P; Palka, M; Constantinescu, S; Jarlskog, G; Lundberg, B L A; Pearce, M; Ellert, M F; Bannikov, A; Fechtchenko, A; Iambourenko, V; Kukhtin, V; Pozdniakov, V; Topilin, N; Vorozhtsov, S; Khassanov, A; Fliaguine, V; Kharchenko, D; Nikolaev, K; Kotenov, K; Kozhin, A; Zenin, A; Ivashin, A; Golubkov, D; Beddall, A; Su, D; Dallapiccola, C J; Cranshaw, J M; Price, L; Stanek, R W; Gieraltowski, G; Zhang, J; Gilchriese, M; Shapiro, M; Ahlen, S; Morii, M; Taylor, F E; Miller, R J; Phillips, F H; Torrence, E C; Wheeler, S J; Benedict, B H; Napier, A; Hamilton, S F; Petrescu, T A; Boyd, G R J; Jayasinghe, A L; Smith, J M; Mc carthy, R L; Adams, D L; Le vine, M J; Zhao, X; Patwa, A M; Baker, M; Kirsch, L; Krstic, J; Simic, L; Filipcic, A; Seidel, S C; Cantore-cavalli, D; Baroncelli, A; Kind, O M; Scarcella, M J; Maidantchik, C L L; Seixas, J; Balabram filho, L E; Vorobel, V; Spousta, M; Strachota, P; Vokac, P; Slavicek, T; Bergmann, B L; Biebel, O; Kersten, S; Srinivasan, M; Trefzger, T; Vazeille, F; Insa, C; Kirk, J; Middleton, R; Burke, S; Klein, U; Morris, J D; Ellis, K V; Millward, L R; 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    2002-01-01

    % ATLAS \\\\ \\\\ ATLAS is a general-purpose experiment for recording proton-proton collisions at LHC. The ATLAS collaboration consists of 144 participating institutions (June 1998) with more than 1750~physicists and engineers (700 from non-Member States). The detector design has been optimized to cover the largest possible range of LHC physics: searches for Higgs bosons and alternative schemes for the spontaneous symmetry-breaking mechanism; searches for supersymmetric particles, new gauge bosons, leptoquarks, and quark and lepton compositeness indicating extensions to the Standard Model and new physics beyond it; studies of the origin of CP violation via high-precision measurements of CP-violating B-decays; high-precision measurements of the third quark family such as the top-quark mass and decay properties, rare decays of B-hadrons, spectroscopy of rare B-hadrons, and $ B ^0 _{s} $-mixing. \\\\ \\\\The ATLAS dectector, shown in the Figure includes an inner tracking detector inside a 2~T~solenoid providing an axial...

  11. tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.

    Science.gov (United States)

    Zheng, Ling-Ling; Xu, Wei-Lin; Liu, Shun; Sun, Wen-Ju; Li, Jun-Hao; Wu, Jie; Yang, Jian-Hua; Qu, Liang-Hu

    2016-07-01

    tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called 'tRFinCancer' was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called 'tRFBrowser' shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/. PMID:27179031

  12. GANDivAWeb: A web server for detecting early folding units ("foldons" from protein 3D structures

    Directory of Open Access Journals (Sweden)

    Krishnan Arun

    2008-03-01

    Full Text Available Abstract Background It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. Results In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c It can take as input an uploaded PDB file and a results file (obtained from functionality (b and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA distributions. Conclusion We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological

  13. ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions.

    Science.gov (United States)

    Sushko, Iurii; Salmina, Elena; Potemkin, Vladimir A; Poda, Gennadiy; Tetko, Igor V

    2012-08-27

    The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly

  14. SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity.

    Science.gov (United States)

    Li, Ying Hong; Xu, Jing Yu; Tao, Lin; Li, Xiao Feng; Li, Shuang; Zeng, Xian; Chen, Shang Ying; Zhang, Peng; Qin, Chu; Zhang, Cheng; Chen, Zhe; Zhu, Feng; Chen, Yu Zong

    2016-01-01

    Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM-Prot web-server employed a machine learning method for predicting protein functional families from protein sequences irrespective of similarity, which complemented those similarity-based and other methods in predicting diverse classes of proteins including the distantly-related proteins and homologous proteins of different functions. Since its publication in 2003, we made major improvements to SVM-Prot with (1) expanded coverage from 54 to 192 functional families, (2) more diverse protein descriptors protein representation, (3) improved predictive performances due to the use of more enriched training datasets and more variety of protein descriptors, (4) newly integrated BLAST analysis option for assessing proteins in the SVM-Prot predicted functional families that were similar in sequence to a query protein, and (5) newly added batch submission option for supporting the classification of multiple proteins. Moreover, 2 more machine learning approaches, K nearest neighbor and probabilistic neural networks, were added for facilitating collective assessment of protein functions by multiple methods. SVM-Prot can be accessed at http://bidd2.nus.edu.sg/cgi-bin/svmprot/svmprot.cgi. PMID:27525735

  15. SVM-Prot 2016: A Web-Server for Machine Learning Prediction of Protein Functional Families from Sequence Irrespective of Similarity

    Science.gov (United States)

    Li, Xiao Feng; Li, Shuang; Zeng, Xian; Chen, Shang Ying; Zhang, Peng; Qin, Chu; Zhang, Cheng; Chen, Zhe; Zhu, Feng; Chen, Yu Zong

    2016-01-01

    Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM-Prot web-server employed a machine learning method for predicting protein functional families from protein sequences irrespective of similarity, which complemented those similarity-based and other methods in predicting diverse classes of proteins including the distantly-related proteins and homologous proteins of different functions. Since its publication in 2003, we made major improvements to SVM-Prot with (1) expanded coverage from 54 to 192 functional families, (2) more diverse protein descriptors protein representation, (3) improved predictive performances due to the use of more enriched training datasets and more variety of protein descriptors, (4) newly integrated BLAST analysis option for assessing proteins in the SVM-Prot predicted functional families that were similar in sequence to a query protein, and (5) newly added batch submission option for supporting the classification of multiple proteins. Moreover, 2 more machine learning approaches, K nearest neighbor and probabilistic neural networks, were added for facilitating collective assessment of protein functions by multiple methods. SVM-Prot can be accessed at http://bidd2.nus.edu.sg/cgi-bin/svmprot/svmprot.cgi. PMID:27525735

  16. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

    Science.gov (United States)

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M; Lin, Jung-Hsin

    2009-07-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design. PMID:19433508

  17. Client Server Model Based DAQ System for Real-Time Air Pollution Monitoring

    Directory of Open Access Journals (Sweden)

    Vetrivel. P

    2014-01-01

    Full Text Available The proposed system consists of client server model based Data-Acquisition Unit. The Embedded Web Server integrates Pollution Server and DAQ that collects air Pollutants levels (CO, NO2, and SO2. The Pollution Server is designed by considering modern resource constrained embedded systems. In contrast, an application server is designed to the efficient execution of programs and scripts for supporting the construction of various applications. While a pollution server mainly deals with sending HTML for display in a web browser on the client terminal, an application server provides access to server side logic for pollutants levels to be use by client application programs. The Embedded Web Server is an arm mcb2300 board with internet connectivity and acts as air pollution server as this standalone device gathers air pollutants levels and as a Server. Embedded Web server is accessed by various clients.

  18. Analysis of Mobile Application Structure and System Construction Based on WebServer%基于WebServer的移动应用结构分析与系统建设

    Institute of Scientific and Technical Information of China (English)

    王永平

    2014-01-01

    Mobile learning device can learn at any time, any place through the portable mobile computing. In the construction process of mobile application system, SSH integrated framework can be used in Web development server procedures. The representation logic and control logic separated are respected by the presentation layer. It uses business logic layer to process, reduce the coupling system architecture. This software structure is clear, expansibility and maintainability of higher.%移动学习通过便携式移动计算设备能够在任何时间、任何地点进行学习,在移动应用系统的建设过程中,利用SSH整合框架进行Web Server程序的开发,把表现逻辑和控制逻辑分离开来,分别由表现层、业务逻辑层来处理,降低了系统总架构的耦合性,使软件结构清晰,可扩展性和可维护性更高。

  19. Dali server update.

    Science.gov (United States)

    Holm, Liisa; Laakso, Laura M

    2016-07-01

    The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo. PMID:27131377

  20. First experience with VMware servers at HLS

    International Nuclear Information System (INIS)

    Hefei Light Source (HLS) is a dedicated second generation VUV light source, which was designed and constructed two decades ago. In order to improve the performance of HLS, especially getting higher brilliance and increasing the number of straight sections, an upgrade project is undergoing, accordingly the new control system is under construction. VMware vSphere 4 Enterprise Plus is used to construct the server system for HLS control system. Four DELL PowerEdge R710 rack servers and one DELL Equallogic PS6000E iSCSI SAN comprises the hardware platform. Some kinds of servers, such as file server, web server, database server, NIS servers etc. together with the softIOC applications are all integrated to this simulation platform. The prototype of softIOC is setup and its performance is also given in this paper. High availability and flexibility are achieved with low cost. (authors)

  1. WMS Server 2.0

    Science.gov (United States)

    Plesea, Lucian; Wood, James F.

    2012-01-01

    This software is a simple, yet flexible server of raster map products, compliant with the Open Geospatial Consortium (OGC) Web Map Service (WMS) 1.1.1 protocol. The server is a full implementation of the OGC WMS 1.1.1 as a fastCGI client and using Geospatial Data Abstraction Library (GDAL) for data access. The server can operate in a proxy mode, where all or part of the WMS requests are done on a back server. The server has explicit support for a colocated tiled WMS, including rapid response of black (no-data) requests. It generates JPEG and PNG images, including 16-bit PNG. The GDAL back-end support allows great flexibility on the data access. The server is a port to a Linux/GDAL platform from the original IRIX/IL platform. It is simpler to configure and use, and depending on the storage format used, it has better performance than other available implementations. The WMS server 2.0 is a high-performance WMS implementation due to the fastCGI architecture. The use of GDAL data back end allows for great flexibility. The configuration is relatively simple, based on a single XML file. It provides scaling and cropping, as well as blending of multiple layers based on layer transparency.

  2. Generic OPC UA Server Framework

    Science.gov (United States)

    Nikiel, Piotr P.; Farnham, Benjamin; Filimonov, Viatcheslav; Schlenker, Stefan

    2015-12-01

    This paper describes a new approach for generic design and efficient development of OPC UA servers. Development starts with creation of a design file, in XML format, describing an object-oriented information model of the target system or device. Using this model, the framework generates an executable OPC UA server application, which exposes the per-design OPC UA address space, without the developer writing a single line of code. Furthermore, the framework generates skeleton code into which the developer adds the necessary logic for integration to the target system or device. This approach allows both developers unfamiliar with the OPC UA standard, and advanced OPC UA developers, to create servers for the systems they are experts in while greatly reducing design and development effort as compared to developments based purely on COTS OPC UA toolkits. Higher level software may further benefit from the explicit OPC UA server model by using the XML design description as the basis for generating client connectivity configuration and server data representation. Moreover, having the XML design description at hand facilitates automatic generation of validation tools. In this contribution, the concept and implementation of this framework is detailed along with examples of actual production-level usage in the detector control system of the ATLAS experiment at CERN and beyond.

  3. EnviroAtlas - Metrics for Austin, TX

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). The layers in this...

  4. Glance traceability - Web system for equipment traceability and radiation monitoring for the ATLAS experiment

    Science.gov (United States)

    Évora, L. H. R. A.; Molina-Pérez, J.; Pommès, K.; Galvão, K. K.; Maidantchik, C.

    2010-04-01

    During the operation, maintenance, and dismantling periods of the ATLAS Experiment, the traceability of all detector equipment must be guaranteed for logistic and safety matters. The running of the Large Hadron Collider will expose the ATLAS detector to radiation. Therefore, CERN must follow specific regulations from both the French and Swiss authorities for equipment removal, transport, repair, and disposal. GLANCE Traceability, implemented in C++ and Java/Java3D, has been developed to fulfill the requirements. The system registers and associates each equipment part to either a functional position in the detector or a zone outside the underground area through a 3D graphical user interface. Radiation control of the equipment is performed using a radiation monitor connected to the system: the local background gets stored and the threshold is automatically calculated. The system classifies the equipment as non radioactive if its radiation dose does not exceed that limit value. History for both location traceability and radiation measurements is ensured, as well as simultaneous management of multiples equipment. The software is fully operational, being used by the Radiation Protection Experts of ATLAS and trained users since the first beam of the LHC. Initially developed for the ATLAS detector, the flexibility of the system has allowed its adaptation for the LHCb detector.

  5. Glance traceability – Web system for equipment traceability and radiation monitoring for the ATLAS experiment

    CERN Document Server

    Ramos de Azevedo Evora, L H; Pommes, K; Galvão, K K; Maidantchik, C

    2010-01-01

    During the operation, maintenance, and dismantling periods of the ATLAS Experiment, the traceability of all detector equipment must be guaranteed for logistic and safety matters. The running of the Large Hadron Collider will expose the ATLAS detector to radiation. Therefore, CERN must follow specific regulations from both the French and Swiss authorities for equipment removal, transport, repair, and disposal. GLANCE Traceability, implemented in C++ and Java/Java3D, has been developed to fulfill the requirements. The system registers and associates each equipment part to either a functional position in the detector or a zone outside the underground area through a 3D graphical user interface. Radiation control of the equipment is performed using a radiation monitor connected to the system: the local background gets stored and the threshold is automatically calculated. The system classifies the equipment as non radioactive if its radiation dose does not exceed that limit value. History for both location traceabi...

  6. EnviroAtlas - Metrics for Memphis, TN

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  7. EnviroAtlas - Metrics for Portland, ME

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  8. EnviroAtlas - Metrics for Phoenix, AZ

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  9. EnviroAtlas - Metrics for Paterson, NJ

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  10. EnviroAtlas - Metrics for Pittsburgh, PA

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in these web...

  11. EnviroAtlas - Metrics for Tampa, FL

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  12. EnviroAtlas - Metrics for Milwaukee, WI

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (http://www.epa.gov/enviroatlas). The layers in these web...

  13. EnviroAtlas - Metrics for Woodbine, IA

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  14. EnviroAtlas - Metrics for Durham, NC

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas ). The layers in these web...

  15. EnviroAtlas - Metrics for Fresno, CA

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  16. EnviroAtlas - Metrics for Portland, OR

    Data.gov (United States)

    U.S. Environmental Protection Agency — These EnviroAtlas web services support research and online mapping activities related to EnviroAtlas (http:/www.epa.gov/enviroatlas). The layers in these web...

  17. GeoServer beginner's guide

    CERN Document Server

    Youngblood, Brian

    2013-01-01

    Step-by-step instructions are included and the needs of a beginner are totally satisfied by the book. The book consists of plenty of examples with accompanying screenshots and code for an easy learning curve. You are a web developer with knowledge of server side scripting, and have experience with installing applications on the server. You have a desire to want more than Google maps, by offering dynamically built maps on your site with your latest geospatial data stored in MySQL, PostGIS, MsSQL or Oracle. If this is the case, this book is meant for you.

  18. The SMARTCyp cytochrome P450 metabolism prediction server

    DEFF Research Database (Denmark)

    Rydberg, Patrik; Gloriam, David Erik Immanuel; Olsen, Lars

    2010-01-01

    The SMARTCyp server is the first web application for site of metabolism prediction of cytochrome P450-mediated drug metabolism.......The SMARTCyp server is the first web application for site of metabolism prediction of cytochrome P450-mediated drug metabolism....

  19. EnviroAtlas - Portland, OR - One Meter Resolution Urban Land Cover (2012) Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Portland, OR land cover web service includes data for the Portland metropolitan area plus the city of Vancouver, Washington and various smaller towns and rural...

  20. Web systems to support the elaboration and publication of the ATLAS data analysis papers

    International Nuclear Information System (INIS)

    Full text: In 2010, the LHC experiment produced 7 TeV and heavy-ions collisions continually. It allowed ATLAS to collect and analyze a huge amount of data and perform several studies. Physicists are now publishing papers and conference notes announcing results and achievements. During the past year, 37 papers were published and for 2011 there are already 39 papers in preparation. A paper publication management involves several aspects, such as keep track of the analysis results status, follow the procedure step-by-step, promote the communication among collaborators, improve the paper initial version, and make an interaction between the Authorship Committee and the Publication Committee to produce a final authors list. The UFRJ group developed the Glance system, a retrieval mechanism to perform data manipulation and operation in distinct and geographically spread repositories. Using Glance as the main application to access data, the Analysis Follow-Up and Analysis CONF Notes systems allow users to manage and update information related to all ATLAS papers and conference notes. Both systems support the process of revision, approval and publication of the analysis outcome. The first step to publish a paper or note is to define an Editorial Board, which main responsibility is to improve the initial versions. The whole process is supervised by the Publication Committee, which will sign-off the final decisions and submit the paper for publishing. Presentations and papers versions are elaborated by the Conveners of the different ATLAS physics groups. The systems also support the registration of meetings, tracking the paper through the official references (like CDS, arXiv, DOI and the published Journal) and insertion of comments about the successive versions. As all steps are traced, automatic e-mails warn the responsible of the next step to take an action. A search engine allows any user to follow an analysis publication stage. The access privileges are based on

  1. ATLAS Offline Data Quality Monitoring

    CERN Document Server

    Adelman, J; Boelaert, N; D'Onofrio, M; Frost, J A; Guyot, C; Hauschild, M; Hoecker, A; Leney, K J C; Lytken, E; Martinez-Perez, M; Masik, J; Nairz, A M; Onyisi, P U E; Roe, S; Schatzel, S; Schaetzel, S; Wilson, M G

    2010-01-01

    The ATLAS experiment at the Large Hadron Collider reads out 100 Million electronic channels at a rate of 200 Hz. Before the data are shipped to storage and analysis centres across the world, they have to be checked to be free from irregularities which render them scientifically useless. Data quality offline monitoring provides prompt feedback from full first-pass event reconstruction at the Tier-0 computing centre and can unveil problems in the detector hardware and in the data processing chain. Detector information and reconstructed proton-proton collision event characteristics are distilled into a few key histograms and numbers which are automatically compared with a reference. The results of the comparisons are saved as status flags in a database and are published together with the histograms on a web server. They are inspected by a 24/7 shift crew who can notify on-call experts in case of problems and in extreme cases signal data taking abort.

  2. Creating A Model HTTP Server Program Using java

    OpenAIRE

    Bala Dhandayuthapani Veerasamy

    2010-01-01

    HTTP Server is a computer programs that serves webpage content to clients. A webpage is a document or resource of information that is suitable for the World Wide Web and can be accessed through a web browser and displayed on a computer screen. This information is usually in HTML format, and may provide navigation to other webpage’s via hypertext links. WebPages may be retrieved from a local computer or from a remote HTTP Server. WebPages are requested and served from HTTP Servers using Hypert...

  3. Web data mining

    Science.gov (United States)

    Wibonele, Kasanda J.; Zhang, Yanqing

    2002-03-01

    A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

  4. EnviroAtlas - Metrics for Des Moines, IA

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). The layers in this...

  5. ATLAS EventIndex monitoring system using the Kibana analytics and visualization platform

    CERN Document Server

    Barberis, Dario; The ATLAS collaboration; Favareto, Andrea; Fernandez Casani, Alvaro; Gallas, Elizabeth; Garcia Montoro, Carlos; Gonzalez de la Hoz, Santiago; Hrivnac, Julius; Malon, David; Prokoshin, Fedor; Salt, Jose; Sanchez, Javier; Toebbicke, Rainer; Yuan, Ruijun

    2016-01-01

    The ATLAS EventIndex is a data catalogue system that stores event-related metadata for all (real and simulated) ATLAS events, on all processing stages. As it consists of different components that depend on other applications (such as distributed storage, and different sources of information) we need to monitor the conditions of many heterogeneous subsystems, to make sure everything is working correctly. This paper describes how we gather information about the EventIndex components and related subsystems: the Producer-Consumer architecture for data collection, health parameters from the servers that run EventIndex components, EventIndex web interface status, and the Hadoop infrastructure that stores EventIndex data. This information is collected, processed, and then displayed using CERN service monitoring software based on the Kibana analytic and visualization package, provided by CERN IT Department. EventIndex monitoring is used both by the EventIndex team and ATLAS Distributed Computing shifts crew

  6. ATLAS detector control system data viewer

    International Nuclear Information System (INIS)

    The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. DCS Data Viewer (DDV) is a web interface application that provides access to historical data of ATLAS Detector Control System (DCS) parameters written to the database (DB). It has a modular and flexible design and is structured using a client-server architecture. The server can be operated stand alone with a command-line interface to the data while the client offers a user friendly, browser independent interface. The selection of the meta-data of DCS parameters is done via a column-tree view or with a powerful search engine. The final visualisation of the data is done using various plug-ins such as 'value over time' charts, data tables, raw ASCII or structured export to ROOT. Excessive access or malicious use of the database is prevented by dedicated protection mechanisms, allowing the exposure of the tool to hundreds of inexperienced users. The meta-data selection and data output features can be used separately by XML configuration files. Security constraints have been taken into account in the implementation allowing the access of DDV by collaborators worldwide. (authors)

  7. Single Page Web Applications Security

    OpenAIRE

    Bogdan Beda

    2015-01-01

    With the constant spread of internet access, the world of software is constantly transforming product shapes into services delivered via web browsers. Modern next generation web applications change the way browsers and users interact with servers. A lot of word scale services have already been delivered by top companies as Single Page Applications. Moving services online poses a big attention towards data protection and web application security. Single Page Application are exposed to server-s...

  8. ATLAS Recordings

    CERN Multimedia

    Steven Goldfarb; Mitch McLachlan; Homer A. Neal

    Web Archives of ATLAS Plenary Sessions, Workshops, Meetings, and Tutorials from 2005 until this past month are available via the University of Michigan portal here. Most recent additions include the Trigger-Aware Analysis Tutorial by Monika Wielers on March 23 and the ROOT Workshop held at CERN on March 26-27.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal.Feedback WelcomeOur group is making arrangements now to record plenary sessions, tutorials, and other important ATLAS events for 2007. Your suggestions for potential recording, as well as your feedback on existing archives is always welcome. Please contact us at wlap@umich.edu. Thank you.Enjoy the Lectures!

  9. Implementation of absolute delay guarantee in database connection pool in Web application servers%绝对延迟保证在Web应用服务器数据库连接池中的实现

    Institute of Scientific and Technical Information of China (English)

    吕健波; 戴冠中; 慕德俊

    2012-01-01

    网络QoS机制不足以提供完全的端到端的性能保证,在由三层结构构成的电子商务网站中,基于反馈控制理论,提出并实现了在应用服务器的数据库连接池中的绝对延迟保证,对数据库连接池作出了改进,确保带有高优先级请求的平均排队延迟不超过设定的阈值.通过系统辨识建立了数据库连接池的近似线性时不变模型(LTI),并设计了绝对延迟保证控制器,为Tomcat Web应用服务器实现了数据库连接池中闭环系统所有部件.测试结果表明,即使在并发请求数量剧烈变化时,控制器的设计也是有效的.%Network QoS mechanisms are insufficient to provide complete end to end performance guarantees. In e-commeree Web sites composed of a three-tiered architecture, this paper proposed and implemented absolute delay guarantee in the database connection pool(DBCP)in Web application servers based on feedback control. It improved the database connection pool to ensure that the response time for requests with high priority was no more than the threshold specified. It set up the approximate linear time-invariant models of the DBCP through system identification and designed the absolute delay guarantee controller. It implemented all the components of closed-loops in a real DBCP for the Tomcat Web application server. Test results show that the controllers designing is effectively even if the number of concurrent requests varies severely.

  10. EnviroAtlas - Metrics for Green Bay, WI

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  11. EnviroAtlas - Metrics for New Bedford, MA

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  12. EnviroAtlas - Metrics for New York, NY

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  13. GeoServer cookbook

    CERN Document Server

    Iacovella, Stefano

    2014-01-01

    This book is ideal for GIS experts, developers, and system administrators who have had a first glance at GeoServer and who are eager to explore all its features in order to configure professional map servers. Basic knowledge of GIS and GeoServer is required.

  14. CERN World-Wide Web Days

    CERN Document Server

    Llewellyn Smith, Christopher Hubert; Breen, J; Brunner, B; Bruno, F; Cailliau, Robert; Elliott, B; Hardy, T; Hunt, D; Innocente, Vincenzo; Isberg, G; Ludvigsen, B; Trudel, P; Williams, D; CERN. Geneva

    1994-01-01

    Switching on a World-Wide Web server in Liverpool. WhAt is the Internet? What is the Web?A potted history How do I connect up to the Web?What will it cost? How do I get my own server onto the Web? Why we are on the Web Legal implications Who controls the Internet?- unsuitable material on the Web Will the Web continue to grow?

  15. Mastering Lync Server 2010

    CERN Document Server

    Winters, Nathan

    2012-01-01

    An in-depth guide on the leading Unified Communications platform Microsoft Lync Server 2010 maximizes communication capabilities in the workplace like no other Unified Communications (UC) solution. Written by experts who know Lync Server inside and out, this comprehensive guide shows you step by step how to administer the newest and most robust version of Lync Server. Along with clear and detailed instructions, learning is aided by exercise problems and real-world examples of established Lync Server environments. You'll gain the skills you need to effectively deploy Lync Server 2010 and be on

  16. CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

    Science.gov (United States)

    Valassi, A.; Bartoldus, R.; Kalkhof, A.; Salnikov, A.; Wache, M.

    2011-12-01

    The CORAL software is widely used at CERN by the LHC experiments to access the data they store on relational databases, such as Oracle. Two new components have recently been added to implement a model involving a middle tier "CORAL server" deployed close to the database and a tree of "CORAL server proxies", providing data caching and multiplexing, deployed close to the client. A first implementation of the two new components, released in the summer 2009, is now deployed in the ATLAS online system to read the data needed by the High Level Trigger, allowing the configuration of a farm of several thousand processes. This paper reviews the architecture of the software, its development status and its usage in ATLAS.

  17. CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

    International Nuclear Information System (INIS)

    The CORAL software is widely used at CERN by the LHC experiments to access the data they store on relational databases, such as Oracle. Two new components have recently been added to implement a model involving a middle tier 'CORAL server' deployed close to the database and a tree of 'CORAL server proxies', providing data caching and multiplexing, deployed close to the client. A first implementation of the two new components, released in the summer 2009, is now deployed in the ATLAS online system to read the data needed by the High Level Trigger, allowing the configuration of a farm of several thousand processes. This paper reviews the architecture of the software, its development status and its usage in ATLAS.

  18. Base-on Cloud Computing A new type of distributed application server system design

    Directory of Open Access Journals (Sweden)

    Ying-ying Chen

    2012-11-01

    Full Text Available At this stage the application server systems, such as e-commerce platform , instant messaging system , enterprise information system and so on, will be led to lose connections , the data latency phenomena because of too much concurrent requests, application server architecture, system architecture, etc. In serious cases, the server is running blocked. The new type of application server system contains four parts: a client program, transfer servers, application servers and databases. Application server is the core of the system. Its performance determines the system’s performance. At the same time the application servers and transfer servers can be designed as the web service open to be used, and they can be achieved as distributed architecture by a number of hardware servers, which can effectively deal with high concurrent client application requests.

  19. Minimizing cache misses in an event-driven network server: A case study of TUX

    DEFF Research Database (Denmark)

    Bhatia, Sapan; Consel, Charles; Lawall, Julia Laetitia

    servers by optimizing their use of the L2 CPU cache in the context of the TUX Web server, known for its robustness to heavy load. Our approach is based on a novel cache-aware memory allocator and a specific scheduling strategy that together ensure that the total working data set of the server stays in the...

  20. DCS data viewer, an application that accesses ATLAS DCS historical data

    International Nuclear Information System (INIS)

    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.

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

    Science.gov (United States)

    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.

  2. Hipax Cluster PACS Server

    OpenAIRE

    Ramin Payrovi

    2007-01-01

    Best Performace: With our Hipax Cluster PACS Server solution we are introducing the parallel computing concept as an extremely fast software system to the PACS world. In contrast to the common PACS servers, the Hipax Cluster PACS software is not only restricted to one or two computers, but can be used on a couple of servers controlling each other."nThus, the same services can be run simultaneously on different computers. The scalable system can also be expanded subsequently without lost ...

  3. ANALYZING OF THE USER ACCESS LOGS OF A WEBSITE USING WEB USAGE MINING METHOD: EXAMPLE OF FIRAT UNIVERSITY

    OpenAIRE

    DAS, Resul

    2008-01-01

    Web usage mining is to analysis Web log files to discover user accessing patterns of Web pages. The web server access logs records very significant information about websites. Information about a web site such as links between the pages, the users' profile, and demographic properties can be obtained from the web server access logs. In this study, user access logs of the Web server of Firat University were analyzed with Web mining software by using Web usage mining method. The end of analysis,...

  4. Web Usage Mining

    OpenAIRE

    Bari, Pranit; P M Chawan

    2013-01-01

    The paper discusses about web usage mining involves the automatic discovery of user access patterns from one or more Web servers. This article provides a survey and analysis of current Web usage mining systems and technologies. The paper also confers about the procedure in which the web usage mining of the data sets is carried out. Finally the paper concludes with the areas in which web usage mining is implemented

  5. Optimizing the NASA Technical Report Server

    Science.gov (United States)

    Nelson, Michael L.; Maa, Ming-Hokng

    1996-01-01

    The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

  6. Integration of ROOT Notebooks as a Web-based ATLAS Analysis tool for public data releases and outreach

    CERN Document Server

    Banda, Tea; CERN. Geneva. EP Department

    2016-01-01

    The project consists in the initial development of ROOT notebooks for a Z boson analysis in C++ programming language that will allow students and researches to perform fast and very useful data analysis, using ATLAS public data and Monte- Carlo simulations. Several tools are considered: ROOT Data Analysis Frame- work, Jupyter Notebook Technology and CERN-ROOT computing service so-called SWAN.

  7. Web database development

    OpenAIRE

    Tsardas, Nikolaos A.

    2001-01-01

    This thesis explores the concept of Web Database Development using Active Server Pages (ASP) and Java Server Pages (JSP). These are among the leading technologies in the web database development. The focus of this thesis was to analyze and compare the ASP and JSP technologies, exposing their capabilities, limitations, and differences between them. Specifically, issues related to back-end connectivity using Open Database Connectivity (ODBC) and Java Database Connectivity (JDBC), application ar...

  8. Analisis Skalabilitas Server Virtualisasi pada Akademi Manajemen Informatika dan Komputer New Media

    Directory of Open Access Journals (Sweden)

    I Gede Eka Sanjaya

    2014-06-01

    Full Text Available Perguruan tinggi yang sudah besar dan sedang berkembang, umumnya memiliki lebih dari satu sistem informasi ataupun fungsi server yang dijalankan. Pada umumnya penggunaan server hanya berkisar 8%-15%. Keadaan ini tidak ideal jika dibandingkan dengan nilai investasi yang cukup besar untuk pengadaan sebuah mesin server. Untuk itu perlu diimplementasikan sebuah teknologi virtualisasi. Virtualisasi merupakan teknik untuk menyembunyikan karakter fisik suatu sumber daya komputer dari cara yang digunakan oleh sistem lain, aplikasi atau pengguna untuk berinteraksi dengan sumber daya tersebut. Implementasi server virtualisasi menggunakan VMWare sebagai perangkat lunak mesin virtual. Pengujian dilakukan untuk memperoleh nilai skalabilitas CPU Utilization, Response Time serta Throughput dengan menggunakan perangkat lunak Top Command, OpenWebLoad dan Performance Monitor. Pengujian dilakukan dengan terlebih dahulu menguji CPU Utilization sebagai threshold dalam mengukur optimalitas jumlah server virtual dalam satu server fisik. Setelah didapatkan jumlah server yang optimal, pengujian dilanjutkan dengan menguji response time dan throughput. Berdasarkan hasil pengujian diketahui bahwa jumlah server virtual yang optimal pada satu server adalah dua, yang terdiri dari web server dan application server. Server konvensional menggunakan resource CPU sejumlah 46% sedangkan virtualisasi 66%. Respond time pada server konvensional adalah 1,24 detik sedangkan virtualisasi 2,08 detik.

  9. Java Applet程序的安全规则与访问第三方WEB服务器%Safety rules and access to third party WEB server Java Applet program

    Institute of Scientific and Technical Information of China (English)

    韩旭东

    2014-01-01

    随着各项技术的进步,计算机技术广泛的应用于我们的日常生活中,在各软件程序开发的过程中,一种面向对象的编程语言取得了广泛的应用,就是Java语言,在实际的应用中,可以应用Java语言进行不同性质程序的编制,其中一种应用程序就是Applet程序,改程序在实际的运行过程中,不能自行运行,只有通过浏览器及小程序查看器来运行,本文主要对其程序的安全规则进行简单分析,并通过安全策略文件使其能够有效实现第三方WEB服务器的方位。%With theprogress of technology,the computer technology is widely used in our daily life,in the process of the software development,an object-oriented programming language has been widely used,is the Java language,in the actual application,can be written using Java language of the different types of applications,including an application program is Applet program,change the program in the actual operation process,not to run,only through the browser and the applet viewer to run,the main safety rules for its program of simple analysis,and through the security policy file so that it can effectively realize the third party WEB server location.

  10. Learning Zimbra Server essentials

    CERN Document Server

    Kouka, Abdelmonam

    2013-01-01

    A standard tutorial approach which will guide the readers on all of the intricacies of the Zimbra Server.If you are any kind of Zimbra user, this book will be useful for you, from newbies to experts who would like to learn how to setup a Zimbra server. If you are an IT administrator or consultant who is exploring the idea of adopting, or have already adopted Zimbra as your mail server, then this book is for you. No prior knowledge of Zimbra is required.

  11. Windows Server 2008 -infrastruktuuri

    OpenAIRE

    Sundgren, Patrik

    2011-01-01

    Tämä työ käsittelee Windows 2008 -verkkoinfrastrukstuuri-kurssin materiaalin suunnittelua ja testausta. Työ toteutettiin Metropolia Ammattikorkeakoululle keväällä 2010. Työn alussa esitellään työssä käytetty virtuaalisointiohjelmisto ja toiminta, sekä Windows Server 2008:n ominaisuuksia. Työssä käydään läpi virtuaaliympäristön luonti sekä Win-dows Server 2008 -palvelinten konfigurointia. Konfigurointi tapahtuu Windows Server 2008 infrastructure -materaalin harjoitustöiden pohjalta. Työssä...

  12. Improving SQL Server Perform

    Directory of Open Access Journals (Sweden)

    Nicolae MERCIOIU

    2010-01-01

    Full Text Available With the development of client server technology and multilayer architectures the systems ef-ficiency issue has been increasingly discussed. Lacking knowledge in optimization methods and tools offered by DBMS's, database administrators and developers of applications based on Microsoft technologies cannot optimally design and service performing systems. In this article we review the objectives that should be considered (in order to improve performance of SQL Server instances and we describe the techniques used to optimize queries. Also, we explain and illustrate the new optimization features offered by SQL Server 2008.

  13. El uso de las Web 2.0 de colaboración en los escenarios virtuales de divulgación científica del Proyecto Atlas The Use of Web 2.0 for Collaboration in the Virtual Scenarios of Scientific Dissemination of the Atlas Project

    Directory of Open Access Journals (Sweden)

    Elias Said-Hung

    2012-04-01

    Full Text Available Este artículo estudia 110 enlaces vinculados al portal principal del proyecto Atlas, con el fin de analizar los rasgos generales que caracterizan el uso de las Web 2.0 de colaboración en los escenarios virtuales de divulgación científica, al interior de este estudio de caso. Los resultados apuntan, entre otras cosas, a que los escenarios estudiados se caracterizan por un bajo nivel de visibilidad en Internet, una política de acceso libre ampliamente apropiada desde esta comunidad científica, pero que tiene un bajo nivel de implementación de modelos de comunicación multiformatos a través de las Web 2.0, en los que se exponen contenidos altamente especializados, dirigidos a la exposición de informes y resultados, bajo un marco de baja apropiación de herramientas de interacción y personalización de la información. Se concluye que la presencia de un escenario virtual analizado aquí presenta limitaciones en relación con la usabilidad de las Web 2.0, en tanto que limita el ejercicio de esta función a expertos pertenecientes al mismo colectivo científico relacionado con el caso de estudio.This article analyzes 110 links related to the Atlas Project's main website, in order to study the general features that characterize the use of Web 2.0 in the virtual scenarios of scientific dissemination, within this case study. The results suggest, among other things, that the dissemination of science is characterized by a low level of visibility on the Internet, an open access policy broadly appropriate by the scientific community, but with low implementation of multi-format communication models through Web 2.0, in which highly specialized contents are exposed, aimed to the presentation of reports and results, presenting low appropriation of tools for interaction and personalization of information. It is concluded that the presence of a virtual scenario discussed here presents limitations in relation to the usability of the Web 2.0 as it limits

  14. Installing and Testing a Server Operating System

    Directory of Open Access Journals (Sweden)

    Lorentz JÄNTSCHI

    2003-08-01

    Full Text Available The paper is based on the experience of the author with the FreeBSD server operating system administration on three servers in use under academicdirect.ro domain.The paper describes a set of installation, preparation, and administration aspects of a FreeBSD server.First issue of the paper is the installation procedure of FreeBSD operating system on i386 computer architecture. Discussed problems are boot disks preparation and using, hard disk partitioning and operating system installation using a existent network topology and a internet connection.Second issue is the optimization procedure of operating system, server services installation, and configuration. Discussed problems are kernel and services configuration, system and services optimization.The third issue is about client-server applications. Using operating system utilities calls we present an original application, which allows displaying the system information in a friendly web interface. An original program designed for molecular structure analysis was adapted for systems performance comparisons and it serves for a discussion of Pentium, Pentium II and Pentium III processors computation speed.The last issue of the paper discusses the installation and configuration aspects of dial-in service on a UNIX-based operating system. The discussion includes serial ports, ppp and pppd services configuration, ppp and tun devices using.

  15. Fuzzy Clustering: An Approachfor Mining Usage Profilesfrom Web

    OpenAIRE

    Ms.Archana N. Boob; Prof. D. M. Dakhane

    2012-01-01

    Web usage mining is an application of data mining technology to mining the data of the web server log file. It can discover the browsing patterns of user and some kind of correlations between the web pages. Web usage mining provides the support for the web site design, providing personalization server and other business making decision, etc. Web mining applies the data mining, the artificial intelligence and the chart technology and so on to the web data and traces users' visiting characteris...

  16. LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays

    Directory of Open Access Journals (Sweden)

    Gao Hongmei

    2011-05-01

    Full Text Available Abstract Background Multiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results. Results We present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings. Conclusions Standardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the Lab

  17. Remote diagnosis server

    Science.gov (United States)

    Deb, Somnath (Inventor); Ghoshal, Sudipto (Inventor); Malepati, Venkata N. (Inventor); Kleinman, David L. (Inventor); Cavanaugh, Kevin F. (Inventor)

    2004-01-01

    A network-based diagnosis server for monitoring and diagnosing a system, the server being remote from the system it is observing, comprises a sensor for generating signals indicative of a characteristic of a component of the system, a network-interfaced sensor agent coupled to the sensor for receiving signals therefrom, a broker module coupled to the network for sending signals to and receiving signals from the sensor agent, a handler application connected to the broker module for transmitting signals to and receiving signals therefrom, a reasoner application in communication with the handler application for processing, and responding to signals received from the handler application, wherein the sensor agent, broker module, handler application, and reasoner applications operate simultaneously relative to each other, such that the present invention diagnosis server performs continuous monitoring and diagnosing of said components of the system in real time. The diagnosis server is readily adaptable to various different systems.

  18. How Public Is the Web?: Robots, Access, and Scholarly Communication.

    Science.gov (United States)

    Snyder, Herbert; Rosenbaum, Howard

    1998-01-01

    Examines the use of Robot Exclusion Protocol (REP) to restrict the access of search engine robots to 10 major United States university Web sites. An analysis of Web site searching and interviews with Web server administrators shows that the decision to use this procedure is largely technical and is typically made by the Web server administrator.…

  19. Mineral Spectroscopy Server

    OpenAIRE

    Rossman, George R.

    2010-01-01

    This server provides information about mineralogy and is primarily dedicated to providing information about color in minerals and access to data on Mineral Absorption Spectra in the visible and infrared regions of the spectrum and Raman spectra of minerals. Most data on the server were obtained in the Caltech mineral spectroscopy labs. Other types of spectroscopic data on minerals are also available. Visible, near-infrared and infrared absorption spectra are available for a number of minerals...

  20. SERVER FOR A BEST SALE APPLICATION

    OpenAIRE

    Patturaj, Ramkumar

    2014-01-01

    The aim of this Master's thesis was to build a web server providing an Rest API endpoint which could be used to develop platform independent applications displaying online advertisement content for mobiles and tablets. Reducing wastage of paper, minimizing the cost of advertisement, improving the accessibility of the best discount offer for the end user/customer and maintaining the statistical data of online advertisements are some of the practical problems discussed in this thesis. To ac...

  1. Hey Fellows, We Shrunk the Server

    OpenAIRE

    Valentim Sousa; Paulo Ferreira; Manuel Gericota

    2012-01-01

    Remote laboratories are an essential part of Web-based engineering lecturing, enabling future engineers 24/7 access to lab resources. Furthermore, they allow sharing expensive resources among multiple universities and research centres. Typical remote lab architectures feature a server, normally a computer that may serve one or more experiments. Computers are generally bulky, somewhat expensive and require heavy resources to run complex operating systems. In this paper, a remote lab for the te...

  2. The NASA Technical Report Server

    Science.gov (United States)

    Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Paulson, Sharon S.; Binkley, Robert L.; Kellogg, Yvonne D.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael J.; Accomazzi, Alberto

    1995-01-01

    The National Aeronautics and Space Act of 1958 established NASA and charged it to "provide for the widest practicable and appropriate dissemination of information concerning its activities and the results thereof." The search for innovative methods to distribute NASA's information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the service. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained ensures that NASA's institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

  3. RS-WebPredictor

    DEFF Research Database (Denmark)

    Zaretzki, J.; Bergeron, C.; Huang, T.-W.;

    2013-01-01

    Regioselectivity-WebPredictor (RS-WebPredictor) is a server that predicts isozyme-specific cytochrome P450 (CYP)-mediated sites of metabolism (SOMs) on drug-like molecules. Predictions may be made for the promiscuous 2C9, 2D6 and 3A4 CYP isozymes, as well as CYPs 1A2, 2A6, 2B6, 2C8, 2C19 and 2E1....... RS-WebPredictor is the first freely accessible server that predicts the regioselectivity of the last six isozymes. Server execution time is fast, taking on average 2s to encode a submitted molecule and 1s to apply a given model, allowing for high-throughput use in lead optimization projects.......Availability: RS-WebPredictor is accessible for free use at http://reccr.chem.rpi.edu/ Software/RS-WebPredictor. © 2013 The Author....

  4. ATLAS Detector Control System Data Viewer

    CERN Document Server

    Tsarouchas, Charilaos; Roe, S; Bitenc, U; Fehling-Kaschek, ML; Winkelmann, S; D’Auria, S; Hoffmann, D; Pisano, O

    2011-01-01

    The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. DCS Data Viewer (DDV) is a web interface application that provides access to historical data of ATLAS Detector Control System [1] (DCS) parameters written to the database (DB). It has a modular andflexible design and is structured using a clientserver architecture. The server can be operated stand alone with a command-line interface to the data while the client offers a user friendly, browser independent interface. The selection of the metadata of DCS parameters is done via a column-tree view or with a powerful search engine. The final visualisation of the data is done using various plugins such as “value over time” charts, data tables, raw ASCII or structured export to ROOT. Excessive access or malicious use of the database is prevented by dedicated protection mechanisms, allowing the exposure of the tool to hundreds of inexperienced users. The metadata selection and data output features can be used separately by XML con...

  5. Dear ATLAS colleagues,

    CERN Multimedia

    PH Department

    2008-01-01

    We are collecting old pairs of glasses to take out to Mali, where they can be re-used by people there. The price for a pair of glasses can often exceed 3 months salary, so they are prohibitively expensive for many people. If you have any old spectacles you can donate, please put them in the special box in the ATLAS secretariat, bldg.40-4-D01 before the Christmas closure on 19 December so we can take them with us when we leave for Africa at the end of the month. (more details in ATLAS e-news edition of 29 September 2008: http://atlas-service-enews.web.cern.ch/atlas-service-enews/news/news_mali.php) many thanks! Katharine Leney co-driver of the ATLAS car on the Charity Run to Mali

  6. ATLAS distributed analysis

    OpenAIRE

    Adams, David; Branco, Miguel; Albrand, Solveig; Rybkine, G.; Orellana, F.; Liko, D.; Tan C.L.; Deng, W.; C. KANNAN; Harrison Karl; Fassi, Farida; Fulachier, J.; Chetan, N.; Haeberli, C.; Soroko, A.

    2004-01-01

    The ATLAS distributed analysis (ADA) system is described. The ATLAS experiment has more that 2000 physicists from 150 insititutions in 34 countries. Users, data and processing are distributed over these sites. ADA makes use of a collection of high-level web services whose interfaces are expressed in terms of AJDL (abstract job definition language) which includes descriptions of datasets, transformations and jobs. The high-level services are implemented using generic parts...

  7. The MultiHttpServer : a parallel pull engine

    OpenAIRE

    Endres, Christoph

    1999-01-01

    Internet agents require fast, concurrent access to many web pages. This service should be stable, central, and easy to access independently from the actual implementation language. This paper describes the MultiHttpServer (MHS), a parallel pull engine implemented in Java with a TCP/IP interface for communication with other programs. A second TCP/IP interface provides information for administration purposes. A simple config-file allows application-oriented tuning of the MultiHttpServer. An opt...

  8. Recent improvements in the NASA technical report server

    Science.gov (United States)

    Maa, Ming-Hokng; Nelson, Michael L.

    1995-01-01

    The NASA Technical Report Server (NTRS), a World Wide Web (WWW) report distribution service, has been modified to allow parallel database queries, significantly decreasing user access time by an average factor of 2.3, access from clients behind firewalls and/or proxies which truncate excessively long Uniform Resource Locators (URL's), access to non-Wide Area Information Server (WAIS) databases, and compatibility with the Z39-50.3 protocol.

  9. ATLAS Recordings

    CERN Multimedia

    Jeremy Herr; Homer A. Neal; Mitch McLachlan

    The University of Michigan Web Archives for the 2006 ATLAS Week Plenary Sessions, as well as the first of 2007, are now online. In addition, there are a wide variety of Software and Physics Tutorial sessions, recorded over the past couple years, to chose from. All ATLAS-specific archives are accessible here.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal. Shaping Collaboration 2006The Michigan group is happy to announce a complete set of recordings from the Shaping Collaboration conference held last December at the CICG in Geneva.The event hosted a mix of Collaborative Tool experts and LHC Users, and featured presentations by the CERN Deputy Director General, Prof. Jos Engelen, the President of Internet2, and chief developers from VRVS/EVO, WLAP, and other tools...

  10. The design and implementation of web mining in web sites security

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guo-yin; GU Guo-chang; LI Jian-li

    2003-01-01

    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.

  11. KFC Server: interactive forecasting of protein interaction hot spots

    OpenAIRE

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

    2008-01-01

    The KFC Server is a web-based implementation of the KFC (Knowledge-based FADE and Contacts) model—a machine learning approach for the prediction of binding hot spots, or the subset of residues that account for most of a protein interface's; binding free energy. The server facilitates the automated analysis of a user submitted protein–protein or protein–DNA interface and the visualization of its hot spot predictions. For each residue in the interface, the KFC Server characterizes its local str...

  12. The ATLAS metadata interface

    International Nuclear Information System (INIS)

    AMI was chosen as the ATLAS dataset selection interface in July 2006. It is the main interface for searching for ATLAS data using physics metadata criteria. AMI has been implemented as a generic database management framework which allows parallel searching over many catalogues, which may have differing schema. The main features of the web interface will be described; in particular the powerful graphic query builder. The use of XML/XLST technology ensures that all commands can be used either on the web or from a command line interface via a web service. We also describe the overall architecture of ATLAS metadata and the different actors and granularity involved, and the place of AMI within this architecture. We discuss the problems involved in the correlation of metadata of differing granularity, and propose a solution for information mediation

  13. EnviroAtlas - Climate Stabilization Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Climate Stabilization...

  14. EnviroAtlas - Clean Air Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Clean Air category in...

  15. EnviroAtlas - Biodiversity Conservation Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Biodiversity Conservation...

  16. WEB GIS: IMPLEMENTATION ISSUES

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    With the rapid expansion and development of Internet and WWW (World Wide Web or Web), Web GIS (Web Geographical Information Systen) is becoming ever more popular and as a result numerous sites have added GIS capability on their Web sites. In this paper, the reasons behind developing a Web GIS instead of a “traditional” GIS are first outlined. Then the current status of Web GIS is reviewed, and their implementation methodologies are explored as well.The underlying technologies for developing Web GIS, such as Web Server, Web browser, CGI (Common Gateway Interface), Java, ActiveX, are discussed, and some typical implementation tools from both commercial and public domain are given as well. Finally, the future development direction of Web GIS is predicted.

  17. ATLAS TDAQ System Administration:

    CERN Document Server

    Lee, Christopher Jon; The ATLAS collaboration; Bogdanchikov, Alexander; Ballestrero, Sergio; Contescu, Alexandru Cristian; Dubrov, Sergei; Fazio, Daniel; Korol, Aleksandr; Scannicchio, Diana; Twomey, Matthew Shaun; Voronkov, Artem

    2015-01-01

    The ATLAS Trigger and Data Acquisition (TDAQ) system is responsible for the online processing of live data, streaming from the ATLAS experiment at the Large Hadron Collider (LHC) at CERN. The online farm is composed of ̃3000 servers, processing the data readout from ̃100 million detector channels through multiple trigger levels. During the two years of the first Long Shutdown (LS1) there has been a tremendous amount of work done by the ATLAS TDAQ System Administrators, implementing numerous new software applications, upgrading the OS and the hardware, changing some design philosophies and exploiting the High Level Trigger farm with different purposes. During the data taking only critical security updates are applied and broken hardware is replaced to ensure a stable operational environment. The LS1 provided an excellent opportunity to look into new technologies and applications that would help to improve and streamline the daily tasks of not only the System Administrators, but also of the scientists who wil...

  18. Commissioning of ATLAS Data Quality Infrastructure with First Collision Data

    International Nuclear Information System (INIS)

    During particle physics data taking, the data being recorded must be monitored and checked continuously and promptly. The data quality system of the ATLAS experiment at the Large Hadron Collider provides the means to investigate and monitor the data recorded. Over the course of 2010, this system has been commissioned successfully with first collision data. Data quality monitoring enables prompt investigation of the first pass of full event processing at the Tier-0 CERN computing centre, the validation of calibration and other reconstruction parameters, and any detector issues to be diagnosed and, wherever possible, fixed. Automatically filled histograms are checked by algorithms and against references, the results of which are stored as status flags in a database, and published onto a web server, where they can be inspected by shifters and experts. The data quality for approximately 100 data quality regions is determined, and propagated in a convenient format for data analysis teams.

  19. Professional SQL Server 2005 administration

    CERN Document Server

    Knight, Brian; Snyder, Wayne; Armand, Jean-Claude; LoForte, Ross; Ji, Haidong

    2007-01-01

    SQL Server 2005 is the largest leap forward for SQL Server since its inception. With this update comes new features that will challenge even the most experienced SQL Server DBAs. Written by a team of some of the best SQL Server experts in the industry, this comprehensive tutorial shows you how to navigate the vastly changed landscape of the SQL Server administration. Drawing on their own first-hand experiences to offer you best practices, unique tips and tricks, and useful workarounds, the authors help you handle even the most difficult SQL Server 2005 administration issues, including blockin

  20. APAX Server and Viewer

    Directory of Open Access Journals (Sweden)

    Morteza Bakhtiary

    2007-08-01

    Full Text Available ‘APAX VIEWER' enables you to see the various medical images. It allows doctors in each clinical part to inquire about the medical images and helps them to diagnose their patient's illness more cor-rectly. Its function related to the management of the database helps the doctors to prepare for the education, research and conference as well as to save the images into their personal computers. And it also can help the doctors to manage effectively the patient's data of diagnosis and treatment, con-nected with the HIS."nAPAX Viewer's features:"n1- Holds HL7. "n2- Improved image quality through non-linear lookup tables, window leveling preset auto-matching. "n3- Various image processing tools."n4- Optimized medical image searching using MIH (Medical Image History."n5- Record and Dictation supported."n‘APAX SERVER' connects RIS to modalities, acquires images, archives images and interpretations with or without compression using multiple storage spaces through following features:"n1-‘APAX Acquisition Server' acquires images and saves and transmits them to the database (exam and image information and deciphering results received through RIS I/S. "n2-‘APAX RIS Broker' receives patient and order information from RIS, and sends to each modality. "n3-‘APAX Archiving Server' stores acquired data with or without compression in the Short-term Storage (Hard disk, ... and when it passes defined days it will be moved to the Long-term Storage (Tape Drives, ... with or without compression."n4-‘APAX Storage Server' checks multiple-storage spaces any time, and assists Acquisition Server selecting a suitable storage space to store."n5-‘APAX DB Gateway' relays to DB requests between the Client and DB Server when the main DB server is ‘Oracle' and a client's PC is not installed the Oracle client program."n6-‘APAX Secondary Capture System' acquires data from non-DICOM modalities, converts

  1. Internet marketing - Discount servers

    OpenAIRE

    Bozděchová, Lenka

    2014-01-01

    Buying on discount servers is a trend of the last few years. It came from the USA, where it originated in 2005. In 2011 it came to the Czech republic and it is really popular way of shopping. The theoretical section of thesis focused on the internet, its development and the benefits for the society, marketing, marketing mix and internet marketing. Next part of thesis is focused on discount servers, discount aggregator and principle of collective buying. The main aim was to evaluate the ret...

  2. Querying Data Providing Web Services

    OpenAIRE

    Sabesan, Manivasakan

    2010-01-01

    Web services are often used for search computing where data is retrieved from servers providing information of different kinds. Such data providing web services return a set of objects for a given set of parameters without any side effects. There is need to enable general and scalable search capabilities of data from data providing web services, which is the topic of this Thesis. The Web Service MEDiator (WSMED) system automatically provides relational views of any data providing web service ...

  3. SHADE3 server

    DEFF Research Database (Denmark)

    Madsen, Anders Østergaard; Hoser, Anna Agnieszka

    2014-01-01

    . Tools are provided to set up the ab initio calculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong...

  4. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

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

    Science.gov (United States)

    Watanabe, Toru; Koizumi, Hisao

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

  6. Implementation of a Cloud Data Server (CDS) for Providing Secure Service in E-Business

    OpenAIRE

    D.Kesavaraja; Balasubramanian, R; D. Sasireka

    2010-01-01

    Cloud Data Servers is the novel approach for providing secure service to e-business .Millions of users are surfing the Cloud for various purposes, therefore they need highly safe and persistent services. Usually hackers target particular Operating Systems or a Particular Controller. Inspiteof several ongoing researches Conventional Web Servers and its Intrusion Detection System might not be able to detect such attacks. So we implement a Cloud Data Server with Session Controller Architecture u...

  7. UNIX secure server : a free, secure, and functional server example

    OpenAIRE

    Sastre, Hugo

    2016-01-01

    The purpose of this thesis work was to introduce UNIX server as a personal server but also as a start point for investigation and developing at a professional level. The objective of this thesis was to build a secure server providing not only a FTP server but also an HTTP server and a cloud system for remote backups. OpenBSD was used as the operating system. OpenBSD is a UNIX-like operating system made by hackers for hackers. The difference with other systems that might partially provid...

  8. Web Technologies And Databases

    OpenAIRE

    Irina-Nicoleta Odoraba

    2011-01-01

    The database means a collection of many types of occurrences of logical records containing relationships between records and data elementary aggregates. Management System database (DBMS) - a set of programs for creating and operation of a database. Theoretically, any relational DBMS can be used to store data needed by a Web server. Basically, it was observed that the simple DBMS such as Fox Pro or Access is not suitable for Web sites that are used intensively. For large-scale Web applications...

  9. Web Mining: An Overview

    Directory of Open Access Journals (Sweden)

    P. V. G. S. Mudiraj B. Jabber K. David raju

    2011-12-01

    Full Text Available Web usage mining is a main research area in Web mining focused on learning about Web users and their interactions with Web sites. The motive of mining is to find users’ access models automatically and quickly from the vast Web log data, such as frequent access paths, frequent access page groups and user clustering. Through web usage mining, the server log, registration information and other relative information left by user provide foundation for decision making of organizations. This article provides a survey and analysis of current Web usage mining systems and technologies. There are generally three tasks in Web Usage Mining: Preprocessing, Pattern analysis and Knowledge discovery. Preprocessing cleans log file of server by removing log entries such as error or failure and repeated request for the same URL from the same host etc... The main task of Pattern analysis is to filter uninteresting information and to visualize and interpret the interesting pattern to users. The statistics collected from the log file can help to discover the knowledge. This knowledge collected can be used to take decision on various factors like Excellent, Medium, Weak users and Excellent, Medium and Weak web pages based on hit counts of the web page in the web site. The design of the website is restructured based on user’s behavior or hit counts which provides quick response to the web users, saves memory space of servers and thus reducing HTTP requests and bandwidth utilization. This paper addresses challenges in three phases of Web Usage mining along with Web Structure Mining.This paper also discusses an application of WUM, an online Recommender System that dynamically generates links to pages that have not yet been visited by a user and might be of his potential interest. Differently from the recommender systems proposed so far, ONLINE MINER does not make use of any off-line component, and is able to manage Web sites made up of pages dynamically generated.

  10. KFC Server: interactive forecasting of protein interaction hot spots.

    Science.gov (United States)

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

    2008-07-01

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

  11. Ecoupling server: A tool to compute and analyze electronic couplings.

    Science.gov (United States)

    Cabeza de Vaca, Israel; Acebes, Sandra; Guallar, Victor

    2016-07-01

    Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login. © 2016 Wiley Periodicals, Inc. PMID:27157013

  12. ATLAS production system

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration; De, Kaushik; Klimentov, Alexei; Golubkov, Dmitry; Maeno, Tadashi; Mashinistov, Ruslan; Wenaus, Torre; Padolski, Siarhei

    2016-01-01

    The second generation of the ATLAS production system called ProdSys2 is a distributed workload manager which used by thousands of physicists to analyze the data remotely, with the volume of processed data is beyond the exabyte scale, across a more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criterias, such as input and output size, memory requirements and CPU consumption with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteering computers. Besides jobs definition Production System also includes flexible web user interface, which implements user-friendly environment for main ATLAS workflows, e.g. simple way of combining different data flows, and real-time monitoring, optimised for using with huge amount of information to present. We present an overview of the ATLAS Production System major components: job and task definition, workflow manager web user i...

  13. Beginning SQL Server 2008 Administration

    CERN Document Server

    Walters, R

    2009-01-01

    Beginning SQL Server 2008 Administration is essential for anyone wishing to learn about implementing and managing SQL Server 2008 database. From college students, to experienced database administrators from other platforms, to those already familiar with SQL Server and wanting to fill in some gaps of knowledge, this book will bring all readers up to speed on the enterprise platform Microsoft SQL Server 2008. * Clearly describes relational database concepts* Explains the SQL Server database engine and supporting tools* Shows various database maintenance scenarios What you'll learn* Understand c

  14. Windows Home Server users guide

    CERN Document Server

    Edney, Andrew

    2008-01-01

    Windows Home Server brings the idea of centralized storage, backup and computer management out of the enterprise and into the home. Windows Home Server is built for people with multiple computers at home and helps to synchronize them, keep them updated, stream media between them, and back them up centrally. Built on a similar foundation as the Microsoft server operating products, it's essentially Small Business Server for the home.This book details how to install, configure, and use Windows Home Server and explains how to connect to and manage different clients such as Windows XP, Windows Vist

  15. Microsoft SQL Server 2012 bible

    CERN Document Server

    Jorgensen, Adam; LeBlanc, Patrick; Cherry, Denny; Nelson, Aaron

    2012-01-01

    Harness the powerful new SQL Server 2012 Microsoft SQL Server 2012 is the most significant update to this product since 2005, and it may change how database administrators and developers perform many aspects of their jobs. If you're a database administrator or developer, Microsoft SQL Server 2012 Bible teaches you everything you need to take full advantage of this major release. This detailed guide not only covers all the new features of SQL Server 2012, it also shows you step by step how to develop top-notch SQL Server databases and new data connections and keep your databases performing at p

  16. Probabilistic Semantic Web Mining Using Artificial Neural Analysis

    CERN Document Server

    Kishore, T Krishna; Narayana, N Lakshmi

    2010-01-01

    Most of the web user's requirements are search or navigation time and getting correctly matched result. These constrains can be satisfied with some additional modules attached to the existing search engines and web servers. This paper proposes that powerful architecture for search engines with the title of Probabilistic Semantic Web Mining named from the methods used. With the increase of larger and larger collection of various data resources on the World Wide Web (WWW), Web Mining has become one of the most important requirements for the web users. Web servers will store various formats of data including text, image, audio, video etc., but servers can not identify the contents of the data. These search techniques can be improved by adding some special techniques including semantic web mining and probabilistic analysis to get more accurate results. Semantic web mining technique can provide meaningful search of data resources by eliminating useless information with mining process. In this technique web servers...

  17. Nearline Web Archiving

    OpenAIRE

    Xie, Zhiwu; Nayyar, Krati; Fox, Edward A

    2016-01-01

    In this paper, we propose a modified approach to real­time transactional web archiving. It leverages the web caching infrastructure that is already prevalent on web servers. Instead of archiving web content at HTTP transaction time, in our approach the archiving happens when the cached copy expires and is about to be expunged. Before the deletion, all expired cache copies are combined and then sent to the web archive in small batches. Since the cache is purged at much lower frequency than HTT...

  18. Ajax and Web Services

    CERN Document Server

    Pruett, Mark

    2006-01-01

    Ajax and web services are a perfect match for developing web applications. Ajax has built-in abilities to access and manipulate XML data, the native format for almost all REST and SOAP web services. Using numerous examples, this document explores how to fit the pieces together. Examples demonstrate how to use Ajax to access publicly available web services fromYahoo! and Google. You'll also learn how to use web proxies to access data on remote servers and how to transform XML data using XSLT.

  19. EarthServer: an Intercontinental Collaboration on Petascale Datacubes

    Science.gov (United States)

    Baumann, P.; Rossi, A. P.

    2015-12-01

    With the unprecedented increase of orbital sensor, in-situ measurement, and simulation data there is a rich, yet not leveraged potential for getting insights from dissecting datasets and rejoining them with other datasets. Obviously, the goal is to allow users to "ask any question, any time" thereby enabling them to "build their own product on the go".One of the most influential initiatives in Big Geo Data is EarthServer which has demonstrated new directions for flexible, scalable EO services based on innovative NewSQL technology. Researchers from Europe, the US and recently Australia have teamed up to rigourously materialize the concept of the datacube. Such a datacube may have spatial and temporal dimensions (such as a satellite image time series) and may unite an unlimited number of scenes. Independently from whatever efficient data structuring a server network may perform internally, users will always see just a few datacubes they can slice and dice. EarthServer has established client and server technology for such spatio-temporal datacubes. The underlying scalable array engine, rasdaman, enables direct interaction, including 3-D visualization, what-if scenarios, common EO data processing, and general analytics. Services exclusively rely on the open OGC "Big Geo Data" standards suite, the Web Coverage Service (WCS) including the Web Coverage Processing Service (WCPS). Conversely, EarthServer has significantly shaped and advanced the OGC Big Geo Data standards landscape based on the experience gained.Phase 1 of EarthServer has advanced scalable array database technology into 100+ TB services; in phase 2, Petabyte datacubes will be built in Europe and Australia to perform ad-hoc querying and merging. Standing between EarthServer phase 1 (from 2011 through 2014) and phase 2 (from 2015 through 2018) we present the main results and outline the impact on the international standards landscape; effectively, the Big Geo Data standards established through initiative of

  20. Liberate Mediacast Server

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ The Mediacast server schedules the retrieval of HTML content from multiple sources, then organizes and broadcasts the content to all clients on the appropriate channels at the specified times. The content is displayed upon subscriber request, when triggered by an event, or automatically. These broadcasts are generally performed in-band, but Mediacast can also broadcast over the out-of-band network. This allows subscribers to display and interact with a wide variety of specialized content without significantly increasing network traffic.

  1. Qualified Mobile Server Signature

    OpenAIRE

    Orthacker, Clemens; Centner, Martin; Kittl, Christian

    2010-01-01

    International audience A legal basis for the use of electronic signatures exists since the introduction of qualified electronic signatures in EU Directive 1999/ 93/EC. Although considered as key enablers for e-Government and e-Commerce, qualified electronic signatures are still not widely used. Introducing amobile component addresses most of the shortcomings of existing qualified signature approaches but poses certain difficulties in the security reasoning. The proposed server based mobile...

  2. ATLAS Maintenance and Operation management system

    CERN Multimedia

    Copy, B

    2007-01-01

    The maintenance and operation of the ATLAS detector will involve thousands of contributors from 170 physics institutes. Planning and coordinating the action of ATLAS members, ensuring their expertise is properly leveraged and that no parts of the detector are understaffed or overstaffed will be a challenging task. The ATLAS Maintenance and Operation application (referred to as Operation Task Planner inside the ATLAS experiment) offers a fluent web based interface that combines the flexibility and comfort of a desktop application, intuitive data visualization and navigation techniques, with a lightweight service oriented architecture. We will review the application, its usage within the ATLAS experiment, its underlying design and implementation.

  3. Oracle announces increased uptake of Oracle9i Application Server

    CERN Multimedia

    2002-01-01

    Oracle Europe this week announced that increasingly, companies in the region are selecting the Oracle9i Application Server (Oracle9iAS) to develop and deploy web-based business application. CERN is one of its customers (1/2 page).

  4. Computers in Small Libraries: Learning Server-Side Scripting

    Science.gov (United States)

    Roberts, Gary

    2005-01-01

    In this column, the author compares and contrasts the most popular scripting languages that are used to create truly dynamic service-oriented Web sites, building a conceptual framework that be can used as a starting point for specific server-side library projects.

  5. Web-based control application using WebSocket

    International Nuclear Information System (INIS)

    The WebSocket allows asynchronous full-duplex communication between a Web-based (i.e. Java Script-based) application and a Web-server. WebSocket started as a part of HTML5 standardization but has now been separated from HTML5 and has been developed independently. Using WebSocket, it becomes easy to develop platform independent presentation layer applications for accelerator and beamline control software. In addition, a Web browser is the only application program that needs to be installed on client computer. The WebSocket-based applications communicate with the WebSocket server using simple text-based messages, so WebSocket is applicable message-based control system like MADOCA, which was developed for the SPring-8 control system. A simple WebSocket server for the MADOCA control system and a simple motor control application were successfully made as a first trial of the WebSocket control application. Using Google-Chrome (version 13.0) on Debian/Linux and Windows 7, Opera (version 11.0) on Debian/Linux and Safari (version 5.0.3) on Mac OS X as clients, the motors can be controlled using a WebSocket-based Web-application. Diffractometer control application use in synchrotron radiation diffraction experiment was also developed. (author)

  6. GRASS: a server for the graphical representation and analysis of structures.

    OpenAIRE

    Nayal, M.; Hitz, B. C.; Honig, B

    1999-01-01

    GRASS (Graphical Representation and Analysis of Structures Server), a new web-based server, is described. GRASS exploits many of the features of the GRASP program and is designed to provide interactive molecular graphics and quantitative analysis tools with a simple interface over the World-Wide Web. Using GRASS, it is now possible to view many surface features of biological macromolecules on either standard workstations used in macromolecular analysis or personal computers. The result is a W...

  7. Gwt analysis for web web application development

    OpenAIRE

    Makorič, Saša

    2013-01-01

    This undergraduate thesis presents the analysis of the GWT framework usage for the development of web applications. GWT offers functionality for the development of complete web applications, as the user interface as the implementation of the application logic on the server. The thesis shows the architectural concepts and the model of framework operation. There is a great emphasis on the compiler, which uses the concept of deffered binding, providing a coherent render on various browsers witho...

  8. Map server of Slovak Environmental Agency

    International Nuclear Information System (INIS)

    The Slovak Environmental Agency (SAZP) is professional organization of the Ministry of Environment of the Slovak Republic. In the area of informatics SAZP is responsible for operation of information system about environment in the Slovak Republic (ISE). The main goal of the ISE is collection, evaluating and accessing of relevant information about environment between organizations of state or administration, public administration, public, scientific institutes etc. SAZP uses technology of publishing of geo-space data so-called WEB maps (dynamic mapping) - maps are formed online. As a technologic part of information system is internet map server

  9. Professional Microsoft SQL Server 2012 Reporting Services

    CERN Document Server

    Turley, Paul; Silva, Thiago; Withee, Ken; Paisley, Grant

    2012-01-01

    A must-have guide for the latest updates to the new release of Reporting Services SQL Server Reporting Services allows you to create reports and business intelligence (BI) solutions. With this updated resource, a team of experts shows you how Reporting Services makes reporting faster, easier and more powerful than ever in web, desktop, and portal solutions. New coverage discusses the new reporting tool called Crescent, BI semantic model's impact on report design and creation, semantic model design, and more. You'll explore the major enhancements to Report Builder and benefit from best practice

  10. RCD+: Fast loop modeling server.

    Science.gov (United States)

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-07-01

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. PMID:27151199

  11. Cybersecurity, massive data processing, community interaction, and other developments at WWW-based computational X-ray Server

    Science.gov (United States)

    Stepanov, Sergey

    2013-03-01

    X-Ray Server (x-server.gmca.aps.anl.gov) is a WWW-based computational server for modeling of X-ray diffraction, reflection and scattering data. The modeling software operates directly on the server and can be accessed remotely either from web browsers or from user software. In the later case the server can be deployed as a software library or a data fitting engine. As the server recently surpassed the milestones of 15 years online and 1.5 million calculations, it accumulated a number of technical solutions that are discussed in this paper. The developed approaches to detecting physical model limits and user calculations failures, solutions to spam and firewall problems, ways to involve the community in replenishing databases and methods to teach users automated access to the server programs may be helpful for X-ray researchers interested in using the server or sharing their own software online.

  12. Cybersecurity, massive data processing, community interaction, and other developments at WWW-based computational X-ray Server

    International Nuclear Information System (INIS)

    X-Ray Server (x-server.gmca.aps.anl.gov) is a WWW-based computational server for modeling of X-ray diffraction, reflection and scattering data. The modeling software operates directly on the server and can be accessed remotely either from web browsers or from user software. In the later case the server can be deployed as a software library or a data fitting engine. As the server recently surpassed the milestones of 15 years online and 1.5 million calculations, it accumulated a number of technical solutions that are discussed in this paper. The developed approaches to detecting physical model limits and user calculations failures, solutions to spam and firewall problems, ways to involve the community in replenishing databases and methods to teach users automated access to the server programs may be helpful for X-ray researchers interested in using the server or sharing their own software online.

  13. CORAL Server and CORAL Server Proxy: Scalable Access to Relational Databases from CORAL Applications

    CERN Document Server

    Valassi, A; Kalkhof, A; Salnikov, A; Wache, M

    2011-01-01

    The CORAL software is widely used at CERN for accessing the data stored by the LHC experiments using relational database technologies. CORAL provides a C++ abstraction layer that supports data persistency for several backends and deployment models, including local access to SQLite files, direct client access to Oracle and MySQL servers, and read-only access to Oracle through the FroNTier web server and cache. Two new components have recently been added to CORAL to implement a model involving a middle tier "CORAL server" deployed close to the database and a tree of "CORAL server proxy" instances, with data caching and multiplexing functionalities, deployed close to the client. The new components are meant to provide advantages for read-only and read-write data access, in both offline and online use cases, in the areas of scalability and performance (multiplexing for several incoming connections, optional data caching) and security (authentication via proxy certificates). A first implementation of the two new c...

  14. Single Page Web Applications Security

    Directory of Open Access Journals (Sweden)

    Bogdan Beda

    2015-06-01

    Full Text Available With the constant spread of internet access, the world of software is constantly transforming product shapes into services delivered via web browsers. Modern next generation web applications change the way browsers and users interact with servers. A lot of word scale services have already been delivered by top companies as Single Page Applications. Moving services online poses a big attention towards data protection and web application security. Single Page Application are exposed to server-side web applications security in a new way. Also, having application logic being executed by untrusted client environment requires close attention on client application security. Single Page Applications are vulnerable to the same security threads as server-side web application thus not making them less secure. Defending techniques can be easily adapted to guard against hacker attacks.

  15. Client/server study

    Science.gov (United States)

    Dezhgosha, Kamyar; Marcus, Robert; Brewster, Stephen

    1995-01-01

    The goal of this project is to find cost-effective and efficient strategies/solutions to integrate existing databases, manage network, and improve productivity of users in a move towards client/server and Integrated Desktop Environment (IDE) at NASA LeRC. The project consisted of two tasks as follows: (1) Data collection, and (2) Database Development/Integration. Under task 1, survey questionnaires and a database were developed. Also, an investigation on commercially available tools for automated data-collection and net-management was performed. As requirements evolved, the main focus has been task 2 which involved the following subtasks: (1) Data gathering/analysis of database user requirements, (2) Database analysis and design, making recommendations for modification of existing data structures into relational database or proposing a common interface to access heterogeneous databases(INFOMAN system, CCNS equipment list, CCNS software list, USERMAN, and other databases), (3) Establishment of a client/server test bed at Central State University (CSU), (4) Investigation of multi-database integration technologies/ products for IDE at NASA LeRC, and (5) Development of prototypes using CASE tools (Object/View) for representative scenarios accessing multi-databases and tables in a client/server environment. Both CSU and NASA LeRC have benefited from this project. CSU team investigated and prototyped cost-effective/practical solutions to facilitate NASA LeRC move to a more productive environment. CSU students utilized new products and gained skills that could be a great resource for future needs of NASA.

  16. WebMapping at school

    Science.gov (United States)

    de Lange, Norbert

    2010-11-01

    The paper discusses the position of GIS in Geography as a subject especially at German schools. It points out that students only need simple GIS-functions in order to explore digital atlases or webbased data viewers. Furthermore it is widely accepted that learning achievements improve if students make use of the idea of self-employed and explorative working on information produced by themselves. These two arguments have led to the development of the WebMapping tool "kartografix_school". It allows users to generate maps with new and individually defined content on the internet. For that purpose the tool contains generalized outlines of all countries of the world as well as of German States. As these boundaries are given users can assign new attribute data to these geoobjects. These data are transferred to a graphic presentation. It is possible to define the classification and colours for each class. Users can change and update all information (data as well as number of classes, definition of classes, colours) at any time. Moreover "kartografix_school" offers the possibility to produce maps which are composed of two layers. All data are stored at a server located in the University of Osnabrück. "kartografix_school" is integrated in an e-Learning environment.

  17. DELPHI event server

    International Nuclear Information System (INIS)

    The World-Wide Web (WWW) is the telecommunications technology area which underwent the biggest technological uprise observed lately. This work presents a case study which demonstrates the benefits brought by WWW in a High Energy Physics environment

  18. Seamless mobility with personal servers

    OpenAIRE

    Bylund, Markus; Segall, Zary

    2003-01-01

    We describe the concept and the taxonomy of personal servers, and their implications in seamless mobility. Personal servers could offer electronic services independently of network availability or quality, provide a greater flexibility in the choice of user access device, and support the key concept of continuous user experience. We describe the organization of mobile and remote personal servers, define three relevant communication modes, and discuss means for users to exploit seamless servic...

  19. Frame architecture for video servers

    Science.gov (United States)

    Venkatramani, Chitra; Kienzle, Martin G.

    1999-11-01

    Video is inherently frame-oriented and most applications such as commercial video processing require to manipulate video in terms of frames. However, typical video servers treat videos as byte streams and perform random access based on approximate byte offsets to be supplied by the client. They do not provide frame or timecode oriented API which is essential for many applications. This paper describes a frame-oriented architecture for video servers. It also describes the implementation in the context of IBM's VideoCharger server. The later part of the paper describes an application that uses the frame architecture and provides fast and slow-motion scanning capabilities to the server.

  20. Mastering Microsoft Exchange Server 2013

    CERN Document Server

    Elfassy, David

    2013-01-01

    The bestselling guide to Exchange Server, fully updated for the newest version Microsoft Exchange Server 2013 is touted as a solution for lowering the total cost of ownership, whether deployed on-premises or in the cloud. Like the earlier editions, this comprehensive guide covers every aspect of installing, configuring, and managing this multifaceted collaboration system. It offers Windows systems administrators and consultants a complete tutorial and reference, ideal for anyone installing Exchange Server for the first time or those migrating from an earlier Exchange Server version.Microsoft

  1. Microsoft Windows Server Administration Essentials

    CERN Document Server

    Carpenter, Tom

    2011-01-01

    The core concepts and technologies you need to administer a Windows Server OS Administering a Windows operating system (OS) can be a difficult topic to grasp, particularly if you are new to the field of IT. This full-color resource serves as an approachable introduction to understanding how to install a server, the various roles of a server, and how server performance and maintenance impacts a network. With a special focus placed on the new Microsoft Technology Associate (MTA) certificate, the straightforward, easy-to-understand tone is ideal for anyone new to computer administration looking t

  2. Sending servers to Morocco

    CERN Multimedia

    Joannah Caborn Wengler

    2012-01-01

    Did you know that computer centres are like people? They breathe air in and out like a person, they have to be kept at the right temperature, and they can even be organ donors. As part of a regular cycle of equipment renewal, the CERN Computer Centre has just donated 161 retired servers to universities in Morocco.   Prof. Abdeslam Hoummada and CERN DG Rolf Heuer seeing off the servers on the beginning of their journey to Morocco. “Many people don’t realise, but the Computer Centre is like a living thing. You don’t just install equipment and it runs forever. We’re continually replacing machines, broken parts and improving things like the cooling.” Wayne Salter, Leader of the IT Computing Facilities Group, watches over the Computer Centre a bit like a nurse monitoring a patient’s temperature, especially since new international recommendations for computer centre environmental conditions were released. “A new international s...

  3. PACS image security server

    Science.gov (United States)

    Cao, Fei; Huang, H. K.

    2004-04-01

    Medical image security in a PACS environment has become a pressing issue as communications of images increasingly extends over open networks, and hospitals are currently hard-pushed by Health Insurance Portability and Accountability Act (HIPAA) to be HIPPA complaint for ensuring health data security. Other security-related guidelines and technical standards continue bringing to the public attention in healthcare. However, there is not an infrastructure or systematic method to implement and deploy these standards in a PACS. In this paper, we first review DICOM Part15 standard for secure communications of medical images and the HIPAA impacts on PACS security, as well as our previous works on image security. Then we outline a security infrastructure in a HIPAA mandated PACS environment using a dedicated PACS image security server. The server manages its own database of all image security information. It acts as an image Authority for checking and certificating the image origin and integrity upon request by a user, as a secure DICOM gateway to the outside connections and meanwhile also as a PACS operation monitor for HIPAA supporting information.

  4. The ATLAS PanDA Monitoring System and its Evolution

    Science.gov (United States)

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

    2011-12-01

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

  5. The PeptideAtlas Project

    OpenAIRE

    Deutsch, Eric W.

    2010-01-01

    PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from the community and reprocessed through a uniform analysis and validation pipeline that continues to advance. The results are loaded into a database and the information derived from the raw data is returned to the community via several web-based data exploration tools. The PeptideAtlas resource is useful for experiment planning, improving g...

  6. Microsoft Office SharePoint Server 2007 organisaation toiminnan tukena

    OpenAIRE

    Laakso, Jani

    2008-01-01

    Tämän tutkimuksen tarkoituksena on selvittää Microsoft Office SharePoint Server 2007 -ohjelmiston mahdollisuudet Lahden tiede- ja yrityspuisto Oy:n intranetverkkopalveluna organisaation toiminnan tukemiseksi. Tarkoituksena on myös selvittää, mitä web-osia Microsoft Office SharePoint Server 2007 tuo Lahden tiede- ja yrityspuisto Oy:n viestinnän ja työnteon helpottamiseksi. Tutkimus tehtiin case-tutkimuksena vuoden 2008 huhti-syyskuussa Lahden tiedeja yrityspuisto Oy:ssä. Yritykselle tote...

  7. Remote Sensing Data Analytics for Planetary Science with PlanetServer/EarthServer

    Science.gov (United States)

    Rossi, Angelo Pio; Figuera, Ramiro Marco; Flahaut, Jessica; Martinot, Melissa; Misev, Dimitar; Baumann, Peter; Pham Huu, Bang; Besse, Sebastien

    2016-04-01

    Planetary Science datasets, beyond the change in the last two decades from physical volumes to internet-accessible archives, still face the problem of large-scale processing and analytics (e.g. Rossi et al., 2014, Gaddis and Hare, 2015). PlanetServer, the Planetary Science Data Service of the EC-funded EarthServer-2 project (#654367) tackles the planetary Big Data analytics problem with an array database approach (Baumann et al., 2014). It is developed to serve a large amount of calibrated, map-projected planetary data online, mainly through Open Geospatial Consortium (OGC) Web Coverage Processing Service (WCPS) (e.g. Rossi et al., 2014; Oosthoek et al., 2013; Cantini et al., 2014). The focus of the H2020 evolution of PlanetServer is still on complex multidimensional data, particularly hyperspectral imaging and topographic cubes and imagery. In addition to hyperspectral and topographic from Mars (Rossi et al., 2014), the use of WCPS is applied to diverse datasets on the Moon, as well as Mercury. Other Solar System Bodies are going to be progressively available. Derived parameters such as summary products and indices can be produced through WCPS queries, as well as derived imagery colour combination products, dynamically generated and accessed also through OGC Web Coverage Service (WCS). Scientific questions translated into queries can be posed to a large number of individual coverages (data products), locally, regionally or globally. The new PlanetServer system uses the the Open Source Nasa WorldWind (e.g. Hogan, 2011) virtual globe as visualisation engine, and the array database Rasdaman Community Edition as core server component. Analytical tools and client components of relevance for multiple communities and disciplines are shared across service such as the Earth Observation and Marine Data Services of EarthServer. The Planetary Science Data Service of EarthServer is accessible on http://planetserver.eu. All its code base is going to be available on GitHub, on

  8. RESTful Web Services Cookbook

    CERN Document Server

    Allamaraju, Subbu

    2010-01-01

    While the REST design philosophy has captured the imagination of web and enterprise developers alike, using this approach to develop real web services is no picnic. This cookbook includes more than 100 recipes to help you take advantage of REST, HTTP, and the infrastructure of the Web. You'll learn ways to design RESTful web services for client and server applications that meet performance, scalability, reliability, and security goals, no matter what programming language and development framework you use. Each recipe includes one or two problem statements, with easy-to-follow, step-by-step i

  9. Antropo Web - První český sociálněvědní server s možností on-line diskuze

    Czech Academy of Sciences Publication Activity Database

    Woitsch, Jiří; Svoboda, M.

    2005-01-01

    Roč. 11, č. 2 (2005), s. 7. ISSN 1211-6866 Institutional research plan: CEZ:AV0Z90580513 Keywords : Social anthropology * Cultural anthropology * Web journal * On-line discussion Subject RIV: AC - Archeology, Anthropology, Ethnology

  10. Web-Based Course Management and Web Services

    Science.gov (United States)

    Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.

    2004-01-01

    The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…

  11. A Dynamic Extension of ATLAS Run Query Service

    CERN Document Server

    Buliga, Alexandru

    2015-01-01

    The ATLAS RunQuery is a primarily web-based service for the ATLAS community to access meta information about the data taking in a concise format. In order to provide a better user experience, the service was moved to use a new technology, involving concepts such as: Web Sockets, on demand data, client-side scripting, memory caching and parallelizing execution.

  12. Research on Web-Based Networked Virtual Instrument System

    International Nuclear Information System (INIS)

    The web-based networked virtual instrument (NVI) system is designed by using the object oriented methodology (OOM). The architecture of the NVI system consists of two major parts: client-web server interaction and instrument server-virtual instrument (VI) communication. The web server communicates with the instrument server and the clients connected to it over the Internet, and it handles identifying the user's name, managing the connection between the user and the instrument server, adding, removing and configuring VI's information. The instrument server handles setting the parameters of VI, confirming the condition of VI and saving the VI's condition information into the database. The NVI system is required to be a general-purpose measurement system that is easy to maintain, adapt and extend. Virtual instruments are connected to the instrument server and clients can remotely configure and operate these virtual instruments. An application of The NVI system is given in the end of the paper

  13. Web proxy cache replacement strategies simulation, implementation, and performance evaluation

    CERN Document Server

    ElAarag, Hala; Cobb, Jake

    2013-01-01

    This work presents a study of cache replacement strategies designed for static web content. Proxy servers can improve performance by caching static web content such as cascading style sheets, java script source files, and large files such as images. This topic is particularly important in wireless ad hoc networks, in which mobile devices act as proxy servers for a group of other mobile devices. Opening chapters present an introduction to web requests and the characteristics of web objects, web proxy servers and Squid, and artificial neural networks. This is followed by a comprehensive review o

  14. Node web development

    CERN Document Server

    Herron, David

    2013-01-01

    Presented in a simple, step-by-step format, this book is an introduction to web development with Node.This book is for anybody looking for an alternative to the ""P"" languages (Perl, PHP, Python), or anyone looking for a new paradigm of server-side application development.The reader should have at least a rudimentary understanding of JavaScript and web application development.

  15. EnviroAtlas - Natural Hazard Mitigation Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Natural Hazard Mitigation...

  16. EnviroAtlas - Food, Fuel, and Materials Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Food, Fuel, and Materials...

  17. EnviroAtlas - Recreation, Culture, and Aesthetics Metrics for Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Recreation, Culture, and...

  18. EnviroAtlas - Clean and Plentiful Water Metrics for the Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The Clean and Plentiful Water...

  19. The ATLAS Detector Control System

    CERN Document Server

    Schlenker, S; Kersten, S; Hirschbuehl, D; Braun, H; Poblaguev, A; Oliveira Damazio, D; Talyshev, A; Zimmermann, S; Franz, S; Gutzwiller, O; Hartert, J; Mindur, B; Tsarouchas, CA; Caforio, D; Sbarra, C; Olszowska, J; Hajduk, Z; Banas, E; Wynne, B; Robichaud-Veronneau, A; Nemecek, S; Thompson, PD; Mandic, I; Deliyergiyev, M; Polini, A; Kovalenko, S; Khomutnikov, V; Filimonov, V; Bindi, M; Stanecka, E; Martin, T; Lantzsch, K; Hoffmann, D; Huber, J; Mountricha, E; Santos, HF; Ribeiro, G; Barillari, T; Habring, J; Arabidze, G; Boterenbrood, H; Hart, R; Marques Vinagre, F; Lafarguette, P; Tartarelli, GF; Nagai, K; D'Auria, S; Chekulaev, S; Phillips, P; Ertel, E; Brenner, R; Leontsinis, S; Mitrevski, J; Grassi, V; Karakostas, K; Iakovidis, G.; Marchese, F; Aielli, G

    2011-01-01

    The ATLAS experiment is one of the multi-purpose experiments at the Large Hadron Collider (LHC), constructed to study elementary particle interactions in collisions of high-energy proton beams. Twelve different sub-detectors as well as the common experimental infrastructure are supervised by the Detector Control System (DCS). The DCS enables equipment supervision of all ATLAS sub-detectors by using a system of >130 server machines running the industrial SCADA product PVSS. This highly distributed system reads, processes and archives of the order of 106 operational parameters. Higher level control system layers allow for automatic control procedures, efficient error recognition and handling, and manage the communication with external systems such as the LHC. This contribution firstly describes the status of the ATLAS DCS and the experience gained during the LHC commissioning and the first physics data taking operation period. Secondly, the future evolution and maintenance constraints for the coming years an...

  20. gWidgetsWWW: Creating Interactive Web Pages within R

    OpenAIRE

    John Verzani

    2012-01-01

    The gWidgetsWWW package provides a framework for easily developing interactive web pages from within R. It uses the API developed in the gWidgets programming interface to specify the layout of the controls and the relationships between them. The web pages may be served locally under R's built-in web server for help pages or from an rApache-enabled web server.