WorldWideScience

Sample records for macintosh web server

  1. 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/....

  2. 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.

  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. 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…

  5. Dynamic Web Pages: Performance Impact on Web Servers.

    Science.gov (United States)

    Kothari, Bhupesh; Claypool, Mark

    2001-01-01

    Discussion of Web servers and requests for dynamic pages focuses on experimentally measuring and analyzing the performance of the three dynamic Web page generation technologies: CGI, FastCGI, and Servlets. Develops a multivariate linear regression model and predicts Web server performance under some typical dynamic requests. (Author/LRW)

  6. 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.

  7. WebLogic Server 9.0

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    8月9日,BEA WebLogic Server 9.0全面上市。BEA公司产品执行副总裁黄卫文(WaiWong)表示:“WebLogic Server9.0将使用户在转向SOA的同时,能够继续在复杂的异构环境中实现提高效率、降低IT成本和零宕机这些核心目标。”

  8. 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.

  9. 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...

  10. Swiss EMBnet node web server.

    Science.gov (United States)

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

    2003-07-01

    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 biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere else.

  11. The BiSearch web server

    Directory of Open Access Journals (Sweden)

    Tusnády Gábor E

    2006-10-01

    Full Text Available Abstract Background A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genomic DNA methylation profiles. Indeed, the number of studies on bisulfite-treated templates exponentially increases as determining DNA methylation becomes more important in the diagnosis of cancers. Bisulfite-treated DNA is difficult to amplify since undesired PCR products are often amplified due to the increased sequence redundancy after the chemical conversion. In order to increase the efficiency of PCR primer-design, we have developed BiSearch web server, an online primer-design tool for both bisulfite-treated and native DNA templates. Results The web tool is composed of a primer-design and an electronic PCR (ePCR algorithm. The completely reformulated ePCR module detects potential mispriming sites as well as undesired PCR products on both cDNA and native or bisulfite-treated genomic DNA libraries. Due to the new algorithm of the current version, the ePCR module became approximately hundred times faster than the previous one and gave the best performance when compared to other web based tools. This high-speed ePCR analysis made possible the development of the new option of high-throughput primer screening. BiSearch web server can be used for academic researchers at the http://bisearch.enzim.hu site. Conclusion BiSearch web server is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. The ePCR tool for fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes are the unique features of the new version of BiSearch software.

  12. 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...... usage, network usage and memory usage. We collect different data sets from monitoring the web server's activity and for each one we predict the server's reliability with the proposed recurrent neural network. © 2012 Taylor & Francis Group...

  13. 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 (t...... usage, network usage and memory usage. We collect different data sets from monitoring the web server's activity and for each one we predict the server's reliability with the proposed recurrent neural network. © 2012 Taylor & Francis Group...

  14. 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.

  15. PSSweb: protein structural statistics web server.

    Science.gov (United States)

    Gaillard, Thomas; Stote, Roland H; Dejaegere, Annick

    2016-07-01

    With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of protein structures, performs a multiple sequence alignment and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An interactive report is generated, containing a summary of the results, tables, figures and 3D visualization of superposed structures. The server is available at http://pssweb.org.

  16. RANCANG BANGUN PERANGKAT LUNAK MANAJEMEN DATABASE SQL SERVER BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Muchammad Husni

    2005-01-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 Microsoft SQL Server merupakan aplikasi desktop database server yang bersifat client/server, karena memiliki komponen client, yang  berfungsi menampilkan dan memanipulasi data; serta komponen server yang berfungsi menyimpan, memanggil, dan mengamankan database. Operasi-operasi manajemen semua server database dalam jaringan dilakukan administrator database dengan menggunakan tool administratif utama SQL Server yang bernama Enterprise Manager. Hal ini mengakibatkan administrator database hanya bisa  melakukan operasi-operasi tersebut di komputer yang telah diinstalasi Microsoft SQL Server. Pada penelitian ini, dirancang suatu aplikasi berbasis web dengan menggunakan ASP.Net untuk melakukan pengaturan database server. Aplikasi ini menggunakan ADO.NET yang memanfaatkan Transact-SQL dan stored procedure pada server untuk melakukan operasi-operasi manajemen database pada suatu server database SQL, dan menampilkannya ke dalam web. Administrator database bisa menjalankan aplikasi berbasis web tersebut dari komputer mana saja pada jaringan dan melakukan koneksi ke server database SQL dengan menggunakan web browser. Dengan demikian memudahkan administrator melakukan tugasnya tanpa harus menggunakan komputer server.   Kata Kunci : Transact-SQL, ASP.Net, ADO.NET, SQL Server

  17. DYNAMIC REQUEST DISPATCHING ALGORITHM FOR WEB SERVER CLUSTER

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The overall increase in traffic on the WWWcauses a disproportionate increase in client requeststo popular web sites.Site administrators constantlyface the requirement to i mprove server's capacity.Web server cluster is a popular solution.It usesgroup of independent servers that are managed as asingle systemfor higher availability,easier manage-ability and greater scalability.Many web sites haveadopted this solution.Request dispatching[1-2]is one of the core tech-nologies used by parallel web server clusters...

  18. Identifying and Analyzing Web Server Attacks

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-08-29

    Abstract: Client honeypots can be used to identify malicious web servers that attack web browsers and push malware to client machines. Merely recording network traffic is insufficient to perform comprehensive forensic analyses of such attacks. Custom tools are required to access and analyze network protocol data. Moreover, specialized methods are required to perform a behavioral analysis of an attack, which helps determine exactly what transpired on the attacked system. This paper proposes a record/replay mechanism that enables forensic investigators to extract application data from recorded network streams and allows applications to interact with this data in order to conduct behavioral analyses. Implementations for the HTTP and DNS protocols are presented and their utility in network forensic investigations is demonstrated.

  19. 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,...

  20. 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.

  1. A Request Distribution Algorithm for Web Server Cluster

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2011-12-01

    Full Text Available With the explosively increasing of web-based applications’ workloads, Web server cluster encounters challenge in response time for requests. Request distribution among servers in web server cluster is the key to address such challenge, especially under heavy workloads. In this paper, we propose a new request distribution algorithm named llac (least load active cache for load balancing switch in web server cluster. The goal of llac is to improve the cache hit rate and reduce response time. Packets are parsed in IP level, and back-end servers are notified to cache hot files using link change technology, neither changing URL information nor modifying the service program. This avoids switching overhead between user mode and kernel mode. The load balancing switch directly creates connection with the selected server, avoiding migrating connection overhead. This policy estimates the current composited load of each server and selects the server with the least load to serve the request. It also improves the resource utilization of web servers. Experimental results show that llac achieves better performance for web applications than wrr (weight round robin which is a popular request distribution.  

  2. 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.

  3. WebSpy: An Architecture for Monitoring Web Server Availability in a Multi-Platform Environment

    Directory of Open Access Journals (Sweden)

    Madhan Mohan Thirukonda

    2002-01-01

    Full Text Available For an electronic business (e-business, customer satisfaction can be the difference between long-term success and short-term failure. Customer satisfaction is highly impacted by Web server availability, as customers expect a Web site to be available twenty-four hours a day and seven days a week. Unfortunately, unscheduled Web server downtime is often beyond the control of the organization. What is needed is an effective means of identifying and recovering from Web server downtime in order to minimize the negative impact on the customer. An automated architecture, called WebSpy, has been developed to notify administration and to take immediate action when Web server downtime is detected. This paper describes the WebSpy architecture and differentiates it from other popular Web monitoring tools. The results of a case study are presented as a means of demonstrating WebSpy's effectiveness in monitoring Web server availability.

  4. PENERAPAN PENGOLAHAN PARALEL MODEL CLUSTER SEBAGAI WEB SERVER

    Directory of Open Access Journals (Sweden)

    Maman Somantri

    2009-06-01

    Full Text Available engolahan paralel merupakan suatu cara yang dilakukan untuk meningkatkan kecepatan pengolahandata dengan melakukan lebih dari satu pengolahan data tersebut secara bersamaan. Salah satu bentuk pengolahanparalel adalah model cluster. Pengolahan paralel model cluster ini akan digunakan untuk mengolah data Web,dengan membangun server Web yang di-cluster. Cluster server Web ini menggunakan teknologi Linux VirtualServer (LVS yang dapat dilakukan dengan NAT, IP tunneling, dan direct routing yang memiliki empat algoritmapenjadwalan.Pada penelitian ini akan digunakan teknologi LVS untuk membuat cluster Web Server denganmenggunakan NAT, diterapkannya teknologi Network File System, dan Network Block Device yang digunakansebagai media penyimpanan dalam jaringan. Dalam pengujian sistem cluster ini, pertama dilakukan pengujianjaringan yang digunakan untuk mengetahui kinerja sistem, dan pengujian sistem cluster dalam mengolah data Webdengan perangkat lunak WebBench dan script benchmark.

  5. 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.

  6. Technical Note: On The Usage and Development of the AWAKE Web Server and Web Applications

    CERN Document Server

    Berger, Dillon Tanner

    2017-01-01

    The purpose of this technical note is to give a brief explanation of the AWAKE Web Server, the current web applications it serves, and how to edit, maintain, and update the source code. The majority of this paper is dedicated to the development of the server and its web applications.

  7. 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.

  8. WSKE: Web Server Key Enabled Cookies

    Science.gov (United States)

    Masone, Chris; Baek, Kwang-Hyun; Smith, Sean

    In this paper, we present the design and prototype of a new approach to cookie management: if a server deposits a cookie only after authenticating itself via the SSL handshake, the browser will return the cookie only to a server that can authenticate itself, via SSL, to the same keypair. This approach can enable usable but secure client authentication. This approach can improve the usability of server authentication by clients. This approach is superior to the prior work on Active Cookies in that it defends against both DNS spoofing and IP spoofing—and does not require binding a user's interaction with a server to individual IP addresses.

  9. The web server of IBM's Bioinformatics and Pattern Discovery group

    OpenAIRE

    Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel,; Shibuya, Tetsuo

    2003-01-01

    We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic ...

  10. A CONFERENCE CONTROL MODEL BETWEEN A WEB SERVER AND A TELECOM APPLICATION SERVER

    Institute of Scientific and Technical Information of China (English)

    Wang Kaixi; Yang Fangchun

    2008-01-01

    The paper proposes a conference control model between a web server and a telecom application server, referred to as the Conference Directed Graph (CDG), and describes an asynchronous communication mechanism between them. The Corba Interface Definition Language (IDL) interfaces are defined, and a message sequence chart is illustrated. This web conference control model provides conference users with a new approach to manage and control a conference and the participants. The performance of the system prototype is analyzed and verified in the 863 project named "The Multimedia and Mobile Services Enabled Soft-switch System".

  11. DYNAMIC REQUEST DISPATCHING ALGORITHM FOR WEB SERVER CLUSTER

    Institute of Scientific and Technical Information of China (English)

    Yang Zhenjiang; Zhang Deyun; Sun Qindong; Sun Qing

    2006-01-01

    Distributed architectures support increased load on popular web sites by dispatching client requests transparently among multiple servers in a cluster. Packet Single-Rewriting technology and client address hashing algorithm in ONE-IP technology which can ensure application-session-keep have been analyzed, an improved request dispatching algorithm which is simple, effective and supports dynamic load balance has been proposed. In this algorithm, dispatcher evaluates which server node will process request by applying a hash function to the client IP address and comparing the result with its assigned identifier subset; it adjusts the size of the subset according to the performance and current load of each server, so as to utilize all servers' resource effectively. Simulation shows that the improved algorithm has better performance than the original one.

  12. 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.

  13. Proactive Web Server Protocol for Complaint Assessment

    OpenAIRE

    Kumar, G. Vijay; Raykundaliya, Ravikumar S.; Prasad, Dr. P. Naga

    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...

  14. Framework to Solve Load Balancing Problem in Heterogeneous Web Servers

    CERN Document Server

    Sharma, Ms Deepti

    2011-01-01

    For popular websites most important concern is to handle incoming load dynamically among web servers, so that they can respond to their client without any wait or failure. Different websites use different strategies to distribute load among web servers but most of the schemes concentrate on only one factor that is number of requests, but none of the schemes consider the point that different type of requests will require different level of processing efforts to answer, status record of all the web servers that are associated with one domain name and mechanism to handle a situation when one of the servers is not working. Therefore, there is a fundamental need to develop strategy for dynamic load allocation on web side. In this paper, an effort has been made to introduce a cluster based frame work to solve load distribution problem. This framework aims to distribute load among clusters on the basis of their operational capabilities. Moreover, the experimental results are shown with the help of example, algorithm...

  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. Management van World-Wide Web Servers

    NARCIS (Netherlands)

    van Hengstum, F.P.H.; Pras, Aiko

    1996-01-01

    Het World Wide Web is een populaire Internet toepassing waarmee het mogelijk is documenten aan willekeurige Internet gebruikers aan te bieden. Omdat hiervoor nog geen voorzieningen zijn getroffen, was het tot voor kort niet goed mogelijk het World Wide Web op afstand te beheren. De Universiteit Twen

  17. Management van World-Wide Web Servers

    NARCIS (Netherlands)

    van Hengstum, F.P.H.; Pras, Aiko

    1996-01-01

    Het World Wide Web is een populaire Internet toepassing waarmee het mogelijk is documenten aan willekeurige Internet gebruikers aan te bieden. Omdat hiervoor nog geen voorzieningen zijn getroffen, was het tot voor kort niet goed mogelijk het World Wide Web op afstand te beheren. De Universiteit

  18. SPEER-SERVER: a web server for prediction of protein specificity determining sites

    Science.gov (United States)

    Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

    2012-01-01

    Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

  19. Visible Human Slice Web Server: a first assessment

    Science.gov (United States)

    Hersch, Roger D.; Gennart, Benoit A.; Figueiredo, Oscar; Mazzariol, Marc; Tarraga, Joaquin; Vetsch, S.; Messerli, Vincent; Welz, R.; Bidaut, Luc M.

    1999-12-01

    The Visible Human Slice Server started offering its slicing services at the end of June 1998. From that date until the end of May, more than 280,000 slices were extracted from the Visible Man, by layman interested in anatomy, by students and by specialists. The Slice Server is based one Bi-Pentium PC and 16 disks. It is a scaled down version of a powerful parallel server comprising 5 Bi-Pentium Pro PCs and 60 disks. The parallel server program was created thanks to a computer-aided parallelization framework, which takes over the task of creating a multi-threaded pipelined parallel program from a high-level parallel program description. On the full blown architecture, the parallel program enables the extraction and resampling of up to 5 color slices per second. Extracting 5 slice/s requires to access the disks and extract subvolumes of the Visible Human at an aggregate throughput of 105 MB/s. The publicly accessible server enables to extract slices having any orientation. The slice position and orientation can either be specified for each slice separately or as a position and orientation offered by a Java applet and possible future improvements. In the very near future, the Web Slice Server will offer additional services, such as the possibility to extract ruled surfaces and to extract animations incorporating slices perpendicular to a user defined trajectory.

  20. Macintosh Plus

    CERN Multimedia

    1986-01-01

    Apple introduced the Macintosh Plus on January 16, 1986. The Macintosh Plus has an 8 MHz 68000 processor and an internal 800K floppy disk drive. It supports up to 4 MB of RAM. The Plus is a significant improvement over the previous compact Macs primarily due to the addition of the SCSI bus. Previous Macs did not have SCSI, thus making it more difficult to find a suitable external hard drive able to connect through the drive port, the printer port, or the modem port. These drives are considerably slower (as much as 4 times slower) than external SCSI hard drives. The Macintosh Plus is a very important computer in the history of the Apple Computers. It set up many of the standards that Apple followed for over a decade going forward.

  1. 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

  2. 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

  3. 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.

  4. Parmodel: a web server for automated comparative modeling of proteins.

    Science.gov (United States)

    Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

    2004-12-24

    Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

  5. Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.

    Science.gov (United States)

    Glanville, Jake Gunn; Kirshner, Dan; Krishnamurthy, Nandini; Sjölander, Kimmen

    2007-07-01

    Phylogenomic analysis addresses the limitations of function prediction based on annotation transfer, and has been shown to enable the highest accuracy in prediction of protein molecular function. The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction and SCI-PHY subfamily identification. The PhyloBuilder web server provides an integrated phylogenomic pipeline starting with a user-supplied protein sequence, proceeding to homolog identification, multiple alignment, phylogenetic tree construction, subfamily identification and structure prediction. The Berkeley Phylogenomics Group resources are available at http://phylogenomics.berkeley.edu.

  6. FRASS: the web-server for RNA structural comparison

    Directory of Open Access Journals (Sweden)

    Carugo Oliviero

    2010-06-01

    Full Text Available Abstract Background The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla are available for the structural comparison of large and intact RNA molecules. Results The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method. Conclusions The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases.

  7. 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.

  8. Alignment-Annotator web server: rendering and annotating sequence alignments.

    Science.gov (United States)

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-07-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Design and Development of ARM9 Based Embedded Web Server

    Directory of Open Access Journals (Sweden)

    Niturkar Priyanka

    2015-08-01

    Full Text Available This paper describes the design of embedded web server based on ARM9 processor and Linux platform. It analyses hardware configuration and software implementation for monitoring and controlling systems or devices. User can monitor and control temperature and smoke information. It consists of application program written in „C‟ for accessing data through the serial port and updating the web page, porting of Linux 2.6.3x Kernel with application program on ARM9 board and booting it from the RAM.

  10. Analysis and Design of Web Server Based on Softbase%基于SOftbase的Web Server分析与设计

    Institute of Scientific and Technical Information of China (English)

    黄松英; 涂征

    2001-01-01

    This paper firstly analyses common structure and function ,then designs a new structure of Web server based on seenre Softbase.%分析了Web Sewer的一般结构及功能特点,设计了一种基于Sofbase安全数据库系统的Web Server.

  11. CCTOP: a Consensus Constrained TOPology prediction web server.

    Science.gov (United States)

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

    2015-07-01

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

  12. 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

  13. 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...

  14. The web server of IBM's Bioinformatics and Pattern Discovery group.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore; Parida, Laxmi; Platt, Daniel; Shibuya, Tetsuo

    2003-07-01

    We herein present and discuss the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server is operational around the clock and provides access to a variety of methods that have been published by the group's members and collaborators. The available tools correspond to applications ranging from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences and the interactive annotation of amino acid sequences. Additionally, annotations for more than 70 archaeal, bacterial, eukaryotic and viral genomes are available on-line and can be searched interactively. The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  15. Web-Beagle: a web server for the alignment of RNA secondary structures.

    Science.gov (United States)

    Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2015-07-01

    Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods.

  16. MISA-web: a web server for microsatellite prediction.

    Science.gov (United States)

    Beier, Sebastian; Thiel, Thomas; Münch, Thomas; Scholz, Uwe; Mascher, Martin

    2017-08-15

    Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. scholz@ipk-gatersleben.de.

  17. WeBIAS: a web server for publishing bioinformatics applications.

    Science.gov (United States)

    Daniluk, Paweł; Wilczyński, Bartek; Lesyng, Bogdan

    2015-11-02

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. When publishing bioinformatic applications, such attitude puts additional burden on the reviewers who have to cope with poorly designed interfaces in order to assess quality of presented methods, as well as impairs actual usefulness to the scientific community at large. In this note we present WeBIAS-a simple, self-contained solution to make command-line programs accessible through web forms. It comprises a web portal capable of serving several applications and backend schedulers which carry out computations. The server handles user registration and authentication, stores queries and results, and provides a convenient administrator interface. WeBIAS is implemented in Python and available under GNU Affero General Public License. It has been developed and tested on GNU/Linux compatible platforms covering a vast majority of operational WWW servers. Since it is written in pure Python, it should be easy to deploy also on all other platforms supporting Python (e.g. Windows, Mac OS X). Documentation and source code, as well as a demonstration site are available at http://bioinfo.imdik.pan.pl/webias . WeBIAS has been designed specifically with ease of installation and deployment of services in mind. Setting up a simple application requires minimal effort, yet it is possible to create visually appealing, feature-rich interfaces for query submission and presentation of results.

  18. 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.

  19. 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.

  20. Mitigating App-DDoS Attacks on Web Servers

    Directory of Open Access Journals (Sweden)

    Manisha M. Patil

    2011-07-01

    Full Text Available In this paper, a lightweight mechanism is proposed to mitigate session flooding and request flooding app-DDoS attacks on web servers. App-DDoS attack is Application layer Distributed Denial of Service attack. This attack prevents legitimate users from accessing services. Numbers of mechanisms are available and can be installed on routers and firewalls to mitigate network layer DDoS attacks like SYNflood attack, ping of death attack. But Network layer solution is not applicable because App-DDoS attacks are indistinguishable based on packets and protocols. A lightweight mechanism is proposed which uses trust to differentiate legitimate users and attackers. Trust to client is evaluated based on his visiting history and requests are scheduled in decreasing order of trust. In this mechanism trust information is stored at client side in the form of cookies. This mitigation mechanism can be implemented as a java package which can run separately and forward valid requests to server. This mechanism also mitigates request flooding attacks by using Client Puzzle Protocol. When server is under request flooding attack source throttling is done by imposing cost on client. Cost is collected in terms of CPU cycles.

  1. Improving Performance of Dynamic Load Balancing among Web Servers by Using Number of Effective Parameters

    Directory of Open Access Journals (Sweden)

    Deepti Sharma

    2016-12-01

    Full Text Available Web application is being challenged to develop methods and techniques for large data processing at optimum response time. There are technical challenges in dealing with the increasing demand to handle vast traffic on these websites. As number of users‟ increases, several problems are faced by web servers like bottleneck, delayed response time, load balancing and density of services. The whole traffic cannot reside on a single server and thus there is a fundamental requirement of allocating this huge traffic on multiple load balanced servers. Distributing requests among servers in the web server clusters is the most important means to address such challenge, especially under intense workloads. In this paper, we propose a new request distribution algorithm for load balancing among web server clusters. The Dynamic Load Balancing among web servers take place based on user‟s request and dynamically estimating server workload using multiple parameters like processing and memory requirement, expected execution time and various time intervals. Our simulation results show that, the proposed method dynamically and efficiently balance the load to scale up the services, calculate average response time, average waiting time and server‟s throughput on different web servers. At the end of the paper, we presented an experimentation of running proposed system which proves the proposed algorithm is effic ient in terms of speed of processing, response time, server utilization and cost efficiency

  2. NOBAI: a web server for character coding of geometrical and statistical features in RNA structure.

    Science.gov (United States)

    Knudsen, Vegeir; Caetano-Anollés, Gustavo

    2008-07-01

    The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at 'http://www.manet.uiuc.edu/nobai/nobai.php'. This web site is free and open to all users and there is no login requirement.

  3. ISPIDER Central: an integrated database web-server for proteomics.

    Science.gov (United States)

    Siepen, Jennifer A; Belhajjame, Khalid; Selley, Julian N; Embury, Suzanne M; Paton, Norman W; Goble, Carole A; Oliver, Stephen G; Stevens, Robert; Zamboulis, Lucas; Martin, Nigel; Poulovassillis, Alexandra; Jones, Philip; Côté, Richard; Hermjakob, Henning; Pentony, Melissa M; Jones, David T; Orengo, Christine A; Hubbard, Simon J

    2008-07-01

    Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics.

  4. Berkeley PHOG: PhyloFacts orthology group prediction web server.

    Science.gov (United States)

    Datta, Ruchira S; Meacham, Christopher; Samad, Bushra; Neyer, Christoph; Sjölander, Kimmen

    2009-07-01

    Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other bioinformatics tasks. We present here the PHOG web server employing a novel algorithm to identify orthologs based on phylogenetic analysis. Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and allows users to target different taxonomic distances and precision levels through the use of tree-distance thresholds. For instance, OrthoMCL-DB achieved 76% recall and 66% precision on this dataset; at a slightly higher precision (68%) PHOG achieves 10% higher recall (86%). InParanoid achieved 87% recall at 24% precision on this dataset, while a PHOG variant designed for high recall achieves 88% recall at 61% precision, increasing precision by 37% over InParanoid. PHOG is based on pre-computed trees in the PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species. Predicted orthologs are linked to GO annotations, pathway information and biological literature. The PHOG web server is available at http://phylofacts.berkeley.edu/orthologs/.

  5. 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.

  6. 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.

  7. 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.

  8. Document distribution algorithm for load balancing on an extensible Web server architecture

    OpenAIRE

    Ng, CP; Wang, CL

    2001-01-01

    Access latency and load balancing are the two main issues in the design of clustered Web server architecture for achieving high performance. We propose a novel document distribution algorithm for load balancing on a cluster of distributed Web servers. We group Web pages that are likely to be accessed during a request session into a migrating unit, which is used as the basic unit of document placement. A modified binning algorithm is developed to distribute the migrating units among the Web se...

  9. 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.

  10. 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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...... 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...

  12. Implementation of Sensor Twitter Feed Web Service Server and Client

    Science.gov (United States)

    2016-12-01

    reasonPhrase> <responseText> <tweet> Hello Twitter 3 from server project</tweet> <tweet> Hello Twitter 2 from server project</tweet> <tweet> Hello ...Twitter 1 from server project</tweet> <tweet> Hello Twitter from server project</tweet> </responseText> <reasonCode>200</reasonCode> </response> b

  13. 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).

  14. 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%.

  15. 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.

  16. Adapting My Weather Impacts Decision Aid (MyWIDA) to Additional Web Application Server Technologies

    Science.gov (United States)

    2015-08-01

    Laboratory Adapting My Weather Impacts Decision Aid (MyWIDA) to Additional Web Application Server Technologies by Jacob C Randall and Jeffrey O...COVERED (From - To) May–Aug 2015 4. TITLE AND SUBTITLE Adapting My Weather Impacts Decision Aid (MyWIDA) to Additional Web Application Server...List of Figures Fig. 1 MyWIDA Web application after calculating impacts ...........................2 Fig. 2 Impact category ranges

  17. 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.

  18. A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

    Science.gov (United States)

    Cohen, Laura B.

    2003-01-01

    Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

  19. 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.

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

    OpenAIRE

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

    2016-01-01

    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 acce...

  1. 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...

  2. 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.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  4. 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.

  5. 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.

  6. METAGENassist: a comprehensive web server for comparative metagenomics.

    Science.gov (United States)

    Arndt, David; Xia, Jianguo; Liu, Yifeng; Zhou, You; Guo, An Chi; Cruz, Joseph A; Sinelnikov, Igor; Budwill, Karen; Nesbø, Camilla L; Wishart, David S

    2012-07-01

    With recent improvements in DNA sequencing and sample extraction techniques, the quantity and quality of metagenomic data are now growing exponentially. This abundance of richly annotated metagenomic data and bacterial census information has spawned a new branch of microbiology called comparative metagenomics. Comparative metagenomics involves the comparison of bacterial populations between different environmental samples, different culture conditions or different microbial hosts. However, in order to do comparative metagenomics, one typically requires a sophisticated knowledge of multivariate statistics and/or advanced software programming skills. To make comparative metagenomics more accessible to microbiologists, we have developed a freely accessible, easy-to-use web server for comparative metagenomic analysis called METAGENassist. Users can upload their bacterial census data from a wide variety of common formats, using either amplified 16S rRNA data or shotgun metagenomic data. Metadata concerning environmental, culture, or host conditions can also be uploaded. During the data upload process, METAGENassist also performs an automated taxonomic-to-phenotypic mapping. Phenotypic information covering nearly 20 functional categories such as GC content, genome size, oxygen requirements, energy sources and preferred temperature range is automatically generated from the taxonomic input data. Using this phenotypically enriched data, users can then perform a variety of multivariate and univariate data analyses including fold change analysis, t-tests, PCA, PLS-DA, clustering and classification. To facilitate data processing, users are guided through a step-by-step analysis workflow using a variety of menus, information hyperlinks and check boxes. METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca.

  7. RNAiFold: a web server for RNA inverse folding and molecular design.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  8. 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.

  9. WebLogic SIP Server 2.2加速通信服务

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    日前,BEA宣布发布WebLogic SIP Server 2.2版本。作为其BEA WebLogic通信平台产品系列中最新的Java EE-SIP应用服务器方案,BEA WebLogic SIP Server 2.2软件为网络营运商提供单一Java EE-SIP应用平台,让其善用IMS、SOA及EDA开创崭新融合服务,加速下一代通信服务发展。

  10. System Software 7 Macintosh

    CERN Multimedia

    1991-01-01

    System 7 is a single-user graphical user interface-based operating system for Macintosh computers and was part of the classic Mac OS line of operating systems. It was introduced on May 13, 1991, by Apple Computer. It succeeded System 6, and was the main Macintosh operating system until it was succeeded by Mac OS 8 in 1997. Features added with the System 7 release included virtual memory, personal file sharing, QuickTime, QuickDraw 3D, and an improved user interface. This is the first real major evolution of the Macintosh system, bringing a significant improvement in the user interface, improved stability and many new features such as the ability to use multiple applications at the same time. "System 7" is the last operating system name of the Macintosh that contains the word "system". Macintosh operating systems were later called "Mac OS" (for Macintosh Operating System).

  11. [Radiology information system using HTML, JavaScript, and Web server].

    Science.gov (United States)

    Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

    1997-12-01

    We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

  12. 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.

  13. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update

    OpenAIRE

    Huynh, Tien; Rigoutsos, Isidore

    2004-01-01

    In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple s...

  14. PBOND: web server for the prediction of proline and non-proline cis/trans isomerization.

    Science.gov (United States)

    Exarchos, Konstantinos P; Exarchos, Themis P; Papaloukas, Costas; Troganis, Anastassios N; Fotiadis, Dimitrios I

    2009-09-01

    PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages: (1) feature extraction, (2) feature selection and (3) peptide bond classification. PBOND can handle both single sequences as well as multiple sequences for batch processing. The predictions can either be directly downloaded from the web site or returned via e-mail. The PBOND web server is freely available at http://195.251.198.21/pbond.html.

  15. PBOND: Web Server for the Prediction of Proline and Non-Proline cis / trans Isomerization

    Institute of Scientific and Technical Information of China (English)

    Konstantinos P. Exarchos; Themis P. Exarchos; Costas Papaloukas; Anastassios N. Troganis; Dimitrios I. Fotiadis

    2009-01-01

    PBOND is a web server that predicts the conformation of the peptide bond be-tween any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide(cis-Pro), cis amide(cis-nonPro), trans imide (trans-Pro)and trans amide(trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages:(1)feature extraction,(2)feature selection and(3)peptide bond clas-sification. PBOND can handle both single sequences as well as multiple sequences for batch processing. The predictions can either be directly downloaded from the web site or returned via e-mail. The PBOND web server is freely available at http://195.251.198.21/pbond.html.

  16. 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.

  17. 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 .

  18. 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.

  19. Are specialized web servers better at predicting protein structures ...

    African Journals Online (AJOL)

    RABAIL HAFEEZ (0973106)

    2012-07-03

    Jul 3, 2012 ... This research study answers the question that technology is the best for predicting protein structures. Stand-alone .... server 3D Jury to show how it produces high quality, accurate ..... Nucleic Acids Res., 32: 14-16. Ginalski K ...

  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. CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

    Science.gov (United States)

    Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

    2015-01-01

    Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/.

  2. CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

    Directory of Open Access Journals (Sweden)

    Mahdi Jalili

    Full Text Available Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv file format or a mapped graphical format as a graph modeling language (GML file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer and R package (centiserve are freely available at http://www.centiserver.org/.

  3. 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.

  4. [Current internet technology for gynecology--from hypertext transfer protocol to embedded web server].

    Science.gov (United States)

    Seufert, R; Woernle, F

    2000-01-01

    The scientific and commercial use of the internet has caused a revolution in information technologies and has influenced medical communication and documentation. Web browsers are the becoming universal starting point for all kinds of client-server applications. Many commercial and medical systems--such as information reservation systems--are being shifted towards web-based systems. This paper describes new techniques. Security problems are the main topics for further developments in medical computing.

  5. Neutralizing SQL Injection Attack Using Server Side Code Modification in Web Applications

    Directory of Open Access Journals (Sweden)

    Asish Kumar Dalai

    2017-01-01

    Full Text Available Reports on web application security risks show that SQL injection is the top most vulnerability. The journey of static to dynamic web pages leads to the use of database in web applications. Due to the lack of secure coding techniques, SQL injection vulnerability prevails in a large set of web applications. A successful SQL injection attack imposes a serious threat to the database, web application, and the entire web server. In this article, the authors have proposed a novel method for prevention of SQL injection attack. The classification of SQL injection attacks has been done based on the methods used to exploit this vulnerability. The proposed method proves to be efficient in the context of its ability to prevent all types of SQL injection attacks. Some popular SQL injection attack tools and web application security datasets have been used to validate the model. The results obtained are promising with a high accuracy rate for detection of SQL injection attack.

  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. From P2P to Web services and grids peers in a client/server world

    CERN Document Server

    Taylor, Ian J

    2005-01-01

    Provides an overview of peer-to-peer (P2P) technologies that have revolutionized the way we think about distributed computing and the internet. This book compares these technologies to alternative solutions, most notably web services and Grid computing but also other technologies, such as client/server based systems and agent technologies.

  8. Developing a Web Server Platform with SAPI support for AJAX RPC using JSON

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Writing a custom web server with SAPI support is a useful task which helps students and future system architects to understand the link between network programming, object oriented programming, enterprise application designing patterns and development best practices because it offers a vision upon interprocess communication and application extensibility in a distributed environment

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

    Science.gov (United States)

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

    2009-07-01

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

  10. Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA

    OpenAIRE

    Smith, Cameron; Heyne, Steffen; Richter, Andreas S.; Will, Sebastian; Backofen, Rolf

    2010-01-01

    The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA–RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.

  11. 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

    2012-01-01

    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

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

    Science.gov (United States)

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

    2015-08-01

    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 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), 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.

  13. 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.

  14. Seq2Ref: a web server to facilitate functional interpretation

    Directory of Open Access Journals (Sweden)

    Li Wenlin

    2013-01-01

    Full Text Available Abstract Background The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of ‘reference proteins’ that have been experimentally characterized or manually curated. Results The Seq2Ref server uses BLAST to detect proteins homologous to a query sequence and identifies the reference proteins among them. Seq2Ref then reports publications with experimental characterizations of the identified reference proteins that might be relevant to the query. Furthermore, a plurality-based rating system is developed to evaluate the homologous relationships and rank the reference proteins by their relevance to the query. Conclusions The reference proteins detected by our server will lend insight into proteins of unknown function and provide extensive information to develop in-depth understanding of uncharacterized proteins. Seq2Ref is available at: http://prodata.swmed.edu/seq2ref.

  15. Management van World-Wide Web servers: een initiatief om World-Wide Web servers te beheren

    NARCIS (Netherlands)

    Hengstum, van F.P.H.; Pras, A.

    1996-01-01

    Het World Wide Web is een populaire Internet toepassing waarmee het mogelijk is documenten aan willekeurige Internet gebruikers aan te bieden. Omdat hiervoor nog geen voorzieningen zijn getroffen, was het tot voor kort niet goed mogelijk het World Wide Web op afstand te beheren. De Universiteit Twen

  16. 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.

  17. SEGEL: A Web Server for Visualization of Smoking Effects on Human Lung Gene Expression.

    Science.gov (United States)

    Xu, Yan; Hu, Brian; Alnajm, Sammy S; Lu, Yin; Huang, Yangxin; Allen-Gipson, Diane; Cheng, Feng

    2015-01-01

    Cigarette smoking is a major cause of death worldwide resulting in over six million deaths per year. Cigarette smoke contains complex mixtures of chemicals that are harmful to nearly all organs of the human body, especially the lungs. Cigarette smoking is considered the major risk factor for many lung diseases, particularly chronic obstructive pulmonary diseases (COPD) and lung cancer. However, the underlying molecular mechanisms of smoking-induced lung injury associated with these lung diseases still remain largely unknown. Expression microarray techniques have been widely applied to detect the effects of smoking on gene expression in different human cells in the lungs. These projects have provided a lot of useful information for researchers to understand the potential molecular mechanism(s) of smoke-induced pathogenesis. However, a user-friendly web server that would allow scientists to fast query these data sets and compare the smoking effects on gene expression across different cells had not yet been established. For that reason, we have integrated eight public expression microarray data sets from trachea epithelial cells, large airway epithelial cells, small airway epithelial cells, and alveolar macrophage into an online web server called SEGEL (Smoking Effects on Gene Expression of Lung). Users can query gene expression patterns across these cells from smokers and nonsmokers by gene symbols, and find the effects of smoking on the gene expression of lungs from this web server. Sex difference in response to smoking is also shown. The relationship between the gene expression and cigarette smoking consumption were calculated and are shown in the server. The current version of SEGEL web server contains 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 Plus 2.0 platform. SEGEL will be an invaluable resource for researchers interested in the effects of smoking on gene expression in the lungs. The server also provides useful information

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

    Science.gov (United States)

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

    2005-12-01

    The Live Access Server (LAS) is a general purpose Web-server for delivering services related to geo-science data sets. Data providers can use the LAS architecture to build custom Web interfaces to their scientific data. Users and client programs can then access the LAS site to search the provider's on-line data holdings, make plots of data, create sub-sets in a variety of formats, compare data sets and perform analysis on the data. The Live Access server software has continued to evolve by expanding the types of data (in-situ observations and curvilinear grids) it can serve and by taking advantages of advances in software infrastructure both in the earth sciences community (THREDDS, the GrADS Data Server, the Anagram framework and Java netCDF 2.2) and in the Web community (Java Servlet and the Apache Jakarta frameworks). This presentation will explore the continued evolution of the LAS architecture towards a complete Web-services-based framework. Additionally, we will discuss the redesign and modernization of some of the support tools available to LAS installers. Soon after the initial implementation, the LAS architecture was redesigned to separate the components that are responsible for the user interaction (the User Interface Server) from the components that are responsible for interacting with the data and producing the output requested by the user (the Product Server). During this redesign, we changed the implementation of the User Interface Server from CGI and JavaScript to the Java Servlet specification using Apache Jakarta Velocity backed by a database store for holding the user interface widget components. The User Interface server is now quite flexible and highly configurable because we modernized the components used for the implementation. Meanwhile, the implementation of the Product Server has remained a Perl CGI-based system. Clearly, the time has come to modernize this part of the LAS architecture. Before undertaking such a modernization it is

  20. 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.

  1. OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences.

    Science.gov (United States)

    Schreiber, Fabian; Wörheide, Gert; Morgenstern, Burkhard

    2009-07-01

    In the absence of whole genome sequences for many organisms, the use of expressed sequence tags (EST) offers an affordable approach for researchers conducting phylogenetic analyses to gain insight about the evolutionary history of organisms. Reliable alignments for phylogenomic analyses are based on orthologous gene sequences from different taxa. So far, researchers have not sufficiently tackled the problem of the completely automated construction of such datasets. Existing software tools are either semi-automated, covering only part of the necessary data processing, or implemented as a pipeline, requiring the installation and configuration of a cascade of external tools, which may be time-consuming and hard to manage. To simplify data set construction for phylogenomic studies, we set up a web server that uses our recently developed OrthoSelect approach. To the best of our knowledge, our web server is the first web-based EST analysis pipeline that allows the detection of orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Additionally, OrthoSelect provides the user with an extensive results section that lists and visualizes all important results, such as annotations, data matrices for each gene/taxon and orthologous gene alignments. The web server is available at http://orthoselect.gobics.de.

  2. 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.

  3. 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.

  4. SIFT web server: predicting effects of amino acid substitutions on proteins.

    Science.gov (United States)

    Sim, Ngak-Leng; Kumar, Prateek; Hu, Jing; Henikoff, Steven; Schneider, Georg; Ng, Pauline C

    2012-07-01

    The Sorting Intolerant from Tolerant (SIFT) algorithm predicts the effect of coding variants on protein function. It was first introduced in 2001, with a corresponding website that provides users with predictions on their variants. Since its release, SIFT has become one of the standard tools for characterizing missense variation. We have updated SIFT's genome-wide prediction tool since our last publication in 2009, and added new features to the insertion/deletion (indel) tool. We also show accuracy metrics on independent data sets. The original developers have hosted the SIFT web server at FHCRC, JCVI and the web server is currently located at BII. The URL is http://sift-dna.org (24 May 2012, date last accessed).

  5. MetalPredator: a web server to predict iron-sulfur cluster binding proteomes.

    Science.gov (United States)

    Valasatava, Yana; Rosato, Antonio; Banci, Lucia; Andreini, Claudia

    2016-09-15

    The prediction of the iron-sulfur proteome is highly desirable for biomedical and biological research but a freely available tool to predict iron-sulfur proteins has not been developed yet. We developed a web server to predict iron-sulfur proteins from protein sequence(s). This tool, called MetalPredator, is able to process complete proteomes rapidly with high recall and precision. The web server is freely available at: http://metalweb.cerm.unifi.it/tools/metalpredator/ andreini@cerm.unifi.it Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures

    Science.gov (United States)

    Chang, Darby Tien-Hau; Chen, Chien-Yu; Chung, Wen-Chin; Oyang, Yen-Jen; Juan, Hsueh-Fen; Huang, Hsuan-Cheng

    2004-01-01

    Analysis of protein–ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein–ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the α-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/. PMID:15215355

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Madadkar-Sobhani, Armin; Guallar, Victor

    2013-07-01

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

  10. PepServe: a web server for peptide analysis, clustering and visualization

    Science.gov (United States)

    Alexandridou, Anastasia; Dovrolis, Nikolas; Tsangaris, George Th.; Nikita, Konstantina; Spyrou, George

    2011-01-01

    Peptides, either as protein fragments or as naturally occurring entities are characterized by their sequence and function features. Many times the researchers need to massively manage peptide lists concerning protein identification, biomarker discovery, bioactivity, immune response or other functionalities. We present a web server that manages peptide lists in terms of feature analysis as well as interactive clustering and visualization of the given peptides. PepServe is a useful tool in the understanding of the peptide feature distribution among a group of peptides. The PepServe web application is freely available at http://bioserver-1.bioacademy.gr/Bioserver/PepServe/. PMID:21572105

  11. 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.

  12. 嵌入式Web Server的设计与实现%Design and realization of embedded Web Server

    Institute of Scientific and Technical Information of China (English)

    史洁; 田云

    2012-01-01

    The embedded Web Server refered to the ability of running in single-chip embedded devices on the webpage file. In 8 or 16 bit single chip microcomputer rmming low-cost, high-performance webpage file will make more sales information of control equipment. In the development of embedded Web Server, SCM was not the traditional PC machine. General webpage file could not be completely in accordance with the traditional webpage technology, to be in compliance with the corresponding standard conditions make the corresponding changes. In order to adapt to the requirements of embedded equipment webpage.%嵌入式WebServer是指能够运行单片机等嵌入式设备上的网页文件。能够在8位或16位单片机上运行低成本,高性能的网页文件,使控制设备更加信息化。在开发嵌入式WebServer时,单片机并不是传统的PC机。通用的网页文件也不能完全依照传统的网页技术,要在遵守相应标准的情况下做相应的改动,以适应嵌入式设备对网页的要求。

  13. WIMP: web server tool for missing data imputation.

    Science.gov (United States)

    Urda, D; Subirats, J L; García-Laencina, P J; Franco, L; Sancho-Gómez, J L; Jerez, J M

    2012-12-01

    The imputation of unknown or missing data is a crucial task on the analysis of biomedical datasets. There are several situations where it is necessary to classify or identify instances given incomplete vectors, and the existence of missing values can much degrade the performance of the algorithms used for the classification/recognition. The task of learning accurately from incomplete data raises a number of issues some of which have not been completely solved in machine learning applications. In this sense, effective missing value estimation methods are required. Different methods for missing data imputations exist but most of the times the selection of the appropriate technique involves testing several methods, comparing them and choosing the right one. Furthermore, applying these methods, in most cases, is not straightforward, as they involve several technical details, and in particular in cases such as when dealing with microarray datasets, the application of the methods requires huge computational resources. As far as we know, there is not a public software application that can provide the computing capabilities required for carrying the task of data imputation. This paper presents a new public tool for missing data imputation that is attached to a computer cluster in order to execute high computational tasks. The software WIMP (Web IMPutation) is a public available web site where registered users can create, execute, analyze and store their simulations related to missing data imputation.

  14. 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.

  15. A web server for mining Comparative Genomic Hybridization (CGH) data

    Science.gov (United States)

    Liu, Jun; Ranka, Sanjay; Kahveci, Tamer

    2007-11-01

    Advances in cytogenetics and molecular biology has established that chromosomal alterations are critical in the pathogenesis of human cancer. Recurrent chromosomal alterations provide cytological and molecular markers for the diagnosis and prognosis of disease. They also facilitate the identification of genes that are important in carcinogenesis, which in the future may help in the development of targeted therapy. A large amount of publicly available cancer genetic data is now available and it is growing. There is a need for public domain tools that allow users to analyze their data and visualize the results. This chapter describes a web based software tool that will allow researchers to analyze and visualize Comparative Genomic Hybridization (CGH) datasets. It employs novel data mining methodologies for clustering and classification of CGH datasets as well as algorithms for identifying important markers (small set of genomic intervals with aberrations) that are potentially cancer signatures. The developed software will help in understanding the relationships between genomic aberrations and cancer types.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Uppsala University, Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology (Sweden); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Faculty of Science – Chemistry, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-08-15

    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.

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

    Science.gov (United States)

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

    2016-07-08

    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.

  18. 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

  19. AVCpred: an integrated web server for prediction and design of antiviral compounds.

    Science.gov (United States)

    Qureshi, Abid; Kaur, Gazaldeep; Kumar, Manoj

    2017-01-01

    Viral infections constantly jeopardize the global public health due to lack of effective antiviral therapeutics. Therefore, there is an imperative need to speed up the drug discovery process to identify novel and efficient drug candidates. In this study, we have developed quantitative structure-activity relationship (QSAR)-based models for predicting antiviral compounds (AVCs) against deadly viruses like human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), human herpesvirus (HHV) and 26 others using publicly available experimental data from the ChEMBL bioactivity database. Support vector machine (SVM) models achieved a maximum Pearson correlation coefficient of 0.72, 0.74, 0.66, 0.68, and 0.71 in regression mode and a maximum Matthew's correlation coefficient 0.91, 0.93, 0.70, 0.89, and 0.71, respectively, in classification mode during 10-fold cross-validation. Furthermore, similar performance was observed on the independent validation sets. We have integrated these models in the AVCpred web server, freely available at http://crdd.osdd.net/servers/avcpred. In addition, the datasets are provided in a searchable format. We hope this web server will assist researchers in the identification of potential antiviral agents. It would also save time and cost by prioritizing new drugs against viruses before their synthesis and experimental testing.

  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

    2016-06-20

    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/.

  1. CATH FunFHMMer web server: protein functional annotations using functional family assignments.

    Science.gov (United States)

    Das, Sayoni; Sillitoe, Ian; Lee, David; Lees, Jonathan G; Dawson, Natalie L; Ward, John; Orengo, Christine A

    2015-07-01

    The widening function annotation gap in protein databases and the increasing number and diversity of the proteins being sequenced presents new challenges to protein function prediction methods. Multidomain proteins complicate the protein sequence-structure-function relationship further as new combinations of domains can expand the functional repertoire, creating new proteins and functions. Here, we present the FunFHMMer web server, which provides Gene Ontology (GO) annotations for query protein sequences based on the functional classification of the domain-based CATH-Gene3D resource. Our server also provides valuable information for the prediction of functional sites. The predictive power of FunFHMMer has been validated on a set of 95 proteins where FunFHMMer performs better than BLAST, Pfam and CDD. Recent validation by an independent international competition ranks FunFHMMer as one of the top function prediction methods in predicting GO annotations for both the Biological Process and Molecular Function Ontology. The FunFHMMer web server is available at http://www.cathdb.info/search/by_funfhmmer.

  2. LDAP: a web server for lncRNA-disease association prediction.

    Science.gov (United States)

    Lan, Wei; Li, Min; Zhao, Kaijie; Liu, Jin; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

    2017-02-01

    Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources. Then, we implement this method as a web server for lncRNA-disease association prediction (LDAP). The input of the LDAP server is the lncRNA sequence. The LDAP predicts potential lncRNA-disease associations by using a bagging SVM classifier based on lncRNA similarity and disease similarity. The web server is available at http://bioinformatics.csu.edu.cn/ldap jxwang@mail.csu.edu.cn. Supplementary data are available at Bioinformatics online.

  3. FOLDNA, a Web Server for Self-Assembled DNA Nanostructure Autoscaffolds and Autostaples

    Directory of Open Access Journals (Sweden)

    Chensheng Zhou

    2012-01-01

    Full Text Available DNA self-assembly is a nanotechnology that folds DNA into desired shapes. Self-assembled DNA nanostructures, also known as origami, are increasingly valuable in nanomaterial and biosensing applications. Two ways to use DNA nanostructures in medicine are to form nanoarrays, and to work as vehicles in drug delivery. The DNA nanostructures perform well as a biomaterial in these areas because they have spatially addressable and size controllable properties. However, manually designing complementary DNA sequences for self-assembly is a technically demanding and time consuming task, which makes it advantageous for computers to do this job instead. We have developed a web server, FOLDNA, which can automatically design 2D self-assembled DNA nanostructures according to custom pictures and scaffold sequences provided by the users. It is the first web server to provide an entirely automatic design of self-assembled DNA nanostructure, and it takes merely a second to generate comprehensive information for molecular experiments including: scaffold DNA pathways, staple DNA directions, and staple DNA sequences. This program could save as much as several hours in the designing step for each DNA nanostructure. We randomly selected some shapes and corresponding outputs from our server and validated its performance in molecular experiments.

  4. AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

    Science.gov (United States)

    Lounnas, V; Vriend, G

    2012-02-27

    Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The

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

    DEFF Research Database (Denmark)

    Amico, M.; Finelli, M.; Rossi, I.;

    2006-01-01

    ://pongo.biocomp.unibo.it/ ) provides the annotation on predictive basis for the all-alpha membrane proteins in the human genome, not only through DAS queries, but also directly using a simple web interface. In order to produce a more comprehensive analysis of the sequence at hand, this annotation is carried out with four selected...... and high scoring predictors: TMHMM2.0, MEMSAT, PRODIV and ENSEMBLE1.0. The stored and pre-computed predictions for the human proteins can be searched and displayed in a graphical view. However the web service allows the prediction of the topology of any kind of putative membrane proteins, regardless...... of the organism and more importantly with the same sequence profile for a given sequence when required. Here we present a new web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously...

  6. Analisis Arsitektur Aplikasi Web Menggunakan Model View Controller (MVC pada Framework Java Server Faces

    Directory of Open Access Journals (Sweden)

    Gunawan Gunawan

    2016-06-01

    Full Text Available Aplikasi web yang khususnya memiliki kompleksitas besar dalam melakukan transaksi data sehingga konsep arsitektur (pattern perlu menjadi perhatian khusus untuk dapat mengoptimalkan kinerja performansi sistem ketika pengguna (user menggunakan dalam waktu yang bersamaan dengan jumlah yang banyak. Analisis performa arsitektur aplikasi web yang menggunakan model 2 (MVC dengan menggunakan framework Java Server Faces (JSF dan model 1 sebagai pembanding. Metode yang digunakan adalah Load dan Scalability Testing dengan dua cara yaitu uji coba terhadap response time karena peningkatan ukuran dari database dan uji coba terhadap response time karena peningkatan jumlah user yang menggunakan sistem secara bersamaan (concurrent users dan waktu tunggu (ramp-up yang ditentukan menggunakan Apache Jmeter. Analisis menunjukkan bahwa dalam implementasi arsitektur web yang menggunakan model 1 waktu rata-rata yang dibutuhkan untuk merespon permintaan user lebih cepat dan efisien dibanding model 2 (MVC.  

  7. A Robust Mechanism For Defending Distributed Denial Of Service Attacks On Web Servers

    Directory of Open Access Journals (Sweden)

    Jaydip Sen

    2011-03-01

    Full Text Available Distributed Denial of Service (DDoS attacks have emerged as a popular means of causing mass targetedservice disruptions, often for extended periods of time. The relative ease and low costs of launching suchattacks, supplemented by the current inadequate sate of any viable defense mechanism, have made themone of the top threats to the Internet community today. Since the increasing popularity of web-basedapplications has led to several critical services being provided over the Internet, it is imperative tomonitor the network traffic so as to prevent malicious attackers from depleting the resources of thenetwork and denying services to legitimate users. This paper first presents a brief discussion on some ofthe important types of DDoS attacks that currently exist and some existing mechanisms to combat theseattacks. It then points out the major drawbacks of the currently existing defense mechanisms andproposes a new mechanism for protecting a web-server against a DDoS attack. In the proposedmechanism, incoming traffic to the server is continuously monitored and any abnormal rise in theinbound traffic is immediately detected. The detection algorithm is based on a statistical analysis of theinbound traffic on the server and a robust hypothesis testing framework. While the detection process ison, the sessions from the legitimate sources are not disrupted and the load on the server is restored to thenormal level by blocking the traffic from the attacking sources. To cater to different scenarios, thedetection algorithm has various modules with varying level of computational and memory overheads fortheir execution. While the approximate modules are fast in detection and involve less overhead, theyprovide lower level of detection accuracy. The accurate modules employ complex detection logic andhence involve more overhead for their execution. However, they have very high detection accuracy.Simulations carried out on the proposed mechanism have produced

  8. The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

    Science.gov (United States)

    Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E; Hofacker, Ivo L; Stadler, Peter F; Gorodkin, Jan

    2013-07-01

    The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, 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/.

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

    Science.gov (United States)

    Pers, Tune H; Dworzyński, Piotr; Thomas, Cecilia Engel; Lage, Kasper; Brunak, Søren

    2013-07-01

    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/MetaRanker-2.0.

  10. 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......Ranker 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/MetaRanker-2.0....

  11. Design and Implementation of WebPACS Based on Web Server%基于Web服务器的WebPACS设计与实现

    Institute of Scientific and Technical Information of China (English)

    梁敏; 陈侃侃; 刘兴淮; 李居河

    2014-01-01

    目的:基于Web服务器,实现企业级PACS的应用。方法以中心Web网站为基础,通过HTTP文件流调阅。系统采用Web Service、浏览器插件、.NET技术等开发。结果该系统的应用成功地实现了患者影像信息的计算机存储和医学影像诊断报告的数字化书写、打印等功能。结论企业级Web PACS充分满足了临床需求。%Objective To implement the enterprise-level PACS based on Web server. Methods The system is developed by using HTTP document lfow retrieval, Web Service, browser plug-in and .NET technology based on a central Web server. Results The computer storage of image information of patients and the writing and printing of diagnostic report of medical images have been implemented with the application of the system. Conclusion Enterprise-level PACS fully meets the clinical needs.

  12. Applied Research of Campus WebGIS Based on ArcGIS Server%基于ArcGIS Server的校园WebGIS应用研究

    Institute of Scientific and Technical Information of China (English)

    于国强

    2011-01-01

    Focused on introducing the basic theory of WebGIS and ArcGIS Server,and based on the relative technique analysis of ArcGIS Server,this paper takes Jilin Normal University campus WebGIS system's construction as an example,and discusses the creation of campus WebGIS system process.%介绍了WebGIS及ArcGIS Server基础理论,在分析了ArcGIS Server等相关技术的基础上,以吉林师范大学校园WebGIS系统的建设为例,论述了校园WebGIS系统的创建过程。

  13. SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.

    Science.gov (United States)

    Norambuena, Tomás; Malig, Rodrigo; Melo, Francisco

    2007-07-01

    We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). The core of the server relies on a database of genomic virtual tags built by a recently described method that attempts to reduce the amount of ambiguous assignments for those tags that are not unique in the genome. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. The output of the server consists of a table in HTML format that contains links to a graphic representation of the results and to some external servers and databases, facilitating the tasks of analysis of gene expression and gene discovery. Also, a table in tab delimited text format is produced, allowing the user to export the results into custom databases and software for further analysis. The current server version provides the most accurate and complete SAGE tag mapping source that is available for the yeast organism. In the near future, this server will also allow the accurate mapping of experimental SAGE-tags from other model organisms such as human, mouse, frog and fly. The server is freely available on the web at: http://dna.bio.puc.cl/SAGExplore.html.

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

    Science.gov (United States)

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

    2012-01-01

    We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein–RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in ‘.pdb’ format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein–RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein–RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein–RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html. PMID:22689640

  15. A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange.

    Science.gov (United States)

    Lobanov, Mikhail Yu; Suvorina, Masha Yu; Dovidchenko, Nikita V; Sokolovskiy, Igor V; Surin, Alexey K; Galzitskaya, Oxana V

    2013-06-01

    To clarify the relationship between structural elements and polypeptide chain mobility, a set of statistical analyses of structures is necessary. Because at present proteins with determined spatial structures are much less numerous than those with amino acid sequence known, it is important to be able to predict the extent of proton protection from hydrogen-deuterium (HD) exchange basing solely on the protein primary structure. Here we present a novel web server aimed to predict the degree of amino acid residue protection against HD exchange solely from the primary structure of the protein chain under study. On the basis of the amino acid sequence, the presented server offers the following three possibilities (predictors) for user's choice. First, prediction of the number of contacts occurring in this protein, which is shown to be helpful in estimating the number of protons protected against HD exchange (sensitivity 0.71). Second, probability of H-bonding in this protein, which is useful for finding the number of unprotected protons (specificity 0.71). The last is the use of an artificial predictor. Also, we report on mass spectrometry analysis of HD exchange that has been first applied to free amino acids. Its results showed a good agreement with theoretical data (number of protons) for 10 globular proteins (correlation coefficient 0.73). We pioneered in compiling two datasets of experimental HD exchange data for 35 proteins. The H-Protection server is available for users at http://bioinfo.protres.ru/ogp/ Supplementary data are available at Bioinformatics online.

  16. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-07-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package.

  17. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-01-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package. PMID:23703210

  18. 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.

  19. The iceLogo web server and SOAP service for determining protein consensus sequences.

    Science.gov (United States)

    Maddelein, Davy; Colaert, Niklaas; Buchanan, Iain; Hulstaert, Niels; Gevaert, Kris; Martens, Lennart

    2015-07-01

    The iceLogo web server and SOAP service implement the previously published iceLogo algorithm. iceLogo builds on probability theory to visualize protein consensus sequences in a format resembling sequence logos. Peptide sequences are compared against a reference sequence set that can be tailored to the studied system and the used protocol. As such, not only over- but also underrepresented residues can be visualized in a statistically sound manner, which further allows the user to easily analyse and interpret conserved sequence patterns in proteins. The web application and SOAP service can be found free and open to all users without the need for a login on http://iomics.ugent.be/icelogoserver/main.html.

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

    Science.gov (United States)

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

    2016-12-01

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

  1. 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

    2016-07-08

    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.

  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.

    2016-03-01

    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/).

  3. iSARST: an integrated SARST web server for rapid protein structural similarity searches.

    Science.gov (United States)

    Lo, Wei-Cheng; Lee, Che-Yu; Lee, Chi-Ching; Lyu, Ping-Chiang

    2009-07-01

    iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARST allows users submitting multiple PDB/SCOP entry IDs or an archive file containing many structures. After scanning the target database using SARST/CPSARST, the ordering of hits are refined with conventional structure alignment tools such as FAST, TM-align and SAMO, which are run in a PC cluster. In this way, iSARST achieves a high running speed while preserving the high precision of refinement engines. The final outputs include tables listing co-linear or circularly permuted homologs of the query proteins and a functional summary of the best hits. Superimposed structures can be examined through an interactive and informative visualization tool. iSARST provides the first batch mode structural comparison web service for both co-linear homologs and circular permutants. It can serve as a rapid annotation system for functionally unknown or hypothetical proteins, which are increasing rapidly in this post-genomics era. The server can be accessed at http://sarst.life.nthu.edu.tw/iSARST/.

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

    Science.gov (United States)

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

    2016-07-08

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

  5. A FPGA embedded web server for remote monitoring and control of smart sensors networks.

    Science.gov (United States)

    Magdaleno, Eduardo; Rodríguez, Manuel; Pérez, Fernando; Hernández, David; García, Enrique

    2013-12-27

    This article describes the implementation of a web server using an embedded Altera NIOS II IP core, a general purpose and configurable RISC processor which is embedded in a Cyclone FPGA. The processor uses the μCLinux operating system to support a Boa web server of dynamic pages using Common Gateway Interface (CGI). The FPGA is configured to act like the master node of a network, and also to control and monitor a network of smart sensors or instruments. In order to develop a totally functional system, the FPGA also includes an implementation of the time-triggered protocol (TTP/A). Thus, the implemented master node has two interfaces, the webserver that acts as an Internet interface and the other to control the network. This protocol is widely used to connecting smart sensors and actuators and microsystems in embedded real-time systems in different application domains, e.g., industrial, automotive, domotic, etc., although this protocol can be easily replaced by any other because of the inherent characteristics of the FPGA-based technology.

  6. 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

    2016-07-08

    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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Meinicke, Peter

    2009-09-02

    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. 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. 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.

  10. 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.

  11. 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

    2014-01-01

    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

  12. A FPGA Embedded Web Server for Remote Monitoring and Control of Smart Sensors Networks

    Directory of Open Access Journals (Sweden)

    Eduardo Magdaleno

    2013-12-01

    Full Text Available This article describes the implementation of a web server using an embedded Altera NIOS II IP core, a general purpose and configurable RISC processor which is embedded in a Cyclone FPGA. The processor uses the μCLinux operating system to support a Boa web server of dynamic pages using Common Gateway Interface (CGI. The FPGA is configured to act like the master node of a network, and also to control and monitor a network of smart sensors or instruments. In order to develop a totally functional system, the FPGA also includes an implementation of the time-triggered protocol (TTP/A. Thus, the implemented master node has two interfaces, the webserver that acts as an Internet interface and the other to control the network. This protocol is widely used to connecting smart sensors and actuators and microsystems in embedded real-time systems in different application domains, e.g., industrial, automotive, domotic, etc., although this protocol can be easily replaced by any other because of the inherent characteristics of the FPGA-based technology.

  13. RNAmutants: a web server to explore the mutational landscape of RNA secondary structures.

    Science.gov (United States)

    Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

    2009-07-01

    The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/.

  14. Shortening full-length aptamer by crawling base deletion – Assisted by Mfold web server application

    Directory of Open Access Journals (Sweden)

    Subash C.B. Gopinath

    2017-06-01

    Full Text Available Systematic Evolution of Ligands by EXponential enrichment (SELEX is the method to select the specific aptamer against a wide range of targets. For this process, the initial library usually has a length of random sequences from ∼25 and it reaches over 100 bases. The lengthy sequences have disadvantages such as difficult to prepare, less stable and expensive. It is wise to prefer shorter version of aptamer for a wide range of applications including drug delivery process. It is a common practice to shorten the full-length aptamer by mapping analyses and it is tedious. Here, we used a crawling method to shorten the aptamer by different sequential deletion of bases from both 5′ and 3′ ends, assisted by Mfold web server application. Two different kinds of aptamer with varied lengths (randomized region of 30 and 74 bases were desired for this study, generated against Influenza A/Panama/2007/1999 (H3N2 and gD protein of Herpes Simplex Virus-1. It was found that shortening the aptamer length by crawling pattern is possible with the assistance of Mfold web server application. The obtained results resemble the shortened aptamer derived by mapping analyses. The proposed strategy is recommended to predict the shorter aptamer without involving any wet experimental section.

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

    Science.gov (United States)

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

    2011-12-15

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

  16. PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins.

    Science.gov (United States)

    Reumann, Sigrun; Buchwald, Daniela; Lingner, Thomas

    2012-01-01

    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.

  17. 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.

  18. 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/.

  19. 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/.

  20. The Collocation of Web Server in the Setting of Windows Server 2003%在Windows Server 2003环境下Web服务器的配置

    Institute of Scientific and Technical Information of China (English)

    贾燕茹

    2008-01-01

    Windows Server 003可以用系统自带的ⅡS或采用第三方软件两种方式来架设Web服务器.同时Windows Server 2003家族中,还有一个Web版,专用于基于Web服务的各种Web接口应用.文章以Windows Server 2003系统自带ⅡS6.0为例,论述了Web服务器的架设过程.

  1. 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.

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

    Science.gov (United States)

    Xie, Yang; Ying, Jinyong; Xie, Dexuan

    2017-03-30

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

  3. DECENTRALIZED SOCIAL NETWORK SERVICE USING THE WEB HOSTING SERVER FOR PRIVACY PRESERVATION

    Directory of Open Access Journals (Sweden)

    Yoonho Nam

    2013-10-01

    Full Text Available In recent years, the number of subscribers of the social network services such as Facebook and Twitter has increased rapidly. In accordance with the increasing popularity of social network services, concerns about user privacy are also growing. Existing social network services have a centralized structure that a service provider collects all the user’s profile and logs until the end of the connection. The information collected typically useful for commercial purposes, but may lead to a serious user privacy violation. The user’s profile can be compromised for malicious purposes, and even may be a tool of surveillance extremely. In this paper, we remove a centralized structure to prevent the service provider from collecting all users’ information indiscriminately, and present a decentralized structure using the web hosting server. The service provider provides only the service applications to web hosting companies, and the user should select a web hosting company that he trusts. Thus, the user’s information is distributed, and the user’s privacy is guaranteed from the service provider.

  4. The BioExtract Server: a web-based bioinformatic workflow platform.

    Science.gov (United States)

    Lushbough, Carol M; Jennewein, Douglas M; Brendel, Volker P

    2011-07-01

    The BioExtract Server (bioextract.org) is an open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet.

  5. Abdominal aortic aneurysms: virtual imaging and analysis through a remote web server

    Energy Technology Data Exchange (ETDEWEB)

    Neri, Emanuele; Bargellini, Irene; Vignali, Claudio; Bartolozzi, Carlo [University of Pisa, Diagnostic and Interventional Radiology, Pisa (Italy); Rieger, Michael; Jaschke, Werner [University of Innsbruck, Diagnostic and Interventional Radiology, Innsbruck (Austria); Giachetti, Andrea; Tuveri, Massimiliano [Center for Research and Study, Sardinia (Italy)

    2005-02-01

    The study describes the application of a web-based software in the planning of the endovascular treatment of abdominal aortic aneurysms (AAA). The software has been developed in the framework of a 2-year research project called Aneurysm QUAntification Through an Internet Collaborative System (AQUATICS); it allows to manage remotely Virtual Reality Modeling Language (VRML) models of the abdominal aorta, derived from multirow computed tomography angiography (CTA) data sets, and to obtain measurements of diameters, angles and centerline lengths. To test the reliability of measurements, two radiologists performed a detailed analysis of multiple 3D models generated from a synthetic phantom, mimicking an AAA. The system was tested on 30 patients with AAA; CTA data sets were mailed and the time required for segmentation and measurement were collected for each case. The Bland-Altman plot analysis showed that the mean intra- and inter-observer differences in measures on phantoms were clinically acceptable. The mean time required for segmentation was 1 h (range 45-120 min). The mean time required for measurements on the web was 7 min (range 4-11 min). The AQUATICS web server may provide a rapid, standardized and accurate tool for the evaluation of AAA prior to the endovascular treatment. (orig.)

  6. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update.

    Science.gov (United States)

    Huynh, Tien; Rigoutsos, Isidore

    2004-07-01

    In this report, we provide an update on the services and content which are available on the web server of IBM's Bioinformatics and Pattern Discovery group. The server, which is operational around the clock, provides access to a large number of methods that have been developed and published by the group's members. There is an increasing number of problems that these tools can help tackle; these problems range from the discovery of patterns in streams of events and the computation of multiple sequence alignments, to the discovery of genes in nucleic acid sequences, the identification--directly from sequence--of structural deviations from alpha-helicity and the annotation of amino acid sequences for antimicrobial activity. Additionally, annotations for more than 130 archaeal, bacterial, eukaryotic and viral genomes are now available on-line and can be searched interactively. The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/.

  7. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.

    Science.gov (United States)

    Xie, Chen; Mao, Xizeng; Huang, Jiaju; Ding, Yang; Wu, Jianmin; Dong, Shan; Kong, Lei; Gao, Ge; Li, Chuan-Yun; Wei, Liping

    2011-07-01

    High-throughput experimental technologies often identify dozens to hundreds of genes related to, or changed in, a biological or pathological process. From these genes one wants to identify biological pathways that may be involved and diseases that may be implicated. Here, we report a web server, KOBAS 2.0, which annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). KOBAS 2.0 can be accessed at http://kobas.cbi.pku.edu.cn.

  8. 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.

  9. 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

  10. 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.

  11. ngLOC: software and web server for predicting protein subcellular localization in prokaryotes and eukaryotes

    Directory of Open Access Journals (Sweden)

    King Brian R

    2012-07-01

    Full Text Available Abstract Background Understanding protein subcellular localization is a necessary component toward understanding the overall function of a protein. Numerous computational methods have been published over the past decade, with varying degrees of success. Despite the large number of published methods in this area, only a small fraction of them are available for researchers to use in their own studies. Of those that are available, many are limited by predicting only a small number of organelles in the cell. Additionally, the majority of methods predict only a single location for a sequence, even though it is known that a large fraction of the proteins in eukaryotic species shuttle between locations to carry out their function. Findings We present a software package and a web server for predicting the subcellular localization of protein sequences based on the ngLOC method. ngLOC is an n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The overall prediction accuracy varies from 89.8% to 91.4% across species. This program can predict 11 distinct locations each in plant and animal species. ngLOC also predicts 4 and 5 distinct locations on gram-positive and gram-negative bacterial datasets, respectively. Conclusions ngLOC is a generic method that can be trained by data from a variety of species or classes for predicting protein subcellular localization. The standalone software is freely available for academic use under GNU GPL, and the ngLOC web server is also accessible at http://ngloc.unmc.edu.

  12. On the Web Server Security Threat and Prevention Tips%Web 服务器安全威胁与防范技巧

    Institute of Scientific and Technical Information of China (English)

    魏江来

    2012-01-01

      The WEB server is mainly oriented to the Internet,with the Internet service the growing demand,all kinds of Internet application services is increasing,Web server will become numerous information application in the most vulnerable of object. This paper mainly introduces several common Web server security threats,and put forward the corresponding security techniques.%  WEB 服务器主要是面向互联网的,随着人们对互联网服务的需求不断扩大,各种互联网应用服务日益增多,Web 服务器便成为众多信息化应用中最容易遭受攻击的对象。文章中主要介绍了几种常见的 Web 服务器安全威胁,并提出了相应的安全防范技巧。

  13. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

    Science.gov (United States)

    Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G

    2013-07-01

    MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

  14. Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

    Directory of Open Access Journals (Sweden)

    Walsh Ian

    2006-09-01

    Full Text Available Abstract Background We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids. Results The servers are state-of-the-art, with secondary structure predicted correctly for nearly 80% of residues (currently the top performance on EVA, 2-class solvent accessibility nearly 80% correct, and contact maps exceeding 50% precision on the top non-diagonal contacts. A preliminary implementation of the predictor of protein Cα traces featured among the top 20 Novel Fold predictors at the last CASP6 experiment as group Distill (ID 0348. The majority of the servers, including the Cα trace predictor, now take into account homology information from the PDB, when available, resulting in greatly improved reliability. Conclusion All predictions are freely available through a simple joint web interface and the results are returned by email. In a single submission the user can send protein sequences for a total of up to 32k residues to all or a selection of the servers. Distill is accessible at the address: http://distill.ucd.ie/distill/.

  15. Evolution of a legacy system to a Web patient record server: leveraging investment while opening the system.

    Science.gov (United States)

    Flanagan, J R; Chun, J; Wagner, J R

    1996-01-01

    A layered system is under development to enhance our legacy system as a backend in a WEB-enabled system. Each layer of the system has defined functionality, leverages the investment in the layer below, and follows the strategy of reducing support requirements for workstations. The mainframe system provides administrative integration of sub-systems, security, and the central data repository for most information. The second layer is a graphical user interface (GUI) to the system for Windows platforms. Support needs are limited by relying chiefly on X-terminals and application servers. The "Intranet" layer is a WEB Server building upon the second layer gateways to provide platform-independent access to selected information and images. The fourth layer, under evaluation, will extend access to the central data repository for Internet users of web browsers that support private-key/public-key encryption.

  16. Web Server Failure Analysis and Treatment Measures%Web服务器故障分析及处理措施

    Institute of Scientific and Technical Information of China (English)

    陈春晓

    2014-01-01

    Web服务器出现故障不仅会对网站的安全运行造成影响,还会影响到人们的正常使用,所以要及时维护和升级服务器,保证其正常运行。以B/S架构的PACS系统为例,其Web服务器采用的是WindowsIIS,客户端浏览器的使用需要WindowsIIS处于正常情况状态。如果WindowsIIS性能出现故障,就会影响PACS系统运行的可靠性。分析了几种故障,并提出解决方法,使Web服务器稳定运行。%Web server failure will not affect the safe operation of the site, but also affect people’s normal use, so in a timely manner to maintain and upgrade the server to ensure their normal operation. With B/S structure PACS system, for example, the Web server uses a WindowsIIS, the client browser is in use need WindowsIIS normal state. If WindowsIIS performance fails, it will affect the reliability of the PACS system operation. Analysis of several failures, and propose solutions to make the Web server and stable operation.

  17. 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, ...

  18. 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.

  19. Power Macintosh 7300/166

    CERN Multimedia

    1997-01-01

    The Power Macintosh 7300 was released in 1997 and was the same case as the Power Macintosh 7600. Its main evolution is that it was equipped with a faster processor. It also had a bigger hard drive (2 GB) and a faster CD-ROM drive (12x to 8x). In return, Apple chose to remove the audiovisual connections that were present on all its predecessors of the range 7x00.

  20. 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)

  1. RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps.

    Science.gov (United States)

    Pandurangan, Arun Prasad; Topf, Maya

    2012-09-15

    To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements. The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk. a.pandurangan@mail.cryst.bbk.ac.uk Supplementary data are available at Bioinformatics online.

  2. ORCAN-a web-based meta-server for real-time detection and functional annotation of orthologs.

    Science.gov (United States)

    Zielezinski, Andrzej; Dziubek, Michal; Sliski, Jan; Karlowski, Wojciech M

    2017-01-05

    ORCAN (ORtholog sCANner) is a web-based meta-server for one-click evolutionary and functional annotation of protein sequences. The server combines information from the most popular orthology-prediction resources, including four tools and four online databases. Functional annotation utilizes five additional comparisons between the query and identified homologs, including: sequence similarity, protein domain architectures, functional motifs, Gene Ontology term assignments and a list of associated articles. Furthermore, the server uses a plurality-based rating system to evaluate the orthology relationships and to rank the reference proteins by their evolutionary and functional relevance to the query. Using a dataset of ∼1 million true yeast orthologs as a sample reference set, we show that combining multiple orthology-prediction tools in ORCAN increases the sensitivity and precision by 1-2 percent points.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

    Lange, Kristian; Kühn, Simone; Filevich, Elisa

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kristian Lange

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

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

    Science.gov (United States)

    Lange, Kristian; Kühn, Simone; Filevich, Elisa

    2015-01-01

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

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

    Science.gov (United States)

    Technology & Learning, 2005

    2005-01-01

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

  9. 基于Web RTC的浏览器端Web服务器的设计与实现%Design and Implementation of Web Server in Browser Based on WebRTC

    Institute of Scientific and Technical Information of China (English)

    缪进; 何加铭

    2015-01-01

    WebRTC has the features of simplicity, easy expansibility, open standard and free & open source. The rapid development of Web applications by means of standard API in WebRTC was introduced and some problems in traditional Web server were researched. The bottleneck of these problems was analyzed and the Web server based on browser was implemented. WebRTC not only provides support to Web server, but brings more solutions to information distribution and sharing.%WebRTC具有简单易扩展、开放标准、开源免费的特点。通过介绍利用WebRTC提供的标准API快速开发Web应用,研究了传统We b服务器存在的问题,分析了其存在问题的瓶颈,并实现了基于浏览器的We b服务器。系统地实现We b RT C技术可以为We b服务器提供支持,并能为信息的传播和分享带来更多的解决方案。

  10. StaRProtein, A Web Server for Prediction of the Stability of Repeat Proteins

    Science.gov (United States)

    Xu, Yongtao; Zhou, Xu; Huang, Meilan

    2015-01-01

    Repeat proteins have become increasingly important due to their capability to bind to almost any proteins and the potential as alternative therapy to monoclonal antibodies. In the past decade repeat proteins have been designed to mediate specific protein-protein interactions. The tetratricopeptide and ankyrin repeat proteins are two classes of helical repeat proteins that form different binding pockets to accommodate various partners. It is important to understand the factors that define folding and stability of repeat proteins in order to prioritize the most stable designed repeat proteins to further explore their potential binding affinities. Here we developed distance-dependant statistical potentials using two classes of alpha-helical repeat proteins, tetratricopeptide and ankyrin repeat proteins respectively, and evaluated their efficiency in predicting the stability of repeat proteins. We demonstrated that the repeat-specific statistical potentials based on these two classes of repeat proteins showed paramount accuracy compared with non-specific statistical potentials in: 1) discriminate correct vs. incorrect models 2) rank the stability of designed repeat proteins. In particular, the statistical scores correlate closely with the equilibrium unfolding free energies of repeat proteins and therefore would serve as a novel tool in quickly prioritizing the designed repeat proteins with high stability. StaRProtein web server was developed for predicting the stability of repeat proteins. PMID:25807112

  11. 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.

  12. Drug-target interaction prediction: databases, web servers and computational models.

    Science.gov (United States)

    Chen, Xing; Yan, Chenggang Clarence; Zhang, Xiaotian; Zhang, Xu; Dai, Feng; Yin, Jian; Zhang, Yongdong

    2016-07-01

    Identification of drug-target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug-target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug-target associations on a large scale. In this review, databases and web servers involved in drug-target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug-target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug-target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug-target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.

  13. 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.

  14. Basic Static Code Analysis Untuk Mendeteksi Backdoor Shell Pada Web Server

    Directory of Open Access Journals (Sweden)

    Nelly Indriani Widiastuti

    2017-05-01

    Full Text Available Mengakses  sistem komputer tanpa ijin merupakan kejahatan yang dilakukan dengan memasuki atau menyusup kedalam suatu sistem jaringan komputer tanpa sepengetahuan dari pemilik sistem tersebut. Kejahatan  tersebut bertujuan untuk mengintai atau mencuri informasi penting dan rahasia. Dalam praktiknya peretas menyisipkan berkas backdoor shell pada lokasi yang sulit ditemukan oleh pemilik sistem. Beberapa perangkat yang sudah ada masih dalam bentuk terminal. Perangkat tersebut melakukan pencarian berkas berdasarkan nama-nama yang telah terdaftar sebelumnya. Akibatnya, pada saat berkas backdoor shell  jenis baru menginfeksi, tools tersebut tidak dapat mendeteksi keberadaannya. Berdasarkan hal tersebut, maka dalam penelitian ini pencarian backdoor shell pada web server menggunakan metode basic static code analysis. File sistem diproses melalui dua tahap utama yaitu string matching dan taint analysis. Dalam proses taint analysis, sistem menghitung peluang kemungkinan setiap signature sebagai backdoor untuk mengatasi kamus backdoor yang tidak lengkap. Berdasarkan  hasil yang didapat dari pengujian yang dilakukan terhadap 3964 berkas diperoleh tingkat akurasi  yang lebih besar dibandingkan dengan aplikasi php shell detector sebesar 75%.

  15. CryoProtect: A Web Server for Classifying Antifreeze Proteins from Nonantifreeze Proteins

    Directory of Open Access Journals (Sweden)

    Reny Pratiwi

    2017-01-01

    Full Text Available Antifreeze protein (AFP is an ice-binding protein that protects organisms from freezing in extremely cold environments. AFPs are found across a diverse range of species and, therefore, significantly differ in their structures. As there are no consensus sequences available for determining the ice-binding domain of AFPs, thus the prediction and characterization of AFPs from their sequence is a challenging task. This study addresses this issue by predicting AFPs directly from sequence on a large set of 478 AFPs and 9,139 non-AFPs using machine learning (e.g., random forest as a function of interpretable features (e.g., amino acid composition, dipeptide composition, and physicochemical properties. Furthermore, AFPs were characterized using propensity scores and important physicochemical properties via statistical and principal component analysis. The predictive model afforded high performance with an accuracy of 88.28% and results revealed that AFPs are likely to be composed of hydrophobic amino acids as well as amino acids with hydroxyl and sulfhydryl side chains. The predictive model is provided as a free publicly available web server called CryoProtect for classifying query protein sequence as being either AFP or non-AFP. The data set and source code are for reproducing the results which are provided on GitHub.

  16. DisArticle: a web server for SVM-based discrimination of articles on traditional medicine.

    Science.gov (United States)

    Kim, Sang-Kyun; Nam, SeJin; Kim, SangHyun

    2017-01-28

    Much research has been done in Northeast Asia to show the efficacy of traditional medicine. While MEDLINE contains many biomedical articles including those on traditional medicine, it does not categorize those articles by specific research area. The aim of this study was to provide a method that searches for articles only on traditional medicine in Northeast Asia, including traditional Chinese medicine, from among the articles in MEDLINE. This research established an SVM-based classifier model to identify articles on traditional medicine. The TAK + HM classifier, trained with the features of title, abstract, keywords, herbal data, and MeSH, has a precision of 0.954 and a recall of 0.902. In particular, the feature of herbal data significantly increased the performance of the classifier. By using the TAK + HM classifier, a total of about 108,000 articles were discriminated as articles on traditional medicine from among all articles in MEDLINE. We also built a web server called DisArticle ( http://informatics.kiom.re.kr/disarticle ), in which users can search for the articles and obtain statistical data. Because much evidence-based research on traditional medicine has been published in recent years, it has become necessary to search for articles on traditional medicine exclusively in literature databases. DisArticle can help users to search for and analyze the research trends in traditional medicine.

  17. Web server for tilt-pair validation of single particle maps from electron cryomicroscopy.

    Science.gov (United States)

    Wasilewski, Sebastian; Rosenthal, Peter B

    2014-04-01

    Three-dimensional structures of biological assemblies may be calculated from images of single particles obtained by electron cryomicroscopy. A key step is the correct determination of the orientation of the particle in individual image projections. A useful tool for validation of the quality of a 3D map and its consistency with images is tilt-pair analysis. In a successful tilt-pair test, the relative angle between orientations assigned to each image of a tilt-pair agrees with the known relative rotation angle of the microscope specimen holder during the experiment. To make the procedure easy to apply to the increasing number of single particle maps, we have developed software and a web server for tilt-pair analysis. The tilt-pair analysis program reports the overall agreement of the assigned orientations with the known tilt angle and axis of the experiment and the distribution of tilt transformations for individual particles recorded in a single image field. We illustrate application of the validation tool to several single particle specimens and describe how to interpret the scores.

  18. 构建Lotus Domino的Brower/Web Server模式%Construction of the Lotus Domino Brower / Web Server model

    Institute of Scientific and Technical Information of China (English)

    李金穗

    2008-01-01

    随着企业原来开发lotus Domino/Notes的Client/Server(客户端朋艮务器)模式,改为现今Brower/Web Serv-er(浏览器/服务器)模式及其实际应用,详细讲述企业局域网B/S模式优势以及如何构建Lotus Domino/Notes的B/S运行模式的具体方法.

  19. 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

    2016-07-08

    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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Research on Web Server Attacks Logs Analysis%Web服务器攻击日志分析研究

    Institute of Scientific and Technical Information of China (English)

    邓诗琪; 刘晓明; 武旭东; 雷敏

    2016-01-01

    The rapid development of Internet Technology has changed people’s lifestyle. And the e-commerce becomes one of the most popular web applications. Nowadays, malicious attacks towards web server of most e-commerce websites appear to be more and more common. However, related attack records can be found through analyzing access logs on web server of those e-commerce websites. The OWASP (Open Web Application Security Project) publishes ten attack technology the web server experienced every year, such as SQL injection, XSS attack and DDoS attack, etc. These attacks have caused great harm to the web server, on the one hand, the e-commerce websites can’t provide normal service for users, on the other hand, most data or privacy of users is leaked. This paper puts forward a solution to analyzing access logs on web server by the classiifcation of web access logs and the matching of attack pattern and characteristics. The system can ifnd out attack sources and types, and then displays the results in a graphical from in a web page, which helps security administrators of e-commerce websites to detect the attacks and improve the ability of resisting various attacks on web server.%互联网技术的飞速发展改变了人们的生活方式,其中电子商务是近年来应用最为广泛的互联网应用之一。越来越多的Web服务器部署在互联网上向外提供服务,因此针对电子商务Web服务器的攻击不断增加。OWASP组织每年都公布Web应用程序遭受到的最多的10种攻击技术,其中攻击危害性较大的有SQL注入、XSS攻击和DDoS攻击等。这些攻击一方面使得电子商务服务器无法向外提供服务,另一方面还可能造成电子商务服务器中数据和用户个人隐私的泄露,因此电子商务服务器的安全防护是Web服务器安全运维最为重要的一个环节。通过对Web服务器日志的分析研究可以对网站的攻击事件进行检测,进而掌握Web服务器被攻击的

  1. 测控设备web网络服务器化研究%Research web server monitoring and control equipment

    Institute of Scientific and Technical Information of China (English)

    胡羽; 张凤登

    2012-01-01

    为实现利用Internet自带的客户端浏览器对现场设备进行远程监控的目的,设计并实施了新型web网络服务器化远程测控系统.系统中测控设备内嵌嵌入式Web服务器,既能自身作为测控终端直接采集数据,又能通过CAN总线与其他测控器进行组网,实现类似网关的功能.硬件设计主要包括:嵌入式web服务器模块、测控器模块以及其接口模块设计与实施.软件设计主要选用Linux操作系统和嵌入式Web服务器Boa实现CGI技术,设计添加CAN控制器驱动程序后完成IE浏览器与嵌入式web服务器以及测控器三者之间的通信.利用该系统进行温度测试,实验成功并能满足实时性,充分表明利用Internet浏览器、嵌入式Web服务器组建并控制CAN网络的新型远程测控系统的先进性与可行性.%In order to monitoring the field devices by the Internet browser, designed and achieved the new web server longdistance observe and control system. In the system, the field device can be used as a control node directly collect data, also can be extend gateway function compatible with the CAN bus. The hardware includes the embedded web server module, the monitoring terminal module and the interfaces module of them. The software used the Linux operating system for OS and BOA for the embedded web server to achieve the CGI technology. After extend CAN controller, the communication between the IE browser, the field device embedded web server and the monitoring terminal can be achieved. Testing temperature measurement by this system, it is successful and can meet the real-time monitoring requirements. The research can show the advance and the feasibility of the new long-distance observe and control system using the Internet browser, web server and the CAN bus.

  2. Design of Measure Data Handler Website Based on Matlab WebServer%基于Matlab WebServer测量数据处理网站设计

    Institute of Scientific and Technical Information of China (English)

    鲍红波; 马国亮; 王坤

    2012-01-01

    采用ASP技术,利用Matlab WebServer编写了一个测量数据处理网站。通过HTML表单输入数据,在基于B/S(Browser/Server结构)结构的情况下,赋予网站进行等高线绘制与遥感图像融合的能力。利用Maflab WebServer与Matlab自带插值函数绘制等高线,解决了Web系统开发程序中数值计算能力差,特别是结果可视化效果差问题,数据结果不仅可以看到二维的等高线图形,还可以及时方便地看到三维曲面图。%By using ASP technology and Matlab WebServer, the authors created a measurement data processing site. Input data through an HTML form, based on B/S (Browser/Server structure) structure, the site was given the ability to contour drawing and remote sensing image fusion. Through Matlab WebServer and Matlab comes with the interpolation function to draw contour lines, the problems of address the web system development process, the numerical calculation ability and results visualization differential problem were solved, through data results can not only see the two-dimensional contour graphics, but also 3-D surface chart.

  3. 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,…

  4. The Biosphere 2 Global Change Testbed world wide web server: closed system research and education using the Internet

    Science.gov (United States)

    Tosteson, J L; Marino, B D

    1996-01-01

    At this time, a fully materially closed system of large scale and complexity has not yet been built. However, Biosphere 2--a unique "living" Earth laboratory--is an example of a large (3.15 acres) and biologically complex (several thousand terrestrial plant species) system that can be operated with minimal exchange of ambient substances (annual exchange of materials is estimated to be approximately 10%). Biosphere 2 provides a multidisciplinary platform for scientific studies related to both Earth system processes and microcosms of the Earth that may be transported into space. The scale and versatility of the facility make Biosphere 2 a unique place to support integrated research and educational activities. The Biosphere 2 Global Change Testbed world wide web server has been developed to facilitate such activities by disseminating information about the facility, as well as current research and education efforts. Currently, these efforts focus of studies on carbon and other elemental cycles, coral reef ecology and physiology, stable isotopic research, studies in biodiversity, and ecophysiological studies of plant responses to elevated CO2. The Biosphere 2 Global Change Testbed web server is briefly described, and goals for use of the server to promote research and education endeavors are outlined.

  5. 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.

  6. System Monitoring And Controlling Water Nutrition aquaponics Using Arduino Uno Based Web Server

    Directory of Open Access Journals (Sweden)

    Amanda Fahmi Maarif

    2016-10-01

    Full Text Available Aquaponics is a sustainable farming system that combines aquaculture and hydroponics systems as an integrated system that is symbiotic. In an aquaponics system results from animal excretion contained in this system will be used as natural nutrients hydroponic plants. As for the animals that live on this system will also result in clean water that has been filtered naturally by the plant roots. In the cultivation of an aquaponics system an important factor affecting the development of the ecosystem is the degree of acidity (PH which have a direct impact on the absorption of nutrients in the roots of plants and development of animals that live in this ecosystem. In addition, factors that are not less important is the electroconductivity (EC is the ability to conduct an electric ion in solution to the plant roots. The degree of acidity (pH of water that is normal for an aquaponics ecosystem at 6-7 and value for EC ranged in value of 0.8-1.2 ms / cm. From this study produced a tool that is capable of monitoring in the form of a web server and conduct automatic action in controlling the levels of PH and EC. Based on the results of system testing results obtained sensor Analog PH Meter Kit and Analog Electrical Conductivity Meter capable of monitoring water tank in accordance with the standard measurement tool used is PH meter and EC Solution and the system is also able to control the changes that occur in the water tank in accordance with the standards of PH and EC.

  7. Macintoshed Libraries 5. Fifth Edition.

    Science.gov (United States)

    Valauskas, Edward J., Ed.; Vaccaro, Bill, Ed.

    This annual collection contains 16 papers about the use of Macintosh computers in libraries which include: "New Horizons in Library Training: Using HyperCard for Computer-Based Staff Training" (Pauline S. Bayne and Joe C. Rader); "Get a Closet!" (Ron Berntson); "Current Periodicals: Subject Access the Mac Way"…

  8. An overview of the BioExtract Server: a distributed, Web-based system for genomic analysis.

    Science.gov (United States)

    Lushbough, C M; Brendel, V P

    2010-01-01

    Genome research is becoming increasingly dependent on access to multiple, distributed data sources, and bioinformatic tools. The importance of integration across distributed databases and Web services will continue to grow as the number of requisite resources expands. Use of bioinformatic workflows has seen considerable growth in recent years as scientific research becomes increasingly dependent on the analysis of large sets of data and the use of distributed resources. The BioExtract Server (http://bioextract.org) is a Web-based system designed to aid researchers in the analysis of distributed genomic data by providing a platform to facilitate the creation of bioinformatic workflows. Scientific workflows are created within the system by recording the analytic tasks preformed by researchers. These steps may include querying multiple data sources, saving query results as searchable data extracts, and executing local and Web-accessible analytic tools. The series of recorded tasks can be saved as a computational workflow simply by providing a name and description.

  9. 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.

  10. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

  12. 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.

  13. RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.

    Science.gov (United States)

    Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

    2015-07-01

    Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular-no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site.

  14. 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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. 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.

  16. Concurrent web server designing based on prethreading technology under Linux system%基于Linux的预线程化并发Web服务器设计

    Institute of Scientific and Technical Information of China (English)

    兰红; 柳显涛; 李文琼

    2012-01-01

    Browsing web pages is the most common service for Internet. Web sever is a kind of software which provides users to get or post web pages. Web server adopts B/S model, follows the standard HTTP protocol. In Linux operating system some web servers designed based on single processing or thread mechanism, have some problems, such as big costs of CPU and lower efficiency etc. This paper introduces a new web sever, using prethreading technology, integrating semaphore mechanism to dispatch shared resource, and producer-consumer model to build web server model. This new web server not only provides basic functions same as other web server, but also has concurrency, better service qualities and system resource utilization.%Web浏览是Internet最为常用的服务,Web服务器为客户提供Web浏览服务,它采用B/S工作模式,遵循HTTP协议.Linux系统中基于进程或单纯基于线程机制设计的Web服务器存在资源消耗大、利用率不高等问题.文中设计的基于预线程化的并发Web服务器利用信号量机制和生产者-消费者模型较好的实现了资源共享及其调度,利用线程的逻辑缓冲流有效节省地址空间.该Web服务器具备了常用Web服务器的基本功能,具有并发处理能力,可以降低系统开销,提高了Web服务器的服务效率和系统资源利用率.

  17. SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser.

    Science.gov (United States)

    Walsh, Thomas P; Webber, Caleb; Searle, Stephen; Sturrock, Shane S; Barton, Geoffrey J

    2008-07-01

    SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance. This combination gives good sensitivity and selectivity that outperforms PSI-BLAST in domain-searching benchmarks. Although computationally expensive, SCANPS exploits onchip parallelism (MMX and SSE2 instructions on Intel chips) as well as MPI parallelism to give acceptable turnround times even for large databases. A web server developed to run SCANPS searches is now available at http://www.compbio.dundee.ac.uk/www-scanps. The server interface allows a range of different protein sequence databases to be searched including the SCOP database of protein domains. The server provides the user with regularly updated versions of the main protein sequence databases and is backed up by significant computing resources which ensure that searches are performed rapidly. For SCOP searches, the results may be viewed in a new tree-based representation that reflects the structure of the SCOP hierarchy; this aids the user in placing each hit in the context of its SCOP classification and understanding its relationship to other domains in SCOP.

  18. SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.

    Science.gov (United States)

    Tuncbag, Nurcan; McCallum, Scott; Huang, Shao-Shan Carol; Fraenkel, Ernest

    2012-07-01

    High-throughput technologies including transcriptional profiling, proteomics and reverse genetics screens provide detailed molecular descriptions of cellular responses to perturbations. However, it is difficult to integrate these diverse data to reconstruct biologically meaningful signaling networks. Previously, we have established a framework for integrating transcriptional, proteomic and interactome data by searching for the solution to the prize-collecting Steiner tree problem. Here, we present a web server, SteinerNet, to make this method available in a user-friendly format for a broad range of users with data from any species. At a minimum, a user only needs to provide a set of experimentally detected proteins and/or genes and the server will search for connections among these data from the provided interactomes for yeast, human, mouse, Drosophila melanogaster and Caenorhabditis elegans. More advanced users can upload their own interactome data as well. The server provides interactive visualization of the resulting optimal network and downloadable files detailing the analysis and results. We believe that SteinerNet will be useful for researchers who would like to integrate their high-throughput data for a specific condition or cellular response and to find biologically meaningful pathways. SteinerNet is accessible at http://fraenkel.mit.edu/steinernet.

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

    Science.gov (United States)

    Zuo, Guanghong; Hao, Bailin

    2015-10-01

    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.

  20. BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

    Science.gov (United States)

    Paz, Inbal; Kligun, Efrat; Bengad, Barak; Mandel-Gutfreund, Yael

    2016-07-08

    Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with yet another known function, are awaiting to be discovered. Here we present a new web server, BindUP, freely accessible through the website http://bindup.technion.ac.il/, for predicting DNA and RNA binding proteins using a non-homology-based approach. Our method is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP predicts nucleic acid binding function given the proteins three-dimensional structure or a structural model. Additionally, BindUP provides information on the largest electrostatic surface patches, visualized on the server. The server was tested on several datasets of DNA and RNA binding proteins, including proteins which do not possess DNA or RNA binding domains and have no similarity to known nucleic acid binding proteins, achieving very high accuracy. BindUP is applicable in either single or batch modes and can be applied for testing hundreds of proteins simultaneously in a highly efficient manner.

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

    Directory of Open Access Journals (Sweden)

    Guanghong Zuo

    2015-10-01

    Full Text Available 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.

  2. 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.

  3. RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

    Science.gov (United States)

    Miao, Zhichao; Westhof, Eric

    2016-07-08

    RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/.

  4. EarthServer2 : The Marine Data Service - Web based and Programmatic Access to Ocean Colour Open Data

    Science.gov (United States)

    Clements, Oliver; Walker, Peter

    2017-04-01

    The ESA Ocean Colour - Climate Change Initiative (ESA OC-CCI) has produced a long-term high quality global dataset with associated per-pixel uncertainty data. This dataset has now grown to several hundred terabytes (uncompressed) and is freely available to download. However, the sheer size of the dataset can act as a barrier to many users; large network bandwidth, local storage and processing requirements can prevent researchers without the backing of a large organisation from taking advantage of this raw data. The EC H2020 project, EarthServer2, aims to create a federated data service providing access to more than 1 petabyte of earth science data. Within this federation the Marine Data Service already provides an innovative on-line tool-kit for filtering, analysing and visualising OC-CCI data. Data are made available, filtered and processed at source through a standards-based interface, the Open Geospatial Consortium Web Coverage Service and Web Coverage Processing Service. This work was initiated in the EC FP7 EarthServer project where it was found that the unfamiliarity and complexity of these interfaces itself created a barrier to wider uptake. The continuation project, EarthServer2, addresses these issues by providing higher level tools for working with these data. We will present some examples of these tools. Many researchers wish to extract time series data from discrete points of interest. We will present a web based interface, based on NASA/ESA WebWorldWind, for selecting points of interest and plotting time series from a chosen dataset. In addition, a CSV file of locations and times, such as a ship's track, can be uploaded and these points extracted and returned in a CSV file allowing researchers to work with the extract locally, such as a spreadsheet. We will also present a set of Python and JavaScript APIs that have been created to complement and extend the web based GUI. These APIs allow the selection of single points and areas for extraction. The

  5. Design of Dynamic Web Server Based on ulP and AJAX%基于uIP与AJAX的动态Web服务器设计

    Institute of Scientific and Technical Information of China (English)

    杜宝祯; 吴志荣; 曾佳

    2012-01-01

    针对远程信息监测系统中数据的实时采集更新问题,将AJAX和CGI应用到嵌入式Web服务器的设计中,实现了服务器与浏览器之间的动态信息交互。本文首先分析了uIP协议栈,并在协议栈之上设计了Web服务器.然后利用CGI服务程序处理来自客户端的XML HttpRequest对象请求,实现动态Web功能。现场实验结果表明,嵌入式Web服务器降低了服务器端的资源开销,提高了响应速度。%Aiming at real-time data collection and update issues in remote information monitoring system, AJAX and CGI are applied to the design of embedded Web server,and dynamic information interaction is achieved between server and browser, uIP protocol stack is first analyzed, and the Web server is designed based on the protocol stack. Then XMLHttpRequest object requests from client are processed by CGI service programs, and the dynamic Web functionality is achieved. Field test results show that this embedded Web server reduces server resource costs and improves response speed.

  6. Botnet-based Distributed Denial of Service (DDoS) Attacks on Web Servers: Classification and Art

    Science.gov (United States)

    Alomari, Esraa; Manickam, Selvakumar; Gupta, B.; Karuppayah, Shankar; Alfaris, Rafeef

    2012-07-01

    Botnets are prevailing mechanisms for the facilitation of the distributed denial of service (DDoS) attacks on computer networks or applications. Currently, Botnet-based DDoS attacks on the application layer are latest and most problematic trends in network security threats. Botnet-based DDoS attacks on the application layer limits resources, curtails revenue, and yields customer dissatisfaction, among others. DDoS attacks are among the most difficult problems to resolve online, especially, when the target is the Web server. In this paper, we present a comprehensive study to show the danger of Botnet-based DDoS attacks on application layer, especially on the Web server and the increased incidents of such attacks that has evidently increased recently. Botnet-based DDoS attacks incidents and revenue losses of famous companies and government websites are also described. This provides better understanding of the problem, current solution space, and future research scope to defend against such attacks efficiently.

  7. SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

    Science.gov (United States)

    Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

    2011-07-01

    The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

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

    Science.gov (United States)

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

    2015-07-01

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

  9. Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking.

    Science.gov (United States)

    Blaszczyk, Maciej; Kurcinski, Mateusz; Kouza, Maksim; Wieteska, Lukasz; Debinski, Aleksander; Kolinski, Andrzej; Kmiecik, Sebastian

    2016-01-15

    Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. 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…

  13. Web Server Benchmark Application WiiBench using Erlang/OTP R11 and Fedora-Core Linux 5.0

    CERN Document Server

    Mutiara, A B

    2007-01-01

    As the web grows and the amount of traffics on the web server increase, problems related to performance begin to appear. Some of the problems, such as the number of users that can access the server simultaneously, the number of requests that can be handled by the server per second (requests per second) to bandwidth consumption and hardware utilization like memories and CPU. To give better quality of service (\\textbf{\\textit{QoS}}), web hosting providers and also the system administrators and network administrators who manage the server need a benchmark application to measure the capabilities of their servers. Later, the application intends to work under Linux/Unix -- like platforms and built using Erlang/OTP R11 as a concurrent oriented language under Fedora Core Linux 5.0. \\textbf{\\textit{WiiBench}} is divided into two main parts, the controller section and the launcher section. Controller is the core of the application. It has several duties, such as read the benchmark scenario file, configure the program b...

  14. PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif

    OpenAIRE

    Tang, Shengnan; Li, Tonghua; Cong, Peisheng; Xiong, Wenwei; Wang, Zhiheng; Sun, Jiangming

    2013-01-01

    Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two innovative characters: building localization motif libraries by a recursive method without alignment and Gene Ontology information; and establishing simple architecture for rapi...

  15. The PPI3D web server for searching, analyzing and modeling protein-protein interactions in the context of 3D structures.

    Science.gov (United States)

    Dapkūnas, Justas; Timinskas, Albertas; Olechnovič, Kliment; Margelevičius, Mindaugas; Dičiūnas, Rytis; Venclovas, Česlovas

    2016-12-22

    The PPI3D web server is focused on searching and analyzing the structural data on protein-protein interactions. Reducing the data redundancy by clustering and analyzing the properties of interaction interfaces using Voronoi tessellation makes this software a highly effective tool for addressing different questions related to protein interactions.

  16. Mobile app versus Web app: a comparison using 2008-2012 "PubMed for Handhelds" server data.

    Science.gov (United States)

    Fontelo, Paul; Liu, Fang

    2013-01-01

    Recent surveys show that mobile apps are more popular than Web apps. Apple's iTunes Store, now has about 800,000 apps and reported to have about 40 billion downloads. Android apps, although fewer, is available to the most number of smartphones today. About 40,000 apps are medical or health related. We developed a PubMed4Hh mobile app for iPhone/iPad users to search MEDLINE/PubMed with same features as our Web-based search tools, in use since 2002. Five-year (2008-2012) server data for PubMed4Hh and Web app were analyzed. Searches using the mobile app significantly increased compared to the same five-year time period. Month-by-month comparison showed a 3 to 5-fold increase in queries. The six-month total accesses comparison increased 280% from the previous four-year average. A review of 500 randomly selected queries revealed that the majority of queries were clinical questions ((97.8%) and 61% of these queries are searches related to therapy.

  17. 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.

  18. 小型Web服务器Boa的移植与验证%Transplantation and Verification of Embedded Web Server Boa

    Institute of Scientific and Technical Information of China (English)

    管华庆

    2016-01-01

    With the development of computer technology and modern communication technology,the device is connected to the network which is available to the general requirements of modern mobile terminals. Compared with the Internet Web applications,the embedded Web server has the advantages of simple structure and low functional requirements. The embedded devices connected to the Internet makes operating state to be easily monitored in real-time through of the network. Then the data can be vividly and intuitively displayed on PC, PDA,Phone and other equipments. Users do not need special application software. This portable communication earth station monitoring system is porting embedded Linux operating system on ARM9 chip. The appropriate application layer Web server on this system is in-stalled,the system uses the Boa server,which is based on B/S structure mode,and user opens a browser on your terminal server to access Web pages stored in the satellite communication earth station,bringing real-time,portable monitor to the user.%现代通信技术和计算机技术都迎来了显著的发展,各个应用领域都要求将可移动设备接入网络。这就要求构建嵌入式Web服务器,让用户可以接入服务器进行数据共享和相互通信。嵌入式Web服务器具有许多优点,如:结构简单、功能低等。把嵌入式设备接入互联网可以实现方便、实时地通过网络监控设备的工作状态,再将数据以直观、形象的网页方式显示在PC、PDA、Phone等设备上,不需要专门的应用软件。文中便携式通信地球站监控系统使用的是ARM9系列芯片,在控制板硬件之上移植Linux操作系统,系统上移植合适的应用层Web服务器。系统采用的是Boa服务器。它是一种B/S(浏览器/服务器)的架构方式,用户在终端上打开浏览器输入网址访问已构建的嵌入式Web服务器,就可以对设备进行方便、实时、简便的监控。

  19. Study on Web Server Method of RHEL5 Configuration%RHEL5配置Web服务器方法初探

    Institute of Scientific and Technical Information of China (English)

    孙莉娜

    2014-01-01

    The Apache server is the most used server in the Linux operating system. As one of the world's most popular Web server software, Apache server's outstanding advantage is that it's a free software, open source code, with stable performance, good portability, support cross platform application etc. This paper mainly discusses the methods of RHEL5 Web server configuration.%在Linux操作系统中,应用最多的Web服务器是Apache服务器。Apache作为世界上最流行的Web服务器软件之一,它的成功之处在于它是一个免费的自由软件,具有源代码开放、性能稳定、可移植性好,支持跨平台应用等特点。本文着重探讨RHEL5配置Web服务器的方法。

  20. DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins.

    Science.gov (United States)

    Tan, Kuan Pern; Varadarajan, Raghavan; Madhusudhan, M S

    2011-07-01

    Depth measures the extent of atom/residue burial within a protein. It correlates with properties such as protein stability, hydrogen exchange rate, protein-protein interaction hot spots, post-translational modification sites and sequence variability. Our server, DEPTH, accurately computes depth and solvent-accessible surface area (SASA) values. We show that depth can be used to predict small molecule ligand binding cavities in proteins. Often, some of the residues lining a ligand binding cavity are both deep and solvent exposed. Using the depth-SASA pair values for a residue, its likelihood to form part of a small molecule binding cavity is estimated. The parameters of the method were calibrated over a training set of 900 high-resolution X-ray crystal structures of single-domain proteins bound to small molecules (molecular weight structures. Users have the option of tuning several parameters to detect cavities of different sizes, for example, geometrically flat binding sites. The input to the server is a protein 3D structure in PDB format. The users have the option of tuning the values of four parameters associated with the computation of residue depth and the prediction of binding cavities. The computed depths, SASA and binding cavity predictions are displayed in 2D plots and mapped onto 3D representations of the protein structure using Jmol. Links are provided to download the outputs. Our server is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis experiments and small molecule docking exercises, in the context of protein functional annotation and drug discovery.

  1. 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.

  2. 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.

    Science.gov (United States)

    Boulos, Maged N Kamel; Honda, Kiyoshi

    2006-01-18

    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(R) 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.

  3. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  4. iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

    Science.gov (United States)

    Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

    2011-06-01

    The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

  5. AthMethPre: a web server for the prediction and query of mRNA m(6)A sites in Arabidopsis thaliana.

    Science.gov (United States)

    Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

    2016-10-18

    N(6)-Methyladenosine (m(6)A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m(6)A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m(6)A functions in plants. Therefore, computational prediction of mRNA m(6)A sites becomes emergently important. Here, we present a method to predict the m(6)A sites for A. thaliana mRNA sequence(s). To predict the m(6)A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m(6)A sites. The server also provides a comprehensive database of predicted transcriptome-wide m(6)A sites and curated m(6)A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m(6)A sites, which is freely accessible for public use at .

  6. Build the Embedded Web Server for Meteorological Acquisition System%气象采集系统中嵌入式Web服务器的构建

    Institute of Scientific and Technical Information of China (English)

    李翠翠; 马尚昌

    2011-01-01

    为了解决远程访问、监测及控制气象采集系统的问题,构建了嵌入式Web服务器.以S3C2440处理器为核心,以Linux为操作系统平台,选用Boa服务器,Sqlite数据库,提出了嵌入式Web服务器通过通用网关接口与Sqlite数据库连接的原理、方法和实现.当客户端发出请求时,服务器调用通用网关接口程序,实现了气象要素实时数据的动态查询.%In order to solve the problem of remote access, monitoring and controlling of automatic weather stations, an embedded web server is built. With s3c2440 processor as the core and Linux operating system as the design platform, using boa web server and sqlite database, the principle, method and the implementation joining embedded web server and sqlite database with cgi are introduced. When a client makes request, the server calls cgi program to achieve dynamic query of real-time meteorological element data.

  7. GoAhead WebServer在以太网交换机中的应用%Application of GoAhead WebServer in Ethernet Switch

    Institute of Scientific and Technical Information of China (English)

    王向群; 渠毅; 徐沛平

    2011-01-01

    In order to realize the Web configuration management of Ethernet switch, the function of dynamic Web page creation is elaborated after presenting the characteristics of GoAhead embedded Web server. The methods of daynamic data creation and function setting by Ej script and GoForm are introduced. The application structure and development process of GoAhead Webserver in Ethernet switch are discussed. The whole dynamic data establishment and the interactive process are concretely analyzed through the management of the aging time of MAC address table. And in the design of dynamic pages, the management of the switch is realized effectively on B/S architecture combined with JavaScript flexibly.%为了实现对以太网交换机进行Web配置管理,在简要介绍了GoAhead嵌入式Web服务器的特点后,阐述了其创建动态页面的功能,详细说明了Ejscript和GoForm创建动态数据和进行功能配置的方法.随后介绍了GoAhead WebServer在交换机中的应用结构和开发过程,并通过对地址表老化时间的管理来具体分析了整个动态数据的建立与交互过程,在动态页面的设计中,与JavaScript的灵活结合,更加有效地实现了B/S架构下对交换机的管理.

  8. 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.

  9. Scientific Graphical Displays on the Macintosh

    Energy Technology Data Exchange (ETDEWEB)

    Grotch, S. [Lawrence Livermore National Lab., CA (United States)

    1994-11-15

    In many organizations scientists have ready access to more than one computer, often both a workstation (e.g., SUN, HP, SGI) as well as a Macintosh or other PC. The scientist commonly uses the work station for `number-crunching` and data analysis whereas the Macintosh is relegated to either word processing or serves as a `dumb terminal` to a larger main-frame computer. In an informal poll of my colleagues, very few of them used their Macintoshes for either statistical analysis or for graphical data display. I believe that this state of affairs is particularly unfortunate because over the last few years both the computational capability, and even more so, the software availability for the Macintosh have become quite formidable. In some instances, very powerful tools are now available on the Macintosh that may not exist (or be far too costly) on the so-called `high end` workstations. Many scientists are simply unaware of the wealth of extremely useful, `off-the-shelf` software that already exists on the Macintosh for scientific graphical and statistical analysis.

  10. Vectronic's Power Macintosh G3 (B & W)

    CERN Multimedia

    1999-01-01

    Apple introduced the Power Macintosh G3 Blue and White (B & W) on January 5, 1999. The Power Macintosh G3 line stayed in production until August 1999, and was replaced by the Power Macintosh G4, which used the same chassis. The Power Macintosh G3 originally cost between $1599 and $2900 depending on options. The three original Power Macintosh G3 models shipped with a 300 MHz, 350 MHz, or 400 MHz PowerPC 750 (G3) processor. Just pull on the small round handle on the side of the tower, and the entire side of the computer opens up. The G3's motherboard is mounted on that surface, giving you easy access for upgrading RAM or installed PCI cards. Apple added new ports (USB and the much-anticipated FireWire) that took the place of historic, and quickly becoming antiquated, Mac serial (printer and modem) ports. The Power Macintosh G3 has two USB (12 Mbps) ports, two FireWire (400 Mbps) ports, one 10/100BaseT Ethernet port, an RJ-11 jack for an optional 56K modem, a sound out and sound in jack, and one ADB (Apple D...

  11. ESAP plus: a web-based server for EST-SSR marker development.

    Science.gov (United States)

    Ponyared, Piyarat; Ponsawat, Jiradej; Tongsima, Sissades; Seresangtakul, Pusadee; Akkasaeng, Chutipong; Tantisuwichwong, Nathpapat

    2016-12-22

    Simple sequence repeats (SSRs) have become widely used as molecular markers in plant genetic studies due to their abundance, high allelic variation at each locus and simplicity to analyze using conventional PCR amplification. To study plants with unknown genome sequence, SSR markers from Expressed Sequence Tags (ESTs), which can be obtained from the plant mRNA (converted to cDNA), must be utilized. With the advent of high-throughput sequencing technology, huge EST sequence data have been generated and are now accessible from many public databases. However, SSR marker identification from a large in-house or public EST collection requires a computational pipeline that makes use of several standard bioinformatic tools to design high quality EST-SSR primers. Some of these computational tools are not users friendly and must be tightly integrated with reference genomic databases. A web-based bioinformatic pipeline, called EST Analysis Pipeline Plus (ESAP Plus), was constructed for assisting researchers to develop SSR markers from a large EST collection. ESAP Plus incorporates several bioinformatic scripts and some useful standard software tools necessary for the four main procedures of EST-SSR marker development, namely 1) pre-processing, 2) clustering and assembly, 3) SSR mining and 4) SSR primer design. The proposed pipeline also provides two alternative steps for reducing EST redundancy and identifying SSR loci. Using public sugarcane ESTs, ESAP Plus automatically executed the aforementioned computational pipeline via a simple web user interface, which was implemented using standard PHP, HTML, CSS and Java scripts. With ESAP Plus, users can upload raw EST data and choose various filtering options and parameters to analyze each of the four main procedures through this web interface. All input EST data and their predicted SSR results will be stored in the ESAP Plus MySQL database. Users will be notified via e-mail when the automatic process is completed and they can

  12. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

    Science.gov (United States)

    Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

    2011-01-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs. PMID:21609950

  13. R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

    Science.gov (United States)

    Vanquelef, Enguerran; Simon, Sabrina; Marquant, Gaelle; Garcia, Elodie; Klimerak, Geoffroy; Delepine, Jean Charles; Cieplak, Piotr; Dupradeau, François-Yves

    2011-07-01

    R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development, charge validation and molecular dynamics simulations. R.E.D. Server interfaces quantum mechanics programs, the RESP program and the latest version of the R.E.D. tools. A two step approach has been developed. The first one consists of preparing P2N file(s) to rigorously define key elements such as atom names, topology and chemical equivalencing needed when building a force field library. Then, P2N files are used to derive RESP or ESP charges embedded in force field libraries in the Tripos mol2 format. In complex cases an entire set of force field libraries or force field topology database is generated. Other features developed in R.E.D. Server include help services, a demonstration, tutorials, frequently asked questions, Jmol-based tools useful to construct PDB input files and parse R.E.D. Server outputs as well as a graphical queuing system allowing any user to check the status of R.E.D. Server jobs.

  14. RNA-Redesign: a web server for fixed-backbone 3D design of RNA.

    Science.gov (United States)

    Yesselman, Joseph D; Das, Rhiju

    2015-07-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment.

  15. 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.

  16. Log files analysis to assess the use and workload of a dynamic web server dedicated to end-stage renal disease.

    Science.gov (United States)

    Ben Said, Mohamed; Le Mignot, Loic; Richard, Jean Baptiste; Le Bihan, Christine; Toubiana, Laurent; Jais, Jean-Philippe; Landais, Paul

    2006-01-01

    A Multi-Source Information System (MSIS), has been designed for the Renal Epidemiology and Information Network (REIN) dedicated to End-Stage Renal Disease (ESRD). MSIS aims at providing reliable follow-up data for ESRD patients. It is based on an n-tier architecture, made out of a universal client, a dynamic Web server connected to a production database and to a data warehouse. MSIS is operational since 2002 and progressively deployed in 9 regions in France. It includes 16,677 patients. We show that the analysis of MSIS web log files allows evaluating the use of the system and the workload in a public-health perspective.

  17. ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices.

    Science.gov (United States)

    Dang, Cuong Cao; Lefort, Vincent; Le, Vinh Sy; Le, Quang Si; Gascuel, Olivier

    2011-10-01

    Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters. http://www.atgc-montpellier.fr/ReplacementMatrix/ olivier.gascuel@lirmm.fr Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/

  18. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders; Sonnhammer, Erik L L

    2007-01-01

    predicted transmembrane topologies overlap. This impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions....... The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius. Udgivelsesdato: 2007-Jul...

  19. PipMaker—A Web Server for Aligning Two Genomic DNA Sequences

    OpenAIRE

    Schwartz, Scott; Zheng ZHANG; Frazer, Kelly A; Smit, Arian; Riemer, Cathy; Bouck, John; Gibbs, Richard; Hardison, Ross; Miller, Webb

    2000-01-01

    PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree of similarity for each aligning segment between the two sequences in a compact and easily understandable form. Positions along the horizontal axis can be labeled with features su...

  20. 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.

  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. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.

    Science.gov (United States)

    Lohse, Marc; Nagel, Axel; Herter, Thomas; May, Patrick; Schroda, Michael; Zrenner, Rita; Tohge, Takayuki; Fernie, Alisdair R; Stitt, Mark; Usadel, Björn

    2014-05-01

    Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

  3. 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.

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

    Science.gov (United States)

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2008-10-27

    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. 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. 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.

  5. 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.

  6. MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

    Directory of Open Access Journals (Sweden)

    Louw Abraham I

    2008-02-01

    Full Text Available Abstract Background Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill. Description MADIBA (MicroArray Data Interface for Biological Annotation facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for Plasmodium, rice and Arabidopsis. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied. Conclusion MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the Plasmodium life cycle, and salt stress treatments of Arabidopsis and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA.

  7. Scientific statistics and graphics on the Macintosh

    Energy Technology Data Exchange (ETDEWEB)

    Grotch, S.L.

    1994-09-01

    In many organizations scientists have ready access to more than one computer, often both a workstation (e.g., SUN, HIP, SGI) as well as a Macintosh or other PC. The scientist commonly uses the work station for {open_quotes}number-crunching{close_quotes} and data analysis whereas the Macintosh is relegated to either word processing or serves as a {open_quotes}dumb terminal{close_quotes} to a larger mainframe computer. In an informal poll of the author`s colleagues, very few of them used their Macintoshes for either statistical analysis or for graphical data display. The author believes that this state of affairs is particularly unfortunate because over the last few years both the computational capability, and even more so, the software availability for the Macintosh have become quite formidable. In some instances, very powerful tools are now available on the Macintosh that may not exist (or be far too costly) on the so-called {open_quotes}high end{close_quotes} workstations. Many scientists are simply unaware of the wealth of extremely useful, {open_quotes}off-the-shelf{close_quote} software that already exists on the Macintosh for scientific graphical and statistical analysis. This paper is a very personal view illustrating several such software packages that have proved valuable in the author`s own work in the analysis and display of climatic datasets. It is not meant to be either an all-inclusive enumeration, nor is it to be taken as an endorsement of these products as the {open_quotes}best{close_quotes} of their class. Rather, it has been found, through extensive use that these few packages were generally capable of satisfying his particular needs for both statistical analysis and graphical data display. In the limited space available, the focus will be on some of the more novel features found to be of value.

  8. Development of Data Acquisition Console and Web Server Using Raspberry Pi for Marine Platforms

    Directory of Open Access Journals (Sweden)

    Aditya Thapliyal

    2016-10-01

    Full Text Available Marine vessels in today’s age are fitted with a number of state of the art systems required for their smooth operation. The compartments which house such systems along with the restricted compartments onboard ships such as the ships galley, dry rations store, cold rooms, battery compartments etc are required to be monitored on real time basis for temperature, pressure, humidity for detecting various hazards like fire, flooding etc. In addition, military platforms also need to monitor compartments such as the armory and magazines to avoid damage to munitions and prevent unauthorized access. The present project aims to develop a proof of concept prototype real time parameter monitoring and motion detection system for critical/restricted compartments on marine platforms with data logging capability. Various sensors forming a sensor suite have been interfaced to the Raspberry Pi board, forming the Data Acquisition Console which is the nodal control center. As most marine vessels are fitted with a shipboard Local Area Network, the project utilizes this existing network for relaying data. The console is placed in the compartment where parameters are to be monitored and the measured data is acquired and transferred via wireless (using Access Points (APs operating on Wi-Fi/ 802.11 network or via wired connectivity with the nearest switch and be accessed by concerned personnel at various nodes/ computer on the . The performance of the DAC was successfully ascertained by comparison of sensor performance with other independent sensor readings. The measurement errors were found to be within the permissible accuracy limits of the sensors. Motion detection was achieved by using PIR motion The probability of detection (Pd for the motion sensor was calculated by conducing iterative motion tests with favorable results. Data is displayed in a web-based dashboard Graphical User Interface. Further, provision has also been made to set visual alarms whenever a

  9. 基于嵌入式web Server的远程数据采集系统的网络实现%Realizes Yu Pengming based on the embedded web Server long range data gathering

    Institute of Scientific and Technical Information of China (English)

    俞鹏明; 裴华刚

    2006-01-01

    研究嵌入式系统作为WEB SERVER,提供远程客户访问本地采集的数据.系统平台采用ARM处理器和嵌入式uClinux操作系统,通过对系统的分析,选择合适的TCP/IP协议来实现远程数据采集系统的服务端功能.

  10. QuatIdent: a web server for identifying protein quaternary structural attribute by fusing functional domain and sequential evolution information.

    Science.gov (United States)

    Shen, Hong-Bin; Chou, Kuo-Chen

    2009-03-01

    Many proteins exist in vivo as oligomers with various different quaternary structural attributes rather than as single individual chains. They are the structural bases of various marvelous biological functions such as cooperative effects, allosteric mechanism, and ion-channel gating. Therefore, with the avalanche of protein sequences generated in the postgenomic era, it is very important for both basic research and drug discovery to identify their quaternary structural attributes in a timely manner. In view of this, a powerful ensemble identifier, called QuatIdent, is developed by fusing the functional domain and sequential evolution information. QuatIdent is a 2-layer predictor. The 1st layer is for identifying a query protein as belonging to which one of the following 10 main quaternary structural attributes: (1) monomer, (2) dimer, (3) trimer, (4) tetramer, (5) pentamer, (6) hexamer, (7) heptamer, (8) octamer, (9) decamer, and (10) dodecamer. If the result thus obtained turns out to be anything but monomer, the process will be automatically continued to further identify it as belonging to a homo-oligomer or hetero-oligomer. The overall success rate by QuatIdent for the 1st layer identification was 71.1% and that for the 2nd layer ranged from 84 to 96%. These rates were derived by the jackknife cross-validation tests on the stringent benchmark data sets where none of proteins has > or =60% pairwise sequence identity to any other in a same subset. QuatIdent is freely accessible to the public as a web server via the site at http://www.csbio.sjtu.edu.cn/bioinf/Quaternary/ , by which one can get the desired 2-level results for a query protein sequence in around 25 seconds. The longer the sequence is, the more time that is needed.

  11. Onto-CC: a web server for identifying Gene Ontology conceptual clusters

    Science.gov (United States)

    Romero-Zaliz, R.; del Val, C.; Cobb, J. P.; Zwir, I.

    2008-01-01

    The Gene Ontology (GO) vocabulary has been extensively explored to analyze the functions of coexpressed genes. However, despite its extended use in Biology and Medical Sciences, there are still high levels of uncertainty about which ontology (i.e. Molecular Process, Cellular Component or Molecular Function) should be used, and at which level of specificity. Moreover, the GO database can contain incomplete information resulting from human annotations, or highly influenced by the available knowledge about a specific branch in an ontology. In spite of these drawbacks, there is a trend to ignore these problems and even use GO terms to conduct searches of gene expression profiles (i.e. expression + GO) instead of more cautious approaches that just consider them as an independent source of validation (i.e. expression versus GO). Consequently, propagating the uncertainty and producing biased analysis of the required gene grouping hypotheses. We proposed a web tool, Onto-CC, as an automatic method specially suited for independent explanation/validation of gene grouping hypotheses (e.g. coexpressed genes) based on GO clusters (i.e. expression versus GO). Onto-CC approach reduces the uncertainty of the queries by identifying optimal conceptual clusters that combine terms from different ontologies simultaneously, as well as terms defined at different levels of specificity in the GO hierarchy. To do so, we implemented the EMO-CC methodology to find clusters in structural databases [GO Directed acyclic Graph (DAG) tree], inspired on Conceptual Clustering algorithms. This approach allows the management of optimal cluster sets as potential parallel hypotheses, guided by multiobjective/multimodal optimization techniques. Therefore, we can generate alternative and, still, optimal explanations of queries that can provide new insights for a given problem. Onto-CC has been successfully used to test different medical and biological hypotheses including the explanation and prediction of

  12. Simulation Modeling on the Macintosh using STELLA.

    Science.gov (United States)

    Costanza, Robert

    1987-01-01

    Describes a new software package for the Apple Macintosh computer which can be used to create elaborate simulation models in a fraction of the time usually required without using a programming language. Illustrates the use of the software which relates to water usage. (TW)

  13. The deployment of a World Wide Web (W3) based medical information system.

    Science.gov (United States)

    Willard, K E; Hallgren, J H; Sielaff, B; Connelly, D P

    1995-01-01

    The development of Web technologies has revolutionized information dissemination on the Internet. The University of Minnesota Hospital and Clinic's Web Clinical Information System (CIS) demonstrates the use of the Web as an infrastructure for deploying a medical information system at a fraction of the developmental cost of more traditional client server systems. This Web CIS has been deployed since December 1994. It makes available laboratory results, including a radically improved clinical microbiology reporting system, ad hoc laboratory order entry, and an embedded expert system protocol laboratory ordering system. It provides these services to any physician or patient care area with TCP (or SLIP/PPP) connection to our hospital network backbone, whether the client computer is running MS Windows, the Macintosh OS, or X-Windows. A formal evaluation of one of this systems subcomponents, the display of clinical microbiology information, demonstrated a significant savings in clinician time (43% p vs 15 p < .01).

  14. Web Instant Messaging System Based on Server Push Technology and php%基于php和服务器推技术的Web即时聊天系统

    Institute of Scientific and Technical Information of China (English)

    王振兴; 黄静

    2012-01-01

    基于http协议应用于Web端,实现一个浏览器无关的、便于移植的、高性能的Web即时聊天系统.系统使用服务器推技术中的ajax长轮询模型构建http通讯模型,利用开源LAMP架构搭建服务器端程序,并使用XML文件系统存储即时聊天内容,前端使用javascript的jquery框架实现与浏览器无关的ajax前端程序.提供包括文本表情模式的聊天,便于整合到社交类型的网站中.项目实践表明,基于php和服务器推技术的Web即时聊天系统稳定性高,具有一定的使用价值.%Based on the http protocol used in the Web side, it realizes a not browser based, easy to transplant, high-performance real-time web chat system. System uses the ajax long polling model of the server push technique to build the http communication, using the open source LAMP architecture to build server-side programs, and use the xml file system to store real-time chat content, the front using the javascript jquery framework to achieve and browse device-independent ajax front-end program. Text chat and expressions, and ease of integration into the sns type of site. Project practice shows that the web php-based server push model real time chat system stability, it has a certain value.

  15. 基于GEP的web服务器安全防护技术研究%Research of Web Server Security Technology Based on GEP

    Institute of Scientific and Technical Information of China (English)

    龙珑; 宁葵

    2011-01-01

    目前网络安全问题日益严重,由于互联网开放性和通信协议的安全缺陷等原因使web服务器面临着越来越多的安全威胁.基因表达式编程( GEP)融合了遗传算法和遗传编程的优点,基于GEP的web服务器安全防护技术开发小组将GEP人工智能技术引入到web服务器,建立了一个多层次的安全防御模型.利用GEP算法的动态学习功能不断地提高安全防御能力,基于GEP的web服务器安全防护技术小组最终目标就是希望把web服务器的安全性提升到一个较为理想的状态.%Nowadays there is a growing concern about the problem of internet security. As the internet and communication protocols open security holes and other reasons,web server is more and more confronted with security threats. Gene Expression Programming (GEP) combines genetic algorithms and genetic programming advantages, GEP artificial intelligence technology will be used for the web server to establish a multi-layered security defense model. Using dynanic learning function in GEP algorithm can improve the security and defense capabilities, the way can better improve the web server security.

  16. NExT server

    CERN Multimedia

    1989-01-01

    The first website at CERN - and in the world - was dedicated to the World Wide Web project itself and was hosted on Berners-Lee's NeXT computer. The website described the basic features of the web; how to access other people's documents and how to set up your own server. This NeXT machine - the original web server - is still at CERN. As part of the project to restore the first website, in 2013 CERN reinstated the world's first website to its original address.

  17. Performance enhancement of a web-based picture archiving and communication system using commercial off-the-shelf server clusters.

    Science.gov (United States)

    Liu, Yan-Lin; Shih, Cheng-Ting; Chang, Yuan-Jen; Chang, Shu-Jun; Wu, Jay

    2014-01-01

    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.

  18. iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition.

    Directory of Open Access Journals (Sweden)

    Yongchun Zuo

    Full Text Available Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design.

  19. SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort.

    Science.gov (United States)

    Rueda, Manuel; Torkamani, Ali

    2017-08-18

    Whole genome and exome sequencing usually include reads containing mitochondrial DNA (mtDNA). Yet, state-of-the-art pipelines and services for human nuclear genome variant calling and annotation do not handle mitochondrial genome data appropriately. As a consequence, any researcher desiring to add mtDNA variant analysis to their investigations is forced to explore the literature for mtDNA pipelines, evaluate them, and implement their own instance of the desired tool. This task is far from trivial, and can be prohibitive for non-bioinformaticians. We have developed SG-ADVISER mtDNA, a web server to facilitate the analysis and interpretation of mtDNA genomic data coming from next generation sequencing (NGS) experiments. The server was built in the context of our SG-ADVISER framework and on top of the MtoolBox platform (Calabrese et al., Bioinformatics 30(21):3115-3117, 2014), and includes most of its functionalities (i.e., assembly of mitochondrial genomes, heteroplasmic fractions, haplogroup assignment, functional and prioritization analysis of mitochondrial variants) as well as a back-end and a front-end interface. The server has been tested with unpublished data from 200 individuals of a healthy aging cohort (Erikson et al., Cell 165(4):1002-1011, 2016) and their data is made publicly available here along with a preliminary analysis of the variants. We observed that individuals over ~90 years old carried low levels of heteroplasmic variants in their genomes. SG-ADVISER mtDNA is a fast and functional tool that allows for variant calling and annotation of human mtDNA data coming from NGS experiments. The server was built with simplicity in mind, and builds on our own experience in interpreting mtDNA variants in the context of sudden death and rare diseases. Our objective is to provide an interface for non-bioinformaticians aiming to acquire (or contrast) mtDNA annotations via MToolBox. SG-ADVISER web server is freely available to all users at https://genomics.scripps.edu/mtdna .

  20. Web server security and protect's new methods%一种Web服务器安全机制的实现方法

    Institute of Scientific and Technical Information of China (English)

    陈伟东; 刘刚; 徐峥; 耿坤英

    2012-01-01

    With the development of Internet, The attacks to Web site incidents continue to occur, the existing firewall, IDS and other equipment can not effectively prevent intruders tampering website pages and other files, steal important information such attacks. This paper presents a more complete Web server security mechanism, the core layer of assurance from the Web site pages tampering by hackers, malicious code in the system will not wantonly attack. The mechanism of reconstruction of the operating system kernel level privileges to access control model, operating system files, registry, process, and network resources such as the use of white list rules, and using a combination of multiple mechanisms to increase resistance to attack Web servers.%针对Web网站点的入侵事件不断发生,现有的防火墙、IDS等设备都不能有效防止入侵者篡改网站中的网页、盗取重要信息等攻击,提出了Web服务器安全较完备机制,从核心层保证Web站点中的网页不会被黑客篡改,恶意代码在系统中不会肆意发作。该机制重构了操作系统核心层权限访问控制模型,对操作系统文件、注册表、进程和网络等资源采用白名单规则,并采用多机制相结合的方式提高Web服务器的抗攻击能力。

  1. 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--

  2. GPCR-GIA: a web-server for identifying G-protein coupled receptors and their families with grey incidence analysis.

    Science.gov (United States)

    Lin, Wei-Zhong; Xiao, Xuan; Chou, Kuo-Chen

    2009-11-01

    G-protein-coupled receptors (GPCRs) play fundamental roles in regulating various physiological processes as well as the activity of virtually all cells. Different GPCR families are responsible for different functions. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop an automated method to address the two problems: given the sequence of a query protein, can we identify whether it is a GPCR? If it is, what family class does it belong to? Here, a two-layer ensemble classifier called GPCR-GIA was proposed by introducing a novel scale called 'grey incident degree'. The overall success rate by GPCR-GIA in identifying GPCR and non-GPCR was about 95%, and that in identifying the GPCRs among their nine family classes was about 80%. These rates were obtained by the jackknife cross-validation tests on the stringent benchmark data sets where none of the proteins has > or = 50% pairwise sequence identity to any other in a same class. Moreover, a user-friendly web-server was established at http://218.65.61.89:8080/bioinfo/GPCR-GIA. For user's convenience, a step-by-step guide on how to use the GPCR-GIA web server is provided. Generally speaking, one can get the desired two-level results in around 10 s for a query protein sequence of 300-400 amino acids; the longer the sequence is, the more time that is needed.

  3. 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.

  4. LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design.

    Science.gov (United States)

    Munteanu, Cristian R; Pedreira, Nieves; Dorado, Julián; Pazos, Alejandro; Pérez-Montoto, Lázaro G; Ubeira, Florencio M; González-Díaz, Humberto

    2014-04-01

    Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non-annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH-INSIDE software to calculate the Markov-Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure-Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this predictor in the web server named LECTINPred, freely available at http://bio-aims.udc.es/LECTINPred.php. This web server showed the following goodness-of-fit statistics: Sensitivity=96.7 % (for Ls), Specificity=87.6 % (non-active proteins), and Accuracy=92.5 % (for all proteins), considering altogether both the training and external prediction series. In mode 2, users can carry out an automatic retrieval of protein structures from PDB. We illustrated the use of this server, in operation mode 1, performing a data mining of PDB. We predicted Ls scores for +2000 proteins with unknown function and selected the top-scored ones as possible lectins. In operation mode 2, LECTINPred can also upload 3D structural models generated with structure-prediction tools like LOMETS or PHYRE2. The new Ls are expected to be of relevance as cancer biomarkers or useful in parasite vaccine design.

  5. Technique of Active Server Page Access to Web Database%ASP技术访问WEB数据库

    Institute of Scientific and Technical Information of China (English)

    洪运锡

    2006-01-01

    作者阐述了Windows操作系统中ⅡS(Internet Information Server)内含的ASP(Active Server Page)和ADO(ActiveX Data Objects)技术的结构和特点,总结了采用ASP技术访问Web数据库的步骤.ASP编写前台动态网页,它采用封装对象,程序调用对象的技术,简化编程,加强程序间合作,通过ADO访问后台WEB数据库.

  6. 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.

  7. Macintosh Troubleshooting Pocket Guide for Mac OS

    CERN Document Server

    Lerner, David; Corporation, Tekserve

    2009-01-01

    The Macintosh Troubleshooting Pocket Guide covers the most common user hardware and software trouble. It's not just a book for Mac OS X (although it includes tips for OS X and Jaguar), it's for anyone who owns a Mac of any type-- there are software tips going back as far as OS 6. This slim guide distills the answers to the urgent questions that Tekserve's employee's answer every week into a handy guide that fits in your back pocket or alongside your keyboard.

  8. Office 2008 for Macintosh The Missing Manual

    CERN Document Server

    Elferdink, Jim

    2008-01-01

    Though Office 2008 has been improved to take advantage of the latest Mac OS X features, you don't get a single page of printed instructions to guide you through the changes. Office 2008 for Macintosh: The Missing Manual gives you the friendly and thorough introduction you need, whether you're a beginner who can't do more than point and click, or a power user who's ready for a few advanced techniques.

  9. 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

  10. 基于ArcGIS Server的林业Web GIS系统的实现%Construction of Forestry Web Geographic Information System Based on ArcGIS Server

    Institute of Scientific and Technical Information of China (English)

    钱发斌; 邓喜庆

    2015-01-01

    在现有研究的基础上,利用ArcGIS Server结合C#语言构建林业Web GIS系统,加快国内基于ArcGIS Server技术的林业Web GIS研究,丰富林业信息化建设理论内容.文中概述了ArcGIS Server理论,阐述系统功能模块设计、集成要求、开发环境以及数据库的准备与设计,系统的实现,通过登录ArcGIS Server Manager来发布地图服务,并讨论了应用效果.

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

    Science.gov (United States)

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

    2017-09-01

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

  12. 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

    Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differe......Background The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis...... from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script. The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evalution results for the first three...

  13. The Erection of a Web Server and Security Configuration%架设Web服务器及安全配置

    Institute of Scientific and Technical Information of China (English)

    黄少娥

    2012-01-01

    目的:在Windows Server 2003下架设Web服务器.方法:建立Web站点以及网站性能配置,保证Web服务器的数据信息安全有效.结论:缓解web服务器风险,web服务器更安全地为医院的医疗保健信息传播工作服务.

  14. Server-side Dynamic Web Page Technique: JSP+Servlet%服务器端动态网页技术--JSP+Servlet

    Institute of Scientific and Technical Information of China (English)

    扬黎明; 董传良; 董玮文

    2001-01-01

    介绍了一种新的、根植于Java跨平台特性的服务器端新技术:Servlet+JSP.它提供了一种灵活、方便,通用的方式来创建动态网页;将HTML编码与Web页面的业务逻辑有效分离;可以高效地通过JDBC与数据库通信.在上海旅委网站建设中采用了该技术进行开发.%he topic introduces a new server-side technique: Servlet and JSP based on the cross-platform characteristic of Java. The technique provides a convenient, agility and universal method to create dynamic Web page, separates the program coding of HTML from the business logic of Web page, and uses JDBC to communicate with database effectively. In the topic we also explain the way to design the Servlet and JSP through the building of the Web site of Shanghai Tour Business Administration Committee.

  15. 嵌入式Web Server在Cable Modem中的设计与实现%Design and Realization of Embedded Web Server in Cable Modem

    Institute of Scientific and Technical Information of China (English)

    张元国

    2009-01-01

    分析了Web Server与浏览器的基本原理,提出了嵌入式Web Server的开发原则、体系结构及基本原理,重点分析了在嵌入式产品Cable Modem中,设计嵌入式Web Server的基本要求及其具体实现.

  16. WebLogic中数据库连接池配置%Design on JDBC Connect Pool in Weblogic Server

    Institute of Scientific and Technical Information of China (English)

    郭俊; 陈梅容; 朱兵章

    2004-01-01

    BEA WebLogic是新一代的用于Web应用的Java应用服务器,连接池模式提供了新的数据库连接方式的解决方案.本文介绍了在BEA WebLogic Server中设置数据库连接池的技术.

  17. Office X for Macintosh the missing manual

    CERN Document Server

    Barber, Nan; Reynolds, David

    2002-01-01

    Mac OS X, Apple's super-advanced, Unix-based operating system, offers every desirable system-software feature known to humans. But without a compatible software library, the Mac of the future was doomed. Microsoft Office X for Macintosh is exactly the software suite most Mac fans were waiting for. Its four programs--Word, Excel, PowerPoint, and Entourage--have been completely overhauled to take advantage of the stunning looks and rock-like stability of Mac OS X. But this magnificent package comes without a single page of printed instructions. Fortunately, Pogue Press/O'Reilly is once again

  18. 一种实用的嵌入式Web服务器设计%Design of a Practical Embedded Web Server

    Institute of Scientific and Technical Information of China (English)

    李英明; 闫志辉; 周水斌

    2012-01-01

    数字化变电站越来越多地采用以太网技术,针对各种保护和控制IED(Integrated Drive Electronics)的参数配置以及状态监测问题,本文通过对Linux平台上的BOA服务器和CGIC的源码进行研究和修改,设计了一种实用的嵌入式web服务器。它可方便地在支持TCP/IP协议的非Linux的嵌入式系统上运行,在不影响IED原有功能的前提下对用户提供Web服务,同时提出了一种适合嵌入式系统使用的访问权限认证和对Web页面的管理及动态生成机制,并支持Web方式下文件的上传与下载。它为变电站现场嵌入式IED的远端访问与控制提供了一种新的思路和方法。%The digital substation using more and more Ethernet technologies, With the problems of all kinds of protection and of controling IED's configuration and monitoring condition, the paper researches and modifies BOA server and CGIC's source code based on Linux, designs an embedded Web server . It can operate convinently in non-Linux embedded system which supports the TCP/IP proto col. The design doesn't affect original function of IED and can provide Web service to users. The paper proposes a certification for access authority and manages the Web page and dynamic generation. It also supports the upload and download of the file based on Web. For remote access and control of the substation site embedded IED, it proposes a new idea and method.

  19. PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

    Directory of Open Access Journals (Sweden)

    Rooman Marianne

    2011-05-01

    Full Text Available Abstract Background The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level. Results PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers. It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability. Conclusion The

  20. 建立安全可靠的Web服务器%Building a Safety's and Credible WEB Server

    Institute of Scientific and Technical Information of China (English)

    姜大为

    2003-01-01

    IIS(Internet Information Server)作为当今流行的Web服务器之一,提供了强大的Internet和Intranet服务功能.如何加强IIS的安全机制,建立高安全性能的可靠的Web服务器,已成为网络管理的重要组成部分.本文就如何利用IIS建立高安全性的Web服务器作了探讨.

  1. Remote Control of Ecological House Based on Embedded Web Server%基于嵌入式Web服务器的生态住宅远程控制

    Institute of Scientific and Technical Information of China (English)

    张振江; 于军琪

    2012-01-01

    针对生态住宅的发展趋势,将无线通信技术、嵌入式技术和Internet三者结合起来应用于生态住宅,设计了基于嵌入式Web服务器的生态住宅远程控制系统方案。运用嵌入式Web网关和ZigBee无线网络的混合通信结构。使用户可通过浏览器远程控制家用设备,具有广阔的应用前景。%According to the development trend of ecological house, took the combination of wireless communication technology, embedded technology and internet technology used in ecological house, designed a scheme of the remote control system of ecological house based on embedded web server, used a mixed communication structure of the embedded web gateways and ZigBee wireless network to allow the user to remotely control home appliances through a browser device. It has wide application prospects.

  2. Application of HTTP Multi Hyperlink in Web Servers%HTTP多路超链接在Web SerVers中的应用

    Institute of Scientific and Technical Information of China (English)

    周刚; 朱晴波; 陈道蓄; 谢立

    2001-01-01

    频繁的WWW访问要求有有效的Web Servers组织方式.针对HTIP超链接不能进行负载平衡的缺点,提出了HTTP多路超链接,并用HTIP超链接对HTTP多路超链接进行了模拟.最后将HTTP多路超链接引入Web Servers设计.

  3. 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.

  4. 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

  5. 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.

  6. Response time accuracy in Apple Macintosh computers.

    Science.gov (United States)

    Neath, Ian; Earle, Avery; Hallett, Darcy; Surprenant, Aimée M

    2011-06-01

    The accuracy and variability of response times (RTs) collected on stock Apple Macintosh computers using USB keyboards was assessed. A photodiode detected a change in the screen's luminosity and triggered a solenoid that pressed a key on the keyboard. The RTs collected in this way were reliable, but could be as much as 100 ms too long. The standard deviation of the measured RTs varied between 2.5 and 10 ms, and the distributions approximated a normal distribution. Surprisingly, two recent Apple-branded USB keyboards differed in their accuracy by as much as 20 ms. The most accurate RTs were collected when an external CRT was used to display the stimuli and Psychtoolbox was able to synchronize presentation with the screen refresh. We conclude that RTs collected on stock iMacs can detect a difference as small as 5-10 ms under realistic conditions, and this dictates which types of research should or should not use these systems.

  7. Design and Implementation of Embedded Web Server System Based on SOPC%基于SOPC的嵌入式Web服务器系统设计与实现

    Institute of Scientific and Technical Information of China (English)

    陈川; 李雪梅; 郭勇

    2011-01-01

    The embedded Web server system is built with the EDK development tools of the FPGA hardware platform of Xilinx company. Based on the HTTP protocol, the TCP/IP socket programming technology is adopted for network communications between PC computer and target, using a high-speed image acquisition system. The equipment's ethemet port is used for the Web server remote access. Through the control commands for input, the system displays the image data, to realize the monitoring and controlling of remote site image data and device activity. In this paper, the functions of the system, the hardware design and the software design based on the Xilkernel Operation System (OS), LwIP protocol stack, XilMFS File System (FS), and socket network programming are discussed. The host end is tested to achieve browsing stored in the embedded Web server in the static page, at the same time, according to the browser input parameters, the indicator's on and off are used to control functions according to the input data. The image data stored in SDRAM could be browsed and the control indicator lamp could be on and off, according to the design.%以Minx公司的现场可编程门阵列(FPGA)作为硬件平台.借助其EDK开发工具.搭建Web服务器运行系统.基于HTTP协议,采用TCP/IP套接字编程技术,实现个人计算机与目标板的网络通信,该系统应用在高速图像采集系统中,经过设备的网口远程访问嵌入式Web服务器,通过翰入控制命令.以及将系统相应的图像数据显示在上位机的Web监控页面上,实现监控远端现场图像数据和设备工作状态.本文对系统功能,系统的硬件设计、软件设计,以及Xilkemel操作系统、LWIP协议栈、XiIMFS文件系统,Socket网络编程等进行了介绍.经过试验测试在主机端实现浏览存储在嵌入式Web服务器中的静态页面;同时根据浏览器中输入参数,控制指示灯的熄灭;并浏览存储在SDRAM中的图像数据.设计达到预期的效果.

  8. NL MIND-BEST: a web server for ligands and proteins discovery--theoretic-experimental study of proteins of Giardia lamblia and new compounds active against Plasmodium falciparum.

    Science.gov (United States)

    González-Díaz, Humberto; Prado-Prado, Francisco; Sobarzo-Sánchez, Eduardo; Haddad, Mohamed; Maurel Chevalley, Séverine; Valentin, Alexis; Quetin-Leclercq, Joëlle; Dea-Ayuela, María A; Teresa Gomez-Muños, María; Munteanu, Cristian R; José Torres-Labandeira, Juan; García-Mera, Xerardo; Tapia, Ricardo A; Ubeira, Florencio M

    2011-05-07

    There are many protein ligands and/or drugs described with very different affinity to a large number of target proteins or receptors. In this work, we selected Ligands or Drug-target pairs (DTPs/nDTPs) of drugs with high affinity/non-affinity for different targets. Quantitative Structure-Activity Relationships (QSAR) models become a very useful tool in this context to substantially reduce time and resources consuming experiments. Unfortunately most QSAR models predict activity against only one protein target and/or have not been implemented in the form of public web server freely accessible online to the scientific community. To solve this problem, we developed here a multi-target QSAR (mt-QSAR) classifier using the MARCH-INSIDE technique to calculate structural parameters of drug and target plus one Artificial Neuronal Network (ANN) to seek the model. The best ANN model found is a Multi-Layer Perceptron (MLP) with profile MLP 20:20-15-1:1. This MLP classifies correctly 611 out of 678 DTPs (sensitivity=90.12%) and 3083 out of 3408 nDTPs (specificity=90.46%), corresponding to training accuracy=90.41%. The validation of the model was carried out by means of external predicting series. The model classifies correctly 310 out of 338 DTPs (sensitivity=91.72%) and 1527 out of 1674 nDTP (specificity=91.22%) in validation series, corresponding to total accuracy=91.30% for validation series (predictability). This model favorably compares with other ANN models developed in this work and Machine Learning classifiers published before to address the same problem in different aspects. We implemented the present model at web portal Bio-AIMS in the form of an online server called: Non-Linear MARCH-INSIDE Nested Drug-Bank Exploration & Screening Tool (NL MIND-BEST), which is located at URL: http://miaja.tic.udc.es/Bio-AIMS/NL-MIND-BEST.php. This online tool is based on PHP/HTML/Python and MARCH-INSIDE routines. Finally we illustrated two practical uses of this server with two

  9. 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

    2016-07-08

    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/.

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

    Science.gov (United States)

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

    2010-12-01

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

  11. 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。

  12. 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.

  13. 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.

  14. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking.

    Directory of Open Access Journals (Sweden)

    Lei Hua

    Full Text Available RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.

  15. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    Science.gov (United States)

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.

  16. THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps.

    Science.gov (United States)

    Cheema, Jitender; Ellis, T H Noel; Dicks, Jo

    2010-07-01

    The estimation of genetic linkage maps is a key component in plant and animal research, providing both an indication of the genetic structure of an organism and a mechanism for identifying candidate genes associated with traits of interest. Because of this importance, several computational solutions to genetic map estimation exist, mostly implemented as stand-alone software packages. However, the estimation process is often largely hidden from the user. Consequently, problems such as a program crashing may occur that leave a user baffled. THREaD Mapper Studio (http://cbr.jic.ac.uk/threadmapper) is a new web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers. The rationale behind the web site is to make the estimation process as transparent and robust as possible, while also allowing users to use their expert knowledge during analysis. Indeed, the 3D visual nature of the tool allows users to spot features in a data set, such as outlying markers and potential structural rearrangements that could cause problems with the estimation procedure and to account for them in their analysis. Furthermore, THREaD Mapper Studio facilitates the visual comparison of genetic map solutions from third party software, aiding users in developing robust solutions for their data sets.

  17. 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

  18. 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

  19. MISS-Prot: web server for self/non-self discrimination of protein residue networks in parasites; theory and experiments in Fasciola peptides and Anisakis allergens.

    Science.gov (United States)

    González-Díaz, Humberto; Muíño, Laura; Anadón, Ana M; Romaris, Fernanda; Prado-Prado, Francisco J; Munteanu, Cristian R; Dorado, Julián; Sierra, Alejandro Pazos; Mezo, Mercedes; González-Warleta, Marta; Gárate, Teresa; Ubeira, Florencio M

    2011-06-01

    Infections caused by human parasites (HPs) affect the poorest 500 million people worldwide but chemotherapy has become expensive, toxic, and/or less effective due to drug resistance. On the other hand, many 3D structures in Protein Data Bank (PDB) remain without function annotation. We need theoretical models to quickly predict biologically relevant Parasite Self Proteins (PSP), which are expressed differentially in a given parasite and are dissimilar to proteins expressed in other parasites and have a high probability to become new vaccines (unique sequence) or drug targets (unique 3D structure). We present herein a model for PSPs in eight different HPs (Ascaris, Entamoeba, Fasciola, Giardia, Leishmania, Plasmodium, Trypanosoma, and Toxoplasma) with 90% accuracy for 15 341 training and validation cases. The model combines protein residue networks, Markov Chain Models (MCM) and Artificial Neural Networks (ANN). The input parameters are the spectral moments of the Markov transition matrix for electrostatic interactions associated with the protein residue complex network calculated with the MARCH-INSIDE software. We implemented this model in a new web-server called MISS-Prot (MARCH-INSIDE Scores for Self-Proteins). MISS-Prot was programmed using PHP/HTML/Python and MARCH-INSIDE routines and is freely available at: . This server is easy to use by non-experts in Bioinformatics who can carry out automatic online upload and prediction with 3D structures deposited at PDB (mode 1). We can also study outcomes of Peptide Mass Fingerprinting (PMFs) and MS/MS for query proteins with unknown 3D structures (mode 2). We illustrated the use of MISS-Prot in experimental and/or theoretical studies of peptides from Fasciola hepatica cathepsin proteases or present on 10 Anisakis simplex allergens (Ani s 1 to Ani s 10). In doing so, we combined electrophoresis (1DE), MALDI-TOF Mass Spectroscopy, and MASCOT to seek sequences, Molecular Mechanics + Molecular Dynamics (MM/MD) to

  20. A new tool for supervised classification of satellite images available on web servers: Google Maps as a case study

    Science.gov (United States)

    García-Flores, Agustín.; Paz-Gallardo, Abel; Plaza, Antonio; Li, Jun

    2016-10-01

    This paper describes a new web platform dedicated to the classification of satellite images called Hypergim. The current implementation of this platform enables users to perform classification of satellite images from any part of the world thanks to the worldwide maps provided by Google Maps. To perform this classification, Hypergim uses unsupervised algorithms like Isodata and K-means. Here, we present an extension of the original platform in which we adapt Hypergim in order to use supervised algorithms to improve the classification results. This involves a significant modification of the user interface, providing the user with a way to obtain samples of classes present in the images to use in the training phase of the classification process. Another main goal of this development is to improve the runtime of the image classification process. To achieve this goal, we use a parallel implementation of the Random Forest classification algorithm. This implementation is a modification of the well-known CURFIL software package. The use of this type of algorithms to perform image classification is widespread today thanks to its precision and ease of training. The actual implementation of Random Forest was developed using CUDA platform, which enables us to exploit the potential of several models of NVIDIA graphics processing units using them to execute general purpose computing tasks as image classification algorithms. As well as CUDA, we use other parallel libraries as Intel Boost, taking advantage of the multithreading capabilities of modern CPUs. To ensure the best possible results, the platform is deployed in a cluster of commodity graphics processing units (GPUs), so that multiple users can use the tool in a concurrent way. The experimental results indicate that this new algorithm widely outperform the previous unsupervised algorithms implemented in Hypergim, both in runtime as well as precision of the actual classification of the images.

  1. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM.

    Science.gov (United States)

    Shen, Hong-Bin; Chou, Kuo-Chen

    2007-11-01

    The life processes of an eukaryotic cell are guided by its nucleus. In addition to the genetic material, the cellular nucleus contains many proteins located at its different compartments, called subnuclear locations. Information of their localization in a nucleus is indispensable for the in-depth study of system biology because, in addition to helping determine their functions, it can provide illuminative insights of how and in what kind of microenvironments these subnuclear proteins are interacting with each other and with other molecules. Facing the deluge of protein sequences generated in the post-genomic age, we are challenged to develop an automated method for fast and effectively annotating the subnuclear locations of numerous newly found nuclear protein sequences. In view of this, a new classifier, called Nuc-PLoc, has been developed that can be used to identify nuclear proteins among the following nine subnuclear locations: (1) chromatin, (2) heterochromatin, (3) nuclear envelope, (4) nuclear matrix, (5) nuclear pore complex, (6) nuclear speckle, (7) nucleolus, (8) nucleoplasm and (9) nuclear promyelocytic leukaemia (PML) body. Nuc-PLoc is featured by an ensemble classifier formed by fusing the evolution information of a protein and its pseudo-amino acid composition. The overall jackknife cross-validation accuracy obtained by Nuc-PLoc is significantly higher than those by the existing methods on the same benchmark data set through the same testing procedure. As a user-friendly web-server, Nuc-PLoc is freely accessible to the public at http://chou.med.harvard.edu/bioinf/Nuc-PLoc.

  2. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM.

    Science.gov (United States)

    Chou, Kuo-Chen; Shen, Hong-Bin

    2007-08-24

    Given an uncharacterized protein sequence, how can we identify whether it is a membrane protein or not? If it is, which membrane protein type it belongs to? These questions are important because they are closely relevant to the biological function of the query protein and to its interaction process with other molecules in a biological system. Particularly, with the avalanche of protein sequences generated in the Post-Genomic Age and the relatively much slower progress in using biochemical experiments to determine their functions, it is highly desired to develop an automated method that can be used to help address these questions. In this study, a 2-layer predictor, called MemType-2L, has been developed: the 1st layer prediction engine is to identify a query protein as membrane or non-membrane; if it is a membrane protein, the process will be automatically continued with the 2nd-layer prediction engine to further identify its type among the following eight categories: (1) type I, (2) type II, (3) type III, (4) type IV, (5) multipass, (6) lipid-chain-anchored, (7) GPI-anchored, and (8) peripheral. MemType-2L is featured by incorporating the evolution information through representing the protein samples with the Pse-PSSM (Pseudo Position-Specific Score Matrix) vectors, and by containing an ensemble classifier formed by fusing many powerful individual OET-KNN (Optimized Evidence-Theoretic K-Nearest Neighbor) classifiers. The success rates obtained by MemType-2L on a new-constructed stringent dataset by both the jackknife test and the independent dataset test are quite high, indicating that MemType-2L may become a very useful high throughput tool. As a Web server, MemType-2L is freely accessible to the public at http://chou.med.harvard.edu/bioinf/MemType.

  3. Development of Water Turbine Regulating System Based on Matlab Web Server%基于Web平台的远程水轮机调节仿真系统开发

    Institute of Scientific and Technical Information of China (English)

    楚清河; 王亚龙; 索宏伟; 牛秀博; 刘团结

    2015-01-01

    Based on the introduction of Matlab Web Server technology,the performance of M files can be easier by using Simulink models. Taking turbine regulating system as an example,the establishment of the network simulation platform for turbine regulating system presented the Matlab web's development and application process. Without installing Matlab software,the costumers just input the data on the website, the data finally would be presented to the users in the form of analysis reports and graphical feedback through Matlab Web Server remote serv-er. The application of server could not only realize the secondary development and maintenance process of programs,but also provide conven-ience for remote training,teaching and other offers in power plant.%在介绍Matlab Web Server技术的基础上,提出利用M文件调用Simulink模型关键技术,降低了M文件编译难度。以水轮机调节系统为例,建立水轮机调节系统网络仿真平台,详细介绍了Matlab Web程序开发及应用过程。用户无需安装Matlab软件,只需通过浏览器手动输入仿真参数,提交给Matlab Web Server远程服务器,利用Matlab强大的数据处理功能,即可实现水轮机调节系统参数改变、不同工况、不同调节方式等仿真过程,最终以网页形式将计算结果和图形反馈至客户端。只需通过服务器端即可实现应用程序的二次开发及维护过程。

  4. 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.

  5. Creating A Model HTTP Server Program Using java

    CERN Document Server

    Veerasamy, Bala Dhandayuthapani

    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 Hypertext Transfer Protocol (HTTP). WebPages may consist of files of static or dynamic text stored within the HTTP Server's file system. Client-side scripting can make WebPages more responsive to user input once in the client browser. This paper encompasses the creation of HTTP server program using java language, which is basically supporting for HTML and JavaScript.

  6. Hamlet on the Macintosh: An Experimental Seminar That Worked.

    Science.gov (United States)

    Strange, William C.

    1987-01-01

    Describes experimental college Shakespeare seminar that used Macintosh computers and software called ELIZA and ADVENTURE to develop character dialogs and adventure games based on Hamlet's characters and plots. Programming languages are examined, particularly their relationship to metaphor, and the use of computers in humanities is discussed. (LRW)

  7. Hamlet on the Macintosh: An Experimental Seminar That Worked.

    Science.gov (United States)

    Strange, William C.

    1987-01-01

    Describes experimental college Shakespeare seminar that used Macintosh computers and software called ELIZA and ADVENTURE to develop character dialogs and adventure games based on Hamlet's characters and plots. Programming languages are examined, particularly their relationship to metaphor, and the use of computers in humanities is discussed. (LRW)

  8. MISTIC: mutual information server to infer coevolution

    DEFF Research Database (Denmark)

    Simonetti, Franco L.; Teppa, Elin; Chernomoretz, Ariel

    2013-01-01

    MISTIC (mutual information server to infer coevolution) is a web server for graphical representation of the information contained within a MSA (multiple sequence alignment) and a complete analysis tool for Mutual Information networks in protein families. The server outputs a graphical visualization...... of several information-related quantities using a circos representation. This provides an integrated view of the MSA in terms of (i) the mutual information (MI) between residue pairs, (ii) sequence conservation and (iii) the residue cumulative and proximity MI scores. Further, an interactive interface...... containing all results can be downloaded. The server is available at http://mistic.leloir.org.ar. In summary, MISTIC allows for a comprehensive, compact, visually rich view of the information contained within an MSA in a manner unique to any other publicly available web server. In particular, the use...

  9. Realization of Embedded Web Server in Smart Home Control System%嵌入式Web服务器在智能家居控制系统的实现

    Institute of Scientific and Technical Information of China (English)

    赵建华; 师振伟

    2013-01-01

    Smart home control system is the indoor household real-time control system through the computer technology,network technol-ogy and control technology. Embedded Web server plays a core role in smart home control system. The user can remotely control the household through the Web server on Internet. It mainly introduces the realization method of the Web server in the smart home control system based on the board of S3C2440. This system is based on S3C2440 and embedded Linux operating system made by Web program-ming (CGI) as the core technology,made to realize a simple network control system. The user can interact with embedded hardware through the Web browser,this system has simple principle and excellent versatility,easy to build,can be used to improve the actual pro-ject after modification and improvement.%  智能家居控制系统是通过计算机技术、网络技术以及控制技术实现的对室内家居进行实时控制的系统。嵌入式Web服务器在智能家居控制系统中具有核心控制作用,用户通过互联网登陆Web服务器对家居进行远程监控。文章主要介绍基于S3C2440进行智能家居控制系统的Web服务器实现方法,系统基于S3C2440和嵌入式Linux操作系统制作,以Web编程(CGI)为核心技术,目的是实现一个简易的网络控制系统,能够使用户通过Web浏览器和嵌入式硬件进行交互。本系统原理简单,易搭建,通用性好,经修改完善后可用于实际项目。

  10. 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....

  11. 嵌入式Web服务器远程监控系统的设计与实现%Design and Implementation of Remote Monitor and Control System Based on Embedded Web Server

    Institute of Scientific and Technical Information of China (English)

    徐叶; 袁敏; 李国军

    2013-01-01

    The rapid development of information technology and the wide application of embedded system have brought revolutionary changes to people's life. The combination of embedded system and Internet has become a trend of the future. Therefore, an embedded Web server is designed. This server uses hyper text transfer protocol and common gateway interface technology, increases database function. In the client, users can monitor local devices and admin historical data through Internet and browser remotely. The use of OPC technology achieves communication between the Web server and PLC. This monitor system can not only meet the needs of supervisory task, reduces the operation and maintenance cost, but also improves the efficiency. The system is of a very high value in use.%信息技术的高速发展和嵌入式系统的广泛应用给人们的生活带来了革命性的变化,嵌入式系统接入Internet成为未来的一个趋势.因此,本文设计一个嵌入式Web服务器,服务器端采用HTTP协议和CGI技术,增加了数据库功能,在客户端的用户可以通过Internet利用浏览器进行远程监控并且可以查看历史数据.利用OPC技术实现了Web服务器与PLC之间的数据通讯.这种监控系统不仅满足了监控任务的需要,而且有效降低了运行维护成本,提高了运行效率,具有很高的使用价值.

  12. CPU Server

    CERN Multimedia

    The CERN computer centre has hundreds of racks like these. They are over a million times more powerful than our first computer in the 1960's. This tray is a 'dual-core' server. This means it effectively has two CPUs in it (eg. two of your home computers minimised to fit into a single box). Also note the copper cooling fins, to help dissipate the heat.

  13. 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.

  14. A reaserch and implementation of embedded remote video monitoring system based on Boa web server%基于boa的嵌入式视频监控系统的研究与实现

    Institute of Scientific and Technical Information of China (English)

    翁彬彬; 徐塞虹

    2014-01-01

    This paper introduces the design and implementation of an embedded video monitoring system based on BOA web server, first expounds the overall structure and the work flow of the system,and the main function modules which will be realized, then respectively introduce the module of BOA web server and the module of PTZ control and presetmo-dule in detail, introduces the realization principle and working process of Boa web server, and how to transplant into the embedded system; introduces the design and the working process of PTZ control and preset module. The design scheme of the system integrate of the embedded technology and network technology, and it has reliable performance and perfect function, compared with the traditional video monitoring system has many advantages. It can be very good application in video monitoring and has important practical application value.%本文介绍了一种基于BOA网络服务器的嵌入式视频监控系统设计与实现,首先主要阐述了该系统的整体结构及工作流程,及其主要将要实现的功能模块,然后针对系统下两大模块BOA web 服务器模块和云台控制与预置位模块分别进行了较为详细的介绍,分别介绍了BOA网络服务器实现原理、工作流程,以及移植到嵌入式系统;云台控制与预置位模块的设计及其工作流程实现。该系统设计方案融合了嵌入式技术网络技术,功能可靠完善,性能与传统视频监控系统相比具有较大的优势,能够很好的应用在视频监控中,具有重要的实际应用价值。

  15. Analisis Performansi Layanan Kluster Server Menggunakan Penyeimbang Beban dan Virtual Box

    Directory of Open Access Journals (Sweden)

    Fajar Zuhroni

    2015-10-01

    Full Text Available Today, the growth of technology is very fast causes people more familiar with the Internet. Web servers are required to more quickly in order to serve a number of user request. Technology uses a single server is underprivileged to handle the load on the web server traffic as the number of users increases, causing the server to fail in serving the request. Technology on cluster server with load balancer is used in order to divide the load evenly so that optimize performance on a web server. Server cluster systems that are designed using six virtual machines using VirtualBox application. Six virtual machine consists of two load balancer servers, two application servers and two database servers. Definition of the system created by outlining system requirements and network topology. System design describes requirements specification of the hardware and software. Analysis and testing conducted to determine the performance of the system designed. Analysis and testing conducted to determine the performance of the system designed. Results of this research is the design of virtual servers that can serve a number of user request. Test result showed maximum ability to serve when all servers are up reach 240 connection, one of the aplication server down is 180 connection and one of the database down is 220.The optimal result when all servers up is 180 connections, one of the aplication server down is 150 connections and when database server down is 160 connections.

  16. Office 2011 for Macintosh The Missing Manual

    CERN Document Server

    Grover, Chris

    2010-01-01

    Office 2011 for Mac is easy to use, but to unleash its full power, you need to go beyond the basics. This entertaining guide not only gets you started with Word, Excel, PowerPoint, and the new Outlook for Mac, it also reveals useful lots of things you didn't know the software could do. Get crystal-clear explanations on the features you use most -- and plenty of power-user tips when you're ready for more. Take advantage of new tools. Navigate with the Ribbon, use SmartArt graphics, and work online with Office Web Apps.Create professional-looking documents. Use Word to craft beautiful reports,

  17. 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......://blast2srs.embl.de/) aims to meet this need. This server therefore combines the two ways to search sequence databases: similarity and keyword....

  18. "MedTRIS" (Medical Triage and Registration Informatics System): A Web-based Client Server System for the Registration of Patients Being Treated in First Aid Posts at Public Events and Mass Gatherings.

    Science.gov (United States)

    Gogaert, Stefan; Vande Veegaete, Axel; Scholliers, Annelies; Vandekerckhove, Philippe

    2016-10-01

    First aid (FA) services are provisioned on-site as a preventive measure at most public events. In Flanders, Belgium, the Belgian Red Cross-Flanders (BRCF) is the major provider of these FA services with volunteers being deployed at approximately 10,000 public events annually. The BRCF has systematically registered information on the patients being treated in FA posts at major events and mass gatherings during the last 10 years. This information has been collected in a web-based client server system called "MedTRIS" (Medical Triage and Registration Informatics System). MedTRIS contains data on more than 200,000 patients at 335 mass events. This report describes the MedTRIS architecture, the data collected, and how the system operates in the field. This database consolidates different types of information with regards to FA interventions in a standardized way for a variety of public events. MedTRIS allows close monitoring in "real time" of the situation at mass gatherings and immediate intervention, when necessary; allows more accurate prediction of resources needed; allows to validate conceptual and predictive models for medical resources at (mass) public events; and can contribute to the definition of a standardized minimum data set (MDS) for mass-gathering health research and evaluation. Gogaert S , Vande veegaete A , Scholliers A , Vandekerckhove P . "MedTRIS" (Medical Triage and Registration Informatics System): a web-based client server system for the registration of patients being treated in first aid posts at public events and mass gatherings. Prehosp Disaster Med. 2016;31(5):557-562.

  19. MIND-BEST: Web server for drugs and target discovery; design, synthesis, and assay of MAO-B inhibitors and theoretical-experimental study of G3PDH protein from Trichomonas gallinae.

    Science.gov (United States)

    González-Díaz, Humberto; Prado-Prado, Francisco; García-Mera, Xerardo; Alonso, Nerea; Abeijón, Paula; Caamaño, Olga; Yáñez, Matilde; Munteanu, Cristian R; Pazos, Alejandro; Dea-Ayuela, María Auxiliadora; Gómez-Muñoz, María Teresa; Garijo, M Magdalena; Sansano, José; Ubeira, Florencio M

    2011-04-01

    Many drugs with very different affinity to a large number of receptors are described. Thus, in this work, we selected drug-target pairs (DTPs/nDTPs) of drugs with high affinity/nonaffinity for different targets. Quantitative structure-activity relationship (QSAR) models become a very useful tool in this context because they substantially reduce time and resource-consuming experiments. Unfortunately, most QSAR models predict activity against only one protein target and/or they have not been implemented on a public Web server yet, freely available online to the scientific community. To solve this problem, we developed a multitarget QSAR (mt-QSAR) classifier combining the MARCH-INSIDE software for the calculation of the structural parameters of drug and target with the linear discriminant analysis (LDA) method in order to seek the best model. The accuracy of the best LDA model was 94.4% (3,859/4,086 cases) for training and 94.9% (1,909/2,012 cases) for the external validation series. In addition, we implemented the model into the Web portal Bio-AIMS as an online server entitled MARCH-INSIDE Nested Drug-Bank Exploration & Screening Tool (MIND-BEST), located at http://miaja.tic.udc.es/Bio-AIMS/MIND-BEST.php . This online tool is based on PHP/HTML/Python and MARCH-INSIDE routines. Finally, we illustrated two practical uses of this server with two different experiments. In experiment 1, we report for the first time a MIND-BEST prediction, synthesis, characterization, and MAO-A and MAO-B pharmacological assay of eight rasagiline derivatives, promising for anti-Parkinson drug design. In experiment 2, we report sampling, parasite culture, sample preparation, 2-DE, MALDI-TOF and -TOF/TOF MS, MASCOT search, 3D structure modeling with LOMETS, and MIND-BEST prediction for different peptides as new protein of the found in the proteome of the bird parasite Trichomonas gallinae, which is promising for antiparasite drug targets discovery.

  20. Win2003系统中基于IPv6的Web服务器架构%Web server architecture in Win2003 system based on IPv6

    Institute of Scientific and Technical Information of China (English)

    刘志荣; 韩春玲

    2012-01-01

    介绍了如何在Windows Server 2003系统中实现基于IPv6技术的Web服务器构建[1],将Linux系统中复杂的配置方法转换成Windows系统中比较简单和易于实现的方法,让更多的用户接触IPv6技术,从而为IPv6的发展和推广奠定基础.所采用的方法是,先在Windows Server 2003系统中安装IPv6,然后设置IPv6的地址、默认网关等信息,再构建基于IPv6技术的DNS服务器,最后再配置Web服务器.结果表明,用户可以像使用IPv4一样显示Web网页,从而实现从IPv4向IPv6技术的过渡和转换.

  1. SAGE FOR MACINTOSH (MSAGE) VERSION 1.0 SOLVENT ALTERNATIVES GUIDE - USER'S GUIDE

    Science.gov (United States)

    The guide provides instructions for using the Solvent Alternatives Guide (SAGE) for Macintosh, version 1.0. The guide assumes that the user is familiar with the fundamentals of operating aMacintosh personal computer under the System 7.0 (or higher) operating system. SAGE for ...

  2. Coping with Computer Viruses: General Discussion and Review of Symantec Anti-Virus for the Macintosh.

    Science.gov (United States)

    Primich, Tracy

    1992-01-01

    Discusses computer viruses that attack the Macintosh and describes Symantec AntiVirus for Macintosh (SAM), a commercial program designed to detect and eliminate viruses; sample screen displays are included. SAM is recommended for use in library settings as well as two public domain virus protection programs. (four references) (MES)

  3. RS-WebPredictor

    DEFF Research Database (Denmark)

    Zaretzki, J.; Bergeron, C.; Huang, T.-W.;

    2013-01-01

    . 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...

  4. 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.

  5. 基于ArcGIS Server开发的Web应用研究%Study of Web application using ArcGIS Server

    Institute of Scientific and Technical Information of China (English)

    龙倩; 周新志

    2007-01-01

    针对基于ArcGIS Server开发的Web应用问题,在结合数据库管理模型的基础上,利用ArcGIS Server.NETADF和ArcObjects组件开发Web应用系统.首先对ArcGIS Server、ArcObjects组件及其相关技术进行了阐述,接着详细说明了基于ArcGIS Server开发Web应用的解决方法和技术流程,最后给出该方法在产品与工程管理系统中的应用实例.

  6. Realizing of Embedded Web Server Based onLight Weight Protocal Stack LwlP and μC/OS-Ⅱ%基于μC/OS-Ⅱ和LwIP的嵌入式Web服务器实现

    Institute of Scientific and Technical Information of China (English)

    杨俊; 吕建平; 徐峰柳

    2011-01-01

    A 32bit-microcontroller LPC1768 based on the core of ARM Cortex-M3 was adopted in this server. Its embedded Ethernet controller was used to construct a web server with μC/OS-Ⅱ as the operating system( OS ). On the basis of μC/OS-Ⅱ , a LwIP protocal stack was transplanted successfully and HTTP( Hyper Text Ttransfer Protocal) service was realized. The process of hardware designing and software developing was introduced in the paper. Adding to it, the paper included transplanting of μC/OS- Ⅱ , the general structure and transplanting of LwIP protocal stack, the handling proceeding of LwlP protocal stack packet, as well as programming of application layer.%采用以ARM Codex-M3为内核的32位微控制器LPC1768,利用其内置以太网控制器搭建web服务器.web服务器以μC/OS-Ⅱ为操作系统,并在其基础上,成功移植了LwIP协议栈,通过该协议栈,实现了HTTP(超文本传输协议)服务.文中介绍了该系统的硬件设计和软件开发过程,涉及μC/OS-Ⅱ的移植、LwIP协议栈的总体架构和移植、LwIP协议栈数据包处理流程、以及网络应用层程序的编写.

  7. Airtraq® versus Macintosh laryngoscope: A comparative study in tracheal intubation

    Science.gov (United States)

    Bhandari, Geeta; Shahi, K. S.; Asad, Mohammad; Bhakuni, Rajani

    2013-01-01

    Background: The curved laryngoscope blade described by Macintosh in 1943 remains the most widely used device to facilitate tracheal intubation. The Airtraq® (Prodol Meditec S.A, Vizcaya, Spain) is a new, single use, indirect laryngoscope introduced into clinical practice in 2005. It has wan exaggerated blade curvature with internal arrangement of optical lenses and a mechanism to prevent fogging of the distal lens. A high quality view of the glottis is provided without the need to align the oral, pharyngeal and tracheal axis. We evaluated Airtraq and Macintosh laryngoscopes for success rate of tracheal intubation, overall duration of successful intubation, optimization maneuvers, POGO (percentage of glottic opening) score, and ease of intubation. Materials and Methods: Patients were randomly allocated by computer-generated random table to one of the two groups, comprising 40 patients each, group I (Airtraq) and group II (Macintosh). After induction of general anesthesia, tracheal intubation was attempted with the Airtraq or the Macintosh laryngoscope as per group. Primary end points were overall success rate of tracheal intubation, overall duration of successful tracheal intubation, optimization maneuvers, POGO score and ease of intubation between the two groups. Results: We observed that Airtraq was better than the Macintosh laryngoscope as duration of successful intubation was shorter in Airtraq 18.15 seconds (±2.74) and in the Macintosh laryngoscope it was 32.72 seconds (±8.31) P < 0.001. POGO was also better in the Airtraq group 100% grade 1 versus 67.5% in the Macintosh group, P < 0.001. Ease of intubation was also better in the Airtraq group. It was easy in 97.5% versus 42.5% in the Macintosh group, P < 0.001. Conclusion: Both Airtraq and Macintosh laryngoscopes are equally effective in tracheal intubation in normal airways. Duration of successful tracheal intubation was shorter in the Airtraq group which was statistically significant. PMID:25885839

  8. 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.

  9. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

    Science.gov (United States)

    Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-François; Notredame, Cedric

    2011-07-01

    This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

  10. CLIPS - C LANGUAGE INTEGRATED PRODUCTION SYSTEM (MACINTOSH VERSION)

    Science.gov (United States)

    Culbert, C.

    1994-01-01

    The C Language Integrated Production System, CLIPS, is a shell for developing expert systems. It is designed to allow artificial intelligence research, development, and delivery on conventional computers. The primary design goals for CLIPS are portability, efficiency, and functionality. For these reasons, the program is written in C. CLIPS meets or outperforms most micro- and minicomputer based artificial intelligence tools. CLIPS is a forward chaining rule-based language. The program contains an inference engine and a language syntax that provide a framework for the construction of an expert system. It also includes tools for debugging an application. CLIPS is based on the Rete algorithm, which enables very efficient pattern matching. The collection of conditions and actions to be taken if the conditions are met is constructed into a rule network. As facts are asserted either prior to or during a session, CLIPS pattern-matches the number of fields. Wildcards and variables are supported for both single and multiple fields. CLIPS syntax allows the inclusion of externally defined functions (outside functions which are written in a language other than CLIPS). CLIPS itself can be embedded in a program such that the expert system is available as a simple subroutine call. Advanced features found in CLIPS version 4.3 include an integrated microEMACS editor, the ability to generate C source code from a CLIPS rule base to produce a dedicated executable, binary load and save capabilities for CLIPS rule bases, and the utility program CRSV (Cross-Reference, Style, and Verification) designed to facilitate the development and maintenance of large rule bases. Five machine versions are available. Each machine version includes the source and the executable for that machine. The UNIX version includes the source and binaries for IBM RS/6000, Sun3 series, and Sun4 series computers. The UNIX, DEC VAX, and DEC RISC Workstation versions are line oriented. The PC version and the Macintosh

  11. DEMAID - A DESIGN MANAGER'S AID FOR INTELLIGENT DECOMPOSITION (MACINTOSH VERSION)

    Science.gov (United States)

    Rogers, J. L.

    1994-01-01

    effects of an output with respect to a change in a particular input. The second method traces backward to determine what modules must be re-executed if the output of a module must be recomputed. DeMAID is available in three machine versions: a Macintosh version which is written in Symantec's Think C 3.01, a Sun version, and an SGI IRIS version, both of which are written in C language. The Macintosh version requires system software 6.0.2 or later and CLIPS 4.3. The source code for the Macintosh version will not compile under version 4.0 of Think C; however, a sample executable is provided on the distribution media. QuickDraw is required for plotting. The Sun version requires GKS 4.1 graphics libraries, OpenWindows 3, and CLIPS 4.3. The SGI IRIS version requires CLIPS 4.3. Since DeMAID is not compatible with CLIPS 5.0 or later, the source code for CLIPS 4.3 is included on the distribution media; however, the documentation for CLIPS 4.3 is not included in the documentation package for DeMAID. It is available from COSMIC separately as the documentation for MSC-21208. The standard distribution medium for the Macintosh version of DeMAID is a set of four 3.5 inch 800K Macintosh format diskettes. The standard distribution medium for the Sun version of DeMAID is a .25 inch streaming magnetic tape cartridge (QIC-24) in UNIX tar format. The standard distribution medium for the IRIS version is a .25 inch IRIX compatible streaming magnetic tape cartridge in UNIX tar format. All versions include sample input. DeMAID was originally developed for use on VAX VMS computers in 1989. The Macintosh version of DeMAID was released in 1991 and updated in 1992. The Sun version of DeMAID was released in 1992 and updated in 1993. The SGI IRIS version was released in 1993.

  12. 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

  13. Discovering More Accurate Frequent Web Usage Patterns

    CERN Document Server

    Bayir, Murat Ali; Cosar, Ahmet; Fidan, Guven

    2008-01-01

    Web usage mining is a type of web mining, which exploits data mining techniques to discover valuable information from navigation behavior of World Wide Web users. As in classical data mining, data preparation and pattern discovery are the main issues in web usage mining. The first phase of web usage mining is the data processing phase, which includes the session reconstruction operation from server logs. Session reconstruction success directly affects the quality of the frequent patterns discovered in the next phase. In reactive web usage mining techniques, the source data is web server logs and the topology of the web pages served by the web server domain. Other kinds of information collected during the interactive browsing of web site by user, such as cookies or web logs containing similar information, are not used. The next phase of web usage mining is discovering frequent user navigation patterns. In this phase, pattern discovery methods are applied on the reconstructed sessions obtained in the first phas...

  14. Endotracheal intubation in patients with cervical spine immobilization: a comparison of macintosh and airtraq laryngoscopes.

    LENUS (Irish Health Repository)

    Maharaj, Chrisen H

    2007-07-01

    The Airtraq laryngoscope (Prodol Ltd., Vizcaya, Spain) is a novel single-use tracheal intubation device. The authors compared ease of intubation with the Airtraq and Macintosh laryngoscopes in patients with cervical spine immobilization in a randomized, controlled clinical trial.

  15. Microcomputer Decisions for the 1990s [and] Apple's Macintosh: A Viable Choice.

    Science.gov (United States)

    Grosch, Audrey N.

    1989-01-01

    Discussion of the factors that should be considered when purchasing or upgrading a microcomputer focuses on the MS-DOS and OS/2 operating systems. Macintosh purchasing decisions are discussed in a sidebar. A glossary is provided. (CLB)

  16. 基于WebLogic Server的多媒体课件发布系统研究%Research on a Multimedia Courseware Publishing System Based on WebLogic Server

    Institute of Scientific and Technical Information of China (English)

    汪海航; 谭成翔; 张量

    2002-01-01

    文章对基于WebLogic Server的多媒体课件发布系统进行了研究与探讨.首先介绍了课件发布系统在远程教育中的重要作用以及国内外发展现状;其次,以WebLogic Server作为中间件,给出了构建多媒体课件发布系统的设计思路和实现方法;最后对用WebLogic Server构建课件发布系统的优势作了分析.

  17. 基于WebLogic Server实现跨域启用集中式身份验证SOA%Implementation of Domain-spanned Concentrated Identity Authentication SOA Based on WebLogic Server

    Institute of Scientific and Technical Information of China (English)

    谢辉; 鲁士文

    2006-01-01

    讨论了如何保护一个基于面向服务架构(SOA)的生产环境和利用WebLogic安全基础来使用网关验证用户身份,分析了在WebLogic中基于周边身份验证的身份验证网关架构之优点.通过身份验证机制被公开为一个服务,而SOA之下可用的所有其他服务都重用该服务,基于WebLogic Server服务器实现跨域启用集中式身份验证的面向服务架构.

  18. 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.

  19. Web Browser/Server方式的GPS车辆管理系统的设计与实现%Design&Realization of GPS Vehicle Control&Supervision System with Web Browser/Server Liu Kaiyang Han Daofan Ma Aimin

    Institute of Scientific and Technical Information of China (English)

    柳开洋; 韩道范; 马爱民

    2001-01-01

    文章介绍了在GSM移动通信网上实现的GPS车辆监控调度系统,用MapInfo公司最近推出的基于Internet/Intranet的地图应用服务器--MapXtreme 实现Web Browser/Server方式的系统运行机制,初步提出了当今比较新颖的Web GIS 思想及实际解决方案。

  20. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

    Directory of Open Access Journals (Sweden)

    Naoki Orii

    Full Text Available Protein-protein interactions (PPIs are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π, a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users

  1. 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.

  2. 嵌入式Linux Webserver软件BOA实现与应用%The Application and Realization of Embedded Linux WebServer BOA

    Institute of Scientific and Technical Information of China (English)

    骆懿; 章坚武

    2004-01-01

    介绍了一种嵌入式Webserver软件BOA在摩托罗拉公司生产的嵌入式CPU MPC823e上的应用.在嵌入式MPC823e平台上成功移植了Linux和BOA webserver.并实现了在串口与嵌入式网页之间交换数据的CGI网关程序.这种嵌入式WebSever方案可以广泛应用在许多实际的应用领域,如自动化设备的远程监控,嵌入式GSM短消息平台,远程家庭医疗等.

  3. PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling.

    Science.gov (United States)

    Pauthenier, Cyrille; Faulon, Jean-Loup

    2014-07-01

    PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Pàgina Web gestió protectora d'animals

    OpenAIRE

    2011-01-01

    Aplicació Web amb ASP visual studio 2010 i Visual C# , Microsoft SQL Server i AJAX. Aplicación Web con ASP visual studio 2010 y Visual C# , Microsoft SQL Server y AJAX. ASP Web Application with Visual Studio 2010 and Visual C #, Microsoft SQL Server and AJAX.

  5. Personalized Web Services for Web Information Extraction

    CERN Document Server

    Jarir, Zahi; Erradi, Mahammed

    2011-01-01

    The field of information extraction from the Web emerged with the growth of the Web and the multiplication of online data sources. This paper is an analysis of information extraction methods. It presents a service oriented approach for web information extraction considering both web data management and extraction services. Then we propose an SOA based architecture to enhance flexibility and on-the-fly modification of web extraction services. An implementation of the proposed architecture is proposed on the middleware level of Java Enterprise Edition (JEE) servers.

  6. MIPortal: A High Capacity Server for Molecular Imaging Research

    Directory of Open Access Journals (Sweden)

    Misha Pivovarov

    2005-10-01

    Full Text Available The introduction of novel molecular tools in research and clinical medicine has created a need for more refined information management systems. This article describes the design and implementation of such a new information platform: the Molecular Imaging Portal (MIPortal. The platform was created to organize, archive, and rapidly retrieve large datasets using Web-based browsers as access points. The system has been implemented in a heterogeneous, academic research environment serving Macintosh, Unix, and Microsoft Windows clients and has been shown to be extraordinarily robust and versatile. In addition, it has served as a useful tool for clinical trials and collaborative multi-institutional small-animal imaging research.

  7. 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.

  8. Disk Storage Server

    CERN Multimedia

    This model was a disk storage server used in the Data Centre up until 2012. Each tray contains a hard disk drive (see the 5TB hard disk drive on the main disk display section - this actually fits into one of the trays). There are 16 trays in all per server. There are hundreds of these servers mounted on racks in the Data Centre, as can be seen.

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

    Science.gov (United States)

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

    2011-03-01

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

  10. Routine Use of Glidescope and Macintosh Laryngoscope by Trainee Anesthetists.

    Science.gov (United States)

    Aqil, Mansoor; Khan, Mueen Ullah; Hussain, Altaf; Khokhar, Rashid Saeed; Mansoor, Saara; Alzahrani, Tariq

    2016-04-01

    To compare intubating conditions, success rate, and ease of intubation by anesthesia trainees using Glidescope Videolaryngoscope (GVL) compared to Macintosh laryngoscope (MCL). Comparative study. King Khalid University Hospital, Riyadh, Saudi Arabia, from January 2012 to February 2015. Eighty adult patients ASAI and II with normal airway, scheduled to undergo elective surgery requiring endotracheal (ET) intubation were enrolled. Patients were randomly divided into 2 groups: GVL and MCL. All intubations were performed by trainee residents having experience of more than 1 year and who had successfully performed more than 50 tracheal intubations with each device. Glottic view based on Cormack and Lehane's (C&L's) score and percentage of glottis opening (POGO) score, time to successful intubation, need of external pressure, and overall difficulty scores were compared using either GVL or MCL. View of glottis based on C&L's classification was better (p < 0.001) and POGO score was higher (88.25 ±22.06 vs. 57.25 ±29.26, p < 0.001) with GVL compared to MCL. Time to intubate in seconds was (32.90 ±8.69 vs. 41.33 ±15.29, p = 0.004) and overall difficulty score was less 2.78 ±1.39 vs. 4.85 ±1.75 (p < 0.001) using GVL compared to MCL. Residents found ET intubation to be faster and easier with superior glottic view using GVL compared to MCL in patients with normal airway.

  11. Energy-efficient server management; Energieeffizientes Servermanagement

    Energy Technology Data Exchange (ETDEWEB)

    Sauter, B.

    2003-07-01

    This final report for the Swiss Federal Office of Energy (SFOE) presents the results of a project that aimed to develop an automatic shut-down system for the servers used in typical electronic data processing installations to be found in small and medium-sized enterprises. The purpose of shutting down these computers - the saving of energy - is discussed. The development of a shutdown unit on the basis of a web-server that automatically shuts down the servers connected to it and then interrupts their power supply is described. The functions of the unit, including pre-set times for switching on and off, remote operation via the Internet and its interaction with clients connected to it are discussed. Examples of the system's user interface are presented.

  12. GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species.

    Directory of Open Access Journals (Sweden)

    Darshan Shimoga Chandrashekar

    Full Text Available Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses.We developed the 'Genomic Repeat Element Analyzer for Mammals' (GREAM for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a enrichment within chromosomal region(s of interest, and b comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20 known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species.GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various

  13. GeoServer: il server geospaziale Open Source novità della nuova versione 2.3.0

    Directory of Open Access Journals (Sweden)

    Simone Giannecchini

    2013-04-01

    Full Text Available GeoServer è un server geospaziale Open Source sviluppato con tecnologia Java Enterprise per la gestione e l’editing di dati geospaziali secondo gli standard OGC e ISO Technical Committee 211. Esso fornisce le funzionalità di base per creareinfrastrutture spaziali di dati (SDI ed è progettato per essere interoperabile potendo pubblicare dati provenienti da ogni tipo di fonte spaziale utilizzando standard aperti.Open Source GeoSpatial server developed with Java Enterprise technology for managing, sharing and editing geospatial data according to the OGC and ISO TC 211 standards. GeoServer provides the basic functionalities to create spatial data infrastructures (SDI.GeoServer is designed for interoperability, it publishes data from any major spatial data source using open standards: it is the reference implementation of the Open Geospatial Consortium (OGC Web Feature Service (WFS and Web Coverage Service (WCS standards, as well as a highperformance certified compliant Web Map Service (WMS. GeoServer forms a core component of the Geospatial Web.

  14. Application of WebLogic Server and EJB in Warehouse Management System%WebLogic服务器和EJB在仓库管理系统中的应用

    Institute of Scientific and Technical Information of China (English)

    朱莉

    2008-01-01

    在分析网络环境下开发部署多层结构的、跨平台的Java应用系统体系结构的基础上,研究了合理利用异构数据库建立相关联系的方法,介绍了基于WebLogic应用服务器和EJB组件进行仓库管理系统设计和实现的过程.

  15. The application of packet classification and queue management in the web QOS system

    Science.gov (United States)

    Bai, Chun; Liu, Jin

    2011-10-01

    The control mechanisms and strategies of QoS are introduced and implemented in the Web server and system, to meet the growing demand of Web performance. And it provides service differentiation and performance guarantees for different types of user or request. And it is now a problems that urgent need to solve for Web development. The paper proposed a program that designs Web QoS software of the middleware to improve the server quality of the LAN Web server.

  16. 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.

  17. 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.

  18. Empirical study of performance of data binding in ASP.NET web applications

    CERN Document Server

    Stojanovski, Toni; Velinov, Ivan

    2012-01-01

    Most developers use default properties of ASP.NET server controls when developing web applications. ASP.NET web applications typically employ server controls to provide dynamic web pages, and data-bound server controls to display and maintain database data. Though the default properties allow for fast creation of workable applications, creating a high-performance, multi-user, and scalable web application requires careful configuring of server controls and their enhancement using custom-made code. In providing commonly required functionality in data-driven ASP.NET web applications such as paging, sorting and filtering, our empirical study evaluated the impact of various technical approaches: automatic data binding in web server controls; data paging and sorting on web server; paging and sorting on database server; indexed and non-indexed database columns; clustered vs. non-clustered indices. The study observed significant performance differences between various technical approaches.

  19. From Newton to Mandelbrot a primer in theoretical physics with fractals for the Macintosh

    CERN Document Server

    Stauffer, Dietrich

    1996-01-01

    From Newton to Mandelbrot A Primer in Theoretical Physics with Fractals for the Macintosh ( ) takes the student on a tour of the most important landmarks of theoretical physics classical, quantum, and statistical mechanics, relativity, electrodynamics, and, the most modern and exciting of all, the physics of fractals The treatment is confined to the essentials of each area, and short computer programs, numerous problems, and beautiful color illustrations round off this unusual textbook Ideally suited for a one-year course in theoretical physics it will also prove useful in preparing and revising for exams This edition is corrected and includes a new appendix on elementary particle physics, answers to all short questions, and a Macintosh diskette where a selection of executable programs exploring the fractal concept can be found The Diskette The program FRACTAL DIMENSION can be used on any 68030-, 68040,- or PowerPC-based Macintosh with 4 Mb RAM and 256 color display running System 67 - 75 - Sierpinski gasket ...

  20. 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.

  1. Interfacing with the WEB

    CERN Document Server

    Dönszelmann, M

    1995-01-01

    Interfacing to the Web or programming interfaces for the Web is used to provide dynamic information for Web users. Using the Web as a transport system of information poses three constraints: namespace, statelessness and performance. To build interfaces on either server or client side of the Web one has to meet these constraints. Several examples, currently in use in High Energy Physics Experiments are described. They range from an interface to show where buildings are located to an interface showing active values of the On-line System of the DELPHI (CERN)..

  2. 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.

  3. 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.

  4. The Design of Smart Home Security System Based on Embedded Web Server%基于嵌入式Web Server的智能家居安防系统设计

    Institute of Scientific and Technical Information of China (English)

    娄德成; 成立

    2014-01-01

    随着科技的发展,舒适、便捷和安全的智能家居环境正逐步被大众所青睐,传统的住宅正向智能化方向转变.在此背景下,设计了一种基于Web Server的嵌入式智能家居安防系统,并给出了系统整体框架及工作原理.该系统以嵌入式系统为核心,结合发展迅猛的网络技术、GPRS通信技术、视频监控技术等实现了智能家居安防功能,此外创造性地架设了嵌入式Web服务器,最后还设计了用于系统管理的网页界面,极大地方便了用户的使用和管理.测试结果表明,该系统可对现场进行实时有效地监控,且数据传输正确率高,可扩展性强,运行稳定,并且成本低廉,对智能家居未来的发展,具有一定的实际应用价值.

  5. NCI's Distributed Geospatial Data Server

    Science.gov (United States)

    Larraondo, P. R.; Evans, B. J. K.; Antony, J.

    2016-12-01

    Earth systems, environmental and geophysics datasets are an extremely valuable source of information about the state and evolution of the Earth. However, different disciplines and applications require this data to be post-processed in different ways before it can be used. For researchers experimenting with algorithms across large datasets or combining multiple data sets, the traditional approach to batch data processing and storing all the output for later analysis rapidly becomes unfeasible, and often requires additional work to publish for others to use. Recent developments on distributed computing using interactive access to significant cloud infrastructure opens the door for new ways of processing data on demand, hence alleviating the need for storage space for each individual copy of each product. The Australian National Computational Infrastructure (NCI) has developed a highly distributed geospatial data server which supports interactive processing of large geospatial data products, including satellite Earth Observation data and global model data, using flexible user-defined functions. This system dynamically and efficiently distributes the required computations among cloud nodes and thus provides a scalable analysis capability. In many cases this completely alleviates the need to preprocess and store the data as products. This system presents a standards-compliant interface, allowing ready accessibility for users of the data. Typical data wrangling problems such as handling different file formats and data types, or harmonising the coordinate projections or temporal and spatial resolutions, can now be handled automatically by this service. The geospatial data server exposes functionality for specifying how the data should be aggregated and transformed. The resulting products can be served using several standards such as the Open Geospatial Consortium's (OGC) Web Map Service (WMS) or Web Feature Service (WFS), Open Street Map tiles, or raw binary arrays under

  6. The BiSearch web server

    National Research Council Canada - National Science Library

    Arányi, Tamás; Váradi, András; Simon, István; Tusnády, Gábor E

    2006-01-01

    A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genomic DNA methylation profiles...

  7. 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.

  8. Library Signage: Applications for the Apple Macintosh and MacPaint.

    Science.gov (United States)

    Diskin, Jill A.; FitzGerald, Patricia

    1984-01-01

    Describes specific applications of the Macintosh computer at Carnegie-Mellon University Libraries, where MacPaint was used as a flexible, easy to use, and powerful tool to produce informational, instructional, and promotional signage. Profiles of system hardware and software, an evaluation of the computer program MacPaint, and MacPaint signage…

  9. Evaluation of the Airtraq and Macintosh laryngoscopes in patients at increased risk for difficult tracheal intubation.

    LENUS (Irish Health Repository)

    Maharaj, C H

    2008-02-01

    The Airtraq, a novel single use indirect laryngoscope, has demonstrated promise in the normal and simulated difficult airway. We compared the ease of intubation using the Airtraq with the Macintosh laryngoscope, in patients at increased risk for difficult tracheal intubation, in a randomised, controlled clinical trial. Forty consenting patients presenting for surgery requiring tracheal intubation, who were deemed to possess at least three characteristics indicating an increased risk for difficulty in tracheal intubation, were randomly assigned to undergo tracheal intubation using a Macintosh (n = 20) or Airtraq (n = 20) laryngoscope. All patients were intubated by one of three anaesthetists experienced in the use of both laryngoscopes. Four patients were not successfully intubated with the Macintosh laryngoscope, but were intubated successfully with the Airtraq. The Airtraq reduced the duration of intubation attempts (mean (SD); 13.4 (6.3) vs 47.7 (8.5) s), the need for additional manoeuvres, and the intubation difficulty score (0.4 (0.8) vs 7.7 (3.0)). Tracheal intubation with the Airtraq also reduced the degree of haemodynamic stimulation and minor trauma compared to the Macintosh laryngoscope.

  10. 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

  11. 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

  12. 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…

  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. 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.

  15. 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

  16. 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.

  17. New web technologies for astronomy

    Science.gov (United States)

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

    2014-12-01

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

  18. APLIKASI WEB CRAWLER UNTUK WEB CONTENT PADA MOBILE PHONE

    Directory of Open Access Journals (Sweden)

    Sarwosri Sarwosri

    2009-01-01

    Full Text Available Crawling is the process behind a search engine, which served through the World Wide Web in a structured and with certain ethics. Applications that run the crawling process is called Web Crawler, also called web spider or web robot. The growth of mobile search services provider, followed by growth of a web crawler that can browse web pages in mobile content type. Crawler Web applications can be accessed by mobile devices and only web pages that type Mobile Content to be explored is the Web Crawler. Web Crawler duty is to collect a number of Mobile Content. A mobile application functions as a search application that will use the results from the Web Crawler. Crawler Web server consists of the Servlet, Mobile Content Filter and datastore. Servlet is a gateway connection between the client with the server. Datastore is the storage media crawling results. Mobile Content Filter selects a web page, only the appropriate web pages for mobile devices or with mobile content that will be forwarded.

  19. 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).

  20. Implementing an Agent Trade Server

    OpenAIRE

    Boman, Magnus; Sandin, Anna

    2003-01-01

    An experimental server for stock trading autonomous agents is presented and made available, together with an agent shell for swift development. The server, written in Java, was implemented as proof-of-concept for an agent trade server for a real financial exchange.

  1. A Cooperative Schema between Web Sever and Search Engine for Improving Freshness of Web Repository

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Because the web is huge and web pages are updated frequently, the index maintained by a search engine has to refresh web pages periodically. This is extremely resource consuming because the search engine needs to crawl the web and download web pages to refresh its index. Based on present technologies of web refreshing, we present a cooperative schema between web server and search engine for maintaining freshness of web repository. The web server provides meta-data defined through XML standard to describe web sites. Before updating the web page the crawler visits the meta-data files. If the meta-data indicates that the page is not modified, then the crawler will not update it. So this schema can save bandwidth resource. A primitive model based on the schema is implemented. The cost and efficiency of the schema are analyzed.

  2. Sending and Addressing Messages in Web Services

    OpenAIRE

    Borkowski, Piotr

    2007-01-01

    This thesis provides an overview of Web Services technology. The concept of Web Services and Service Oriented Architecture are explained. The thesis focuses on the mechanisms for transporting and addressing messages in web services, especially SOAP. It presents the development history of SOAP, an overview of the SOAP 1.2 specification, and the differences between SOAP in version 1.1 and 1.2. Further, the thesis presents two web servers for development and deployment of web services using Java...

  3. A Runtime System for Interactive Web Services

    DEFF Research Database (Denmark)

    Brabrand, Claus; Møller, Anders; Sandholm, Anders

    1999-01-01

    Interactive web services are increasingly replacing traditional static web pages. Producing web services seems to require a tremendous amount of laborious low-level coding due to the primitive nature of CGI programming. We present ideas for an improved runtime system for interactive web services ...... built on top of CGI running on virtually every combination of browser and HTTP/CGI server. The runtime system has been implemented and used extensively in , a tool for producing interactive web services....

  4. Benchmarking Performance of Web Service Operations

    OpenAIRE

    Zhang, Shuai

    2011-01-01

    Web services are often used for retrieving data from servers providing information of different kinds. A data providing web service operation returns collections of objects for a given set of arguments without any side effects. In this project a web service benchmark (WSBENCH) is developed to simulate the performance of web service calls. Web service operations are specified as SQL statements. The function generator of WSBENCH converts user specified SQL queries into functions and automatical...

  5. A Runtime System for Interactive Web Services

    DEFF Research Database (Denmark)

    Brabrand, Claus; Møller, Anders; Sandholm, Anders

    1999-01-01

    Interactive web services are increasingly replacing traditional static web pages. Producing web services seems to require a tremendous amount of laborious low-level coding due to the primitive nature of CGI programming. We present ideas for an improved runtime system for interactive web services...... built on top of CGI running on virtually every combination of browser and HTTP/CGI server. The runtime system has been implemented and used extensively in , a tool for producing interactive web services....

  6. 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.

  7. SFOMC Data Management/Interactive Web

    Science.gov (United States)

    2003-09-30

    included website design , oceanographic data acquisition, oceanographic data processing for internet viewing, obtaining official DOD clearance for public...Internet Map Server is complete and nearly functional. The work breakdown included website design , geographical data acquisition, geographical data...breakdown included website design , acoustic data acquisition, acoustic data processing for Internet viewing, and uploading acoustic data to web server

  8. 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

  9. Lexical Server of Polish Language

    Directory of Open Access Journals (Sweden)

    Marek Gajecki

    2001-01-01

    Full Text Available This paper presents Lexical Server of Polish Language, the tool that aids natural language processing (NLP. Database of the server consists of dictionary units enriched by lexical information. The lexical server should be able to perform identification of word forms and generations of all inflected forms of the word. The server is dedicated to the people who are looking for NLP algorithms or implement them. The algorithms can be implemented in different kinds of programming languages and different operating systems. There are some examples of problems when lexical server can be useful: automatic text correction, tcxt indexing, keywords extraction, text profile building.

  10. Mastering Microsoft Exchange Server 2010

    CERN Document Server

    McBee, Jim

    2010-01-01

    A top-selling guide to Exchange Server-now fully updated for Exchange Server 2010. Keep your Microsoft messaging system up to date and protected with the very newest version, Exchange Server 2010, and this comprehensive guide. Whether you're upgrading from Exchange Server 2007 SP1 or earlier, installing for the first time, or migrating from another system, this step-by-step guide provides the hands-on instruction, practical application, and real-world advice you need.: Explains Microsoft Exchange Server 2010, the latest release of Microsoft's messaging system that protects against spam and vir

  11. 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

  12. 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

  13. Hidden Page WebCrawler Model for Secure Web Pages

    Directory of Open Access Journals (Sweden)

    K. F. Bharati

    2013-03-01

    Full Text Available The traditional search engines available over the internet are dynamic in searching the relevant content over the web. The search engine has got some constraints like getting the data asked from a varied source, where the data relevancy is exceptional. The web crawlers are designed only to more towards a specific path of the web and are restricted in moving towards a different path as they are secured or at times restricted due to the apprehension of threats. It is possible to design a web crawler that will have the capability of penetrating through the paths of the web, not reachable by the traditional web crawlers, in order to get a better solution in terms of data, time and relevancy for the given search query. The paper makes use of a newer parser and indexer for coming out with a novel idea of web crawler and a framework to support it. The proposed web crawler is designed to attend Hyper Text Transfer Protocol Secure (HTTPS based websites and web pages that needs authentication to view and index. User has to fill a search form and his/her creditionals will be used by the web crawler to attend secure web server for authentication. Once it is indexed the secure web server will be inside the web crawler’s accessible zone

  14. Integrating Live Access Server into Google Earth

    Science.gov (United States)

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

    2006-12-01

    The Live Access Server (LAS) is a highly configurable Web server designed to provide flexible access to visualization and analysis products generated from geo-referenced scientific data sets. Now at version 7.0, LAS has been in operation since 1994. The current ~{!0~}Armstrong?release of LAS V7 consists of a set of modular components in a three tiered architecture -- user interface, workflow orchestration and services to access data and generate scientific products. The LAS user interface (UI) helps the user make requests, preventing requests that are impossible or unreasonable. The UI communicates with the LAS Product Server (LPS the workflow orchestration component) via an XML string with an HTTP GET. When a request is received by the LPS, business logic converts this request into a series of Web Service requests invoked via SOAP. The SOAP services perform data access and generate products (visualizations, data subsets, analyses, etc.). LPS packages these outputs into final products via Jakarta Velocity templates for delivery to the end user. Back-end services are most often a legacy application wrapped in a Java class. The Java wrapper classes are deployed as Web Services accessible via SOAP using the AxisServlet and a custom Web Services Deployment Descriptor file. Ferret is the default visualization application used by LAS, though other applications (e.g. Matlab, CDAT, and GrADS) can also be used. This application demonstrates how Keyhole Markup Language (KML) can be used to provide simple integration of LAS and Google Earth. KML makes access to "Virtual Globe" capabilities so simple that it can be added as an option to existing systems. This application is one such example. The ability to package an image in KML was added to the LAS as a new SOAP service. On the LAS user interface, users can select a Google Earth product in the same manner that any other LAS product is requested. The server will dynamically generate a KML file, which contains the 2D plot

  15. 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

  16. Implementing bioinformatic workflows within the bioextract server.

    Science.gov (United States)

    Lushbough, Carol M; Bergman, Michael K; Lawrence, Carolyn J; Jennewein, Doug; Brendel, Volker

    2008-01-01

    Computational workflows in bioinformatics are becoming increasingly important in the achievement of scientific advances. These workflows typically require the integrated use of multiple, distributed data sources and analytic tools. The BioExtract Server (http://bioextract.org) is a distributed service designed to provide researchers with the web ability to query multiple data sources, save results as searchable data sets, and execute analytic tools. As the researcher works with the system, their tasks are saved in the background. At any time these steps can be saved as a workflow that can then be executed again and/or modified later.

  17. An Evaluation of Windows-Based Computer Forensics Application Software Running on a Macintosh

    Directory of Open Access Journals (Sweden)

    Gregory H. Carlton

    2008-09-01

    Full Text Available The two most common computer forensics applications perform exclusively on Microsoft Windows Operating Systems, yet contemporary computer forensics examinations frequently encounter one or more of the three most common operating system environments, namely Windows, OS-X, or some form of UNIX or Linux. Additionally, government and private computer forensics laboratories frequently encounter budget constraints that limit their access to computer hardware. Currently, Macintosh computer systems are marketed with the ability to accommodate these three common operating system environments, including Windows XP in native and virtual environments. We performed a series of experiments to measure the functionality and performance of the two most commonly used Windows-based computer forensics applications on a Macintosh running Windows XP in native mode and in two virtual environments relative to a similarly configured Dell personal computer. The research results are directly beneficial to practitioners, and the process illustrates affective pedagogy whereby students were engaged in applied research.

  18. 我如何在Windows Server 2008 R2中为Remote Data Services(RDS) Web Access启用单-登录(SSO)?

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    当具有正常的RDS Web Access(官方名称为TS Web Access)权限的用户单击RDS Web Access中的应用程序时,系统将提示他们提供凭证,即便他们在访问使用基于表单的身份验证的RDS Web Access时已经输入了用户凭证。

  19. Using SAS/IntrNet for Evaluating Web-Based Courses.

    Science.gov (United States)

    Yu, Chong-ho; Jannasch-Pennell, Angel; Digangi, Sam; Wasson, Barnaby

    1998-01-01

    Describes the use of SAS/IntrNet, a Web service rather than a Web server, to evaluate and enhance university level Web-based courses. IntrNet provides the ability to create both static and dynamic Web pages, using Web publishing tools to convert SAS output to hypertext markup language for the creation of static Web pages. (Author/LRW)

  20. Using SAS/IntrNet for Evaluating Web-Based Courses.

    Science.gov (United States)

    Yu, Chong-ho; Jannasch-Pennell, Angel; Digangi, Sam; Wasson, Barnaby

    1998-01-01

    Describes the use of SAS/IntrNet, a Web service rather than a Web server, to evaluate and enhance university level Web-based courses. IntrNet provides the ability to create both static and dynamic Web pages, using Web publishing tools to convert SAS output to hypertext markup language for the creation of static Web pages. (Author/LRW)

  1. Retention of tracheal intubation skills by novice personnel: a comparison of the Airtraq and Macintosh laryngoscopes.

    LENUS (Irish Health Repository)

    Maharaj, C H

    2007-03-01

    Direct laryngoscopic tracheal intubation is a potentially lifesaving manoeuvre, but it is a difficult skill to acquire and to maintain. These difficulties are exacerbated if the opportunities to utilise this skill are infrequent, and by the fact that the consequences of poorly performed intubation attempts may be severe. Novice users find the Airtraq laryngoscope easier to use than the conventional Macintosh laryngoscope. We therefore wished to determine whether novice users would have greater retention of intubation skills with the Airtraq rather than the Macintosh laryngoscope. Twenty medical students who had no prior airway management experience participated in this study. Following brief didactic instruction, each took turns performing laryngoscopy and intubation using the Macintosh and Airtraq devices in easy and simulated difficult laryngoscopy scenarios. The degree of success with each device, the time taken to perform intubation and the assistance required, and the potential for complications were then assessed. Six months later, the assessment process was repeated. No didactic instruction or practice attempts were provided on this latter occasion. Tracheal intubation skills declined markedly with both devices. However, the Airtraq continued to provide better intubating conditions, resulting in greater success of intubation, with fewer optimisation manoeuvres required, and reduced potential for dental trauma, particularly in the difficult laryngoscopy scenarios. The substantial decline in direct laryngoscopy skills over time emphasise the need for continued reinforcement of this complex skill.

  2. [McGRATH® MAC Is Useful to Learn Tracheal Intubation Using a Macintosh Laryngoscope].

    Science.gov (United States)

    Wakasugi, Keiko; Niyama, Yukitoshi; Kita, Asuka; Sonoda, Hajime; Yamakage, Michiaki

    2015-10-01

    Learning tracheal intubation using a Macintosh laryngoscope (McL) is important although video laryngoscope is becoming popular. The purpose of this study was to compare the usefulness as a training device for intubation technique using McL with three devices; McGRATH® MAC (MAC), Airwayscope® (AWS) and McL. In this prospective study, 60 nurses not experienced in tracheal intubation were randomly assigned to MAC, AWS, and McL groups (each group: n=20), and 10 times of practice using each device were carried out. We compared the intubation time using McL and the nurse's anatomical understanding of the larynx before and after the practice. The intubation time before the practice was comparable among the three groups, but the time after the practice was significantly shorter in the McL and MAC groups compared to the AWS group (P=0.001). The practice significantly improved anatomical understanding of the larynx in all groups (PMAC and AWS groups compared with the McL group (PMAC may possess advantages compared to Airwayscope® and Macintosh laryngoscope as a training device for learning intubation technique using Macintosh laryngoscope and understanding anatomy of the larynx.

  3. Measurement of forces applied during Macintosh direct laryngoscopy compared with GlideScope® videolaryngoscopy.

    Science.gov (United States)

    Russell, T; Khan, S; Elman, J; Katznelson, R; Cooper, R M

    2012-06-01

    Laryngoscopy can induce stress responses that may be harmful in susceptible patients. We directly measured the force applied to the base of the tongue as a surrogate for the stress response. Force measurements were obtained using three FlexiForce Sensors(®) (Tekscan Inc, Boston, MA, USA) attached along the concave surface of each laryngoscope blade. Twenty-four 24 adult patients of ASA physical status 1-2 were studied. After induction of anaesthesia and neuromuscular blockade, laryngoscopy and tracheal intubation was performed using either a Macintosh or a GlideScope(®) (Verathon, Bothell, WA, USA) laryngoscope. Complete data were available for 23 patients. Compared with the Macintosh, we observed lower median (IQR [range]) peak force (9 (5-13 [3-25]) N vs 20 (14-28 [4-41]) N; p = 0.0001), average force (5 (3-7 [2-19]) N vs 11 (6-16 [1-24]) N; p = 0.0003) and impulse force (98 (42-151 [26-444]) Ns vs 150 (93-207 [17-509]) Ns; p = 0.017) with the GlideScope. Our study shows that the peak lifting force on the base of the tongue during laryngoscopy is less with the GlideScope videolaryngoscope compared with the Macintosh laryngoscope.

  4. Designing sgRNAs with CRISPy web

    DEFF Research Database (Denmark)

    Blin, Kai; Lee, Sang Yup; Weber, Tilmann

    2017-01-01

    Tilmann Weber’s group at the Novo Nordisk Foundation Center for Biosustainability developed a user-friendly, web server implementation of the sgRNA prediction software, CRISPy, for non-computer scientists.......Tilmann Weber’s group at the Novo Nordisk Foundation Center for Biosustainability developed a user-friendly, web server implementation of the sgRNA prediction software, CRISPy, for non-computer scientists....

  5. Caching Servers for ATLAS

    CERN Document Server

    Gardner, Robert; The ATLAS collaboration

    2016-01-01

    As many Tier 3 and some Tier 2 centers look toward streamlining operations, they are considering autonomously managed storage elements as part of the solution. These storage elements are essentially file caching servers. They can operate as whole file or data block level caches. Several implementations exist. In this paper we explore using XRootD caching servers that can operate in either mode. They can also operate autonomously (i.e. demand driven), be centrally managed (i.e. a Rucio managed cache), or operate in both modes. We explore the pros and cons of various configurations as well as practical requirements for caching to be effective. While we focus on XRootD caches, the analysis should apply to other kinds of caches as well.

  6. Caching Servers for ATLAS

    CERN Document Server

    Gardner, Robert; The ATLAS collaboration

    2017-01-01

    As many LHC Tier-3 and some Tier-2 centers look toward streamlining operations, they are considering autonomously managed storage elements as part of the solution. These storage elements are essentially file caching servers. They can operate as whole file or data block level caches. Several implementations exist. In this paper we explore using XRootD caching servers that can operate in either mode. They can also operate autonomously (i.e. demand driven), be centrally managed (i.e. a Rucio managed cache), or operate in both modes. We explore the pros and cons of various configurations as well as practical requirements for caching to be effective. While we focus on XRootD caches, the analysis should apply to other kinds of caches as well.

  7. 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.

  8. RCD+: Fast loop modeling server.

    Science.gov (United States)

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-07-08

    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. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. A comparison of GlideScope videolaryngoscope with Macintosh laryngoscope for laryngeal views

    Institute of Scientific and Technical Information of China (English)

    LI Jin-bao; DENG Xiao-ming; WANG Xiao-lin; XIONG Yuan-chang; FAN Xiao-hua; LIU Yi; XU Hua; MA Yu; DU Jian-er; ZHAI Rong

    2007-01-01

    Objective: To describe the use of the GlideScope in comparison with direct laryngoscopy for elective surgical patients requiring tracheal intubation. Methods: Two hundred patients, ASA Ⅰ-Ⅱ scheduled for elective surgery under general anesthesia requiring orotracheal intubation were selected. Information was collected identifying the patient demographics and airway assessment features (Mallampati oropharyngeal scale, thyromenta distance and mouth opening). In a random crossover design, after induction of anesthesia and neuromuscular block, the laryngoscopes were inserted in turn, and the views of the glottis at laryngoscopy (Cormack and Lehane scores) were compared. The tracchea was intubated using either the standard Macintosh laryngoscope or GlideScope after the second grading at laryngoscopy was done. Complications associated with intubating were recorded. Results: There were 200 patients including 107 males and 93 females, with mean age being 52±13 years, height 164. 8±11.3 cm, weight 64.0±11.5 kg, thyromental distance 6.9±1.1 cm, and mouth opening 5.7±0.5 cm. There was a significant association between the preoperative view of the oropharynx (Mallampati score) and the view of the glottis at laryngoscopy for both the direct Macintosh laryngoscope (P<0.001) and the GlideScope (P<0.001). Among 200 patients, 106 patients had the same C&L grade, 91 of remaining patients showed improvement in the C&L grade (P<0.001) obtained with GlideScope compared with the direct Macintosh laryngoscope.3 of remaining patients showed better view of the glottis(C&L grade) with the direct Macintosh laryngoscope (grade 1) than with GlideScope (grade 2). There were no cases of failure to be intubated. There were no cases of dental or mucosal injury in all patients. Conclusion: GlideScope videolaryngoscope yielded comparable or superior laryngeal view compared with Macintosh laryngoscope. The new type of laryngoscope may have potential advantages for managing the difficult

  10. The Program Management Challenges of Web 2.0

    Science.gov (United States)

    2010-06-01

    internal networks. Web servers and pages existed that supported multi-media in a limited fashion. Most were static Web environments with initial...read-only Web from 1992–1994 with static Web page content that used Mosaic or Netscape browsers to access static HTML Webpages. These pages had

  11. 运用C++Builder6开发ISAPI的Web服务器应用程序%Using C++Builder6 to Develop ISAPI for Web Server Program

    Institute of Scientific and Technical Information of China (English)

    丁鹏飞

    2008-01-01

    通过对开发工具的分析和对使用最为广泛的服务器端程序标准CGI(Common Gateway Interface)、ASP(Active Server Page)和ISAPI(Internet Sever Application Programming Interface)比较,提出了运用C++Builder开发ISAPI的web服务器应用程序.利用C++Builder对数据库的强大支持能力和强大的网络编程功能.开发安全、高效、可靠的Web服务器应用程序.

  12. 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

  13. Designing a Framework to Develop WEB Graphical Interfaces for ORACLE Databases - Web Dialog

    Directory of Open Access Journals (Sweden)

    Georgiana-Petruţa Fîntîneanu

    2009-01-01

    Full Text Available The present article aims to describe a project consisting in designing a framework of applications used to create graphical interfaces with an Oracle distributed database. The development of the project supposed the use of the latest technologies: database Oracle server, Tomcat web server, JDBC (Java library used for accessing a database, JSP and Tag Library (for the development of graphical interfaces.

  14. Huygens file server and storage architecture

    NARCIS (Netherlands)

    Bosch, Peter; Mullender, Sape; Stabell-Kulo, Tage

    1993-01-01

    The Huygens file server is a high-performance file server which is able to deliver multi-media data in a timely manner while also providing clients with ordinary “Unix” like file I/O. The file server integrates client machines, file servers and tertiary storage servers in the same storage architectu

  15. An Efficient Cluster Based Web Object Filters From Web Pre-Fetching And Web Caching On Web User Navigation

    Directory of Open Access Journals (Sweden)

    A. K. Santra

    2012-05-01

    Full Text Available The World Wide Web is a distributed internet system, which provides dynamic and interactive services includes on line tutoring, video/audio conferencing, e-commerce, and etc., which generated heavy demand on network resources and web servers. It increase over the past few year at a very rapidly rate, due to which the amount of traffic over the internet is increasing. As a result, the network performance has now become very slow. Web Pre-fetching and Caching is one of the effective solutions to reduce the web access latency and improve the quality of service. The existing model presented a Cluster based pre-fetching scheme identified clusters of correlated Web pages based on users access patterns. Web Pre-fetching and Caching cause significant improvements on the performance of Web infrastructure. In this paper, we present an efficient Cluster based Web Object Filters from Web Pre-fetching and Web caching scheme to evaluate the web user navigation patterns and user references of product search. Clustering of web page objects obtained from pre-fetched and web cached contents. User Navigation is evaluated from the web cluster objects with similarity retrieval in subsequent user sessions. Web Object Filters are built with the interpretation of the cluster web pages related to the unique users by discarding redundant pages. Ranking is done on users web page product preferences at multiple sessions of each individual user. The performance is measured in terms of Objective function, Number of clusters and cluster accuracy.

  16. The UMLS Knowledge Source server.

    Science.gov (United States)

    McCray, A T; Razi, A

    1995-01-01

    The UMLS Knowledge Source server is an evolving tool for accessing information stored in the UMLS Knowledge Sources. The system architecture is based on the client-server paradigm wherein remote site users send their requests to a centrally managed server at the U.S. National Library of Medicine. The client programs can run on platforms supporting the TCP/IP communication protocol. Access to the system is provided through a command-line interface and through an Application Programming Interface.

  17. 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

  18. 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

  19. Overview of Ontology Servers Research

    Directory of Open Access Journals (Sweden)

    Robert M. Colomb

    2007-06-01

    Full Text Available An ontology is increasingly becoming an essential tool for solving problems in many research areas. The ontology is a complex information object. It can contain millions of concepts in complex relationships. When we want to manage complex information objects, we generally turn to information systems technology. An information system intended to manage ontology is called an ontology server. The ontology server technology is at the time of writing quite immature. Therefore, this paper reviews and compares the main ontology servers that have been reported in the literatures. As a result, we point out several research questions related to server technology.

  20. Collaborative web hosting challenges and research directions

    CERN Document Server

    Ahmed, Reaz

    2014-01-01

    This brief presents a peer-to-peer (P2P) web-hosting infrastructure (named pWeb) that can transform networked, home-entertainment devices into lightweight collaborating Web servers for persistently storing and serving multimedia and web content. The issues addressed include ensuring content availability, Plexus routing and indexing, naming schemes, web ID, collaborative web search, network architecture and content indexing. In pWeb, user-generated voluminous multimedia content is proactively uploaded to a nearby network location (preferably within the same LAN or at least, within the same ISP)

  1. Testing of a novel web browser interface for the Chinese market

    OpenAIRE

    Shen, Siu-Tsen; Prior, Stephen D.; Chen, Kuen-Meau

    2009-01-01

    This paper compares the perspicacity, appropriateness and preference of web browser icons from leading software providers with those of a culture-specific design. This online study was conducted in Taiwan and involved 103 participants, who were given three sets of web browser icons to review, namely Microsoft Internet Explorer, Macintosh Safari, and culturally specific icons created using the Culture-Centred Design methodology. The findings of the study show that all three sets have generally...

  2. CERN Document Server Software: the integrated digital library

    CERN Document Server

    Pepe, Alberto; Gracco, Maja; Le Meur, Jean-Yves; Robinson, Nicholas; Simko, Tibor; Vesely, Martin

    2005-01-01

    CERN as the international European Organization for Nuclear Research has been involved since its early beginnings with the open dissemination of scientific results. The dissemination started by free paper distribution of preprints by CERN Library and continued electronically via FTP bulletin boards, the World Wide Web to the current OAI-compliant CERN Document Server. CERN Document Server Software (CDSware) is a suite of applications which provides the framework and tools for building and managing an autonomous digital library server. In this paper, we discuss the design philosophy of CDSware and its modular, extensible, architecture. Each module comes as an independent entity embodying a specific aspect of digital library workflow. By means of a flow-chart we present the operational workflow of the system, depicting its module interactions. Hence, some of the key features in the CDSware technology are introduced more in detail, namely metadata representation, acquisition and delivery, indexing and ranking te...

  3. Migration of legacy mumps applications to relational database servers.

    Science.gov (United States)

    O'Kane, K C

    2001-07-01

    An extended implementation of the Mumps language is described that facilitates vendor neutral migration of legacy Mumps applications to SQL-based relational database servers. Implemented as a compiler, this system translates Mumps programs to operating system independent, standard C code for subsequent compilation to fully stand-alone, binary executables. Added built-in functions and support modules extend the native hierarchical Mumps database with access to industry standard, networked, relational database management servers (RDBMS) thus freeing Mumps applications from dependence upon vendor specific, proprietary, unstandardized database models. Unlike Mumps systems that have added captive, proprietary RDMBS access, the programs generated by this development environment can be used with any RDBMS system that supports common network access protocols. Additional features include a built-in web server interface and the ability to interoperate directly with programs and functions written in other languages.

  4. SQL Server Integration Services

    CERN Document Server

    Hamilton, Bill

    2007-01-01

    SQL Server 2005 Integration Services (SSIS) lets you build high-performance data integration solutions. SSIS solutions wrap sophisticated workflows around tasks that extract, transform, and load (ETL) data from and to a wide variety of data sources. This Short Cut begins with an overview of key SSIS concepts, capabilities, standard workflow and ETL elements, the development environment, execution, deployment, and migration from Data Transformation Services (DTS). Next, you'll see how to apply the concepts you've learned through hands-on examples of common integration scenarios. Once you've

  5. SHADE3 server

    DEFF Research Database (Denmark)

    Madsen, Anders Østergaard; Hoser, Anna Agnieszka

    2014-01-01

    A major update of the SHADE server (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H-atom anisotropic displacement parameters (ADPs) that were offered by SHADE2, the newest version offers two new methods. The first method combines the original...... translation-libration-screw analysis with input from periodic ab initio calculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms...

  6. Beginning JSP, JSF, and Tomcat web development from novice to professional

    CERN Document Server

    Zambon, Giulio

    2008-01-01

    A comprehensive introduction to JavaServer Pages (JSP), JavaServer Faces (JSF), and the Apache Tomcat Web application server, this manual makes key concepts easy to grasp by numerous working examples and a walk-through of the development of a complete e-commerce project.

  7. A Graphical Client-Server Approach to Financial Management

    CERN Document Server

    Möller, M

    1994-01-01

    At the European Laboratory for Particle Physics (CERN), we have an annual budget of around 600 million US dollars. In order to manage this budget successfully, fast, accurate and easy information access is required throughout the management hierarchy. To meet these goals we have focused on the powerful combination of Relational Database Technology, Fourth Generation Tools and Client-Server architecture. Using these technologies we have developed a powerful and easy-to-use management information tool (known as the BHT) which allows the follow up and tracking of expenditure at all levels throughout the organization. Executives may instantaneously produce up-to-date graphics showing the expenditure profile of the organization. These graphics may then be used as a basis for ‘zooming in’ to view more and more details until the individual financial transactions are reached (all of which are on-line and available on the user’s desktop). The graphical user interface runs on both Macintosh and PC. Using ORACLE�...

  8. An Improved Approach to perform Crawling and avoid Duplicate Web Pages

    Directory of Open Access Journals (Sweden)

    Dhiraj Khurana

    2012-06-01

    Full Text Available When a web search is performed it includes many duplicate web pages or the websites. It means we can get number of similar pages at different web servers. We are proposing a Web Crawling Approach to Detect and avoid Duplicate or Near Duplicate WebPages. In this proposed work we are presenting a keyword Prioritization based approach to identify the web page over the web. As such pages will beidentified it will optimize the web search.

  9. Evaluation of Truview evo2 Laryngoscope In Anticipated Difficult Intubation - A Comparison To Macintosh Laryngoscope.

    Science.gov (United States)

    Singh, Ishwar; Khaund, Abhijit; Gupta, Abhishek

    2009-04-01

    The aim of the study was to assess and compare laryngoscopic view of Truview evo2 laryngoscope with that of Macintosh laryngoscope in patients with one or more predictors of difficult intubation (PDI). Moreover ease of intubation with Truview evo2 in terms of absolute time requirement was also aimed at. Patients for elective surgery requiring endotracheal intubation were initially assessed for three PDI parameters - modified Mallampati test, thyro-mental distance & Atlanto-occipital (AO) joint extension. Patients with cumulative PDI scores of 2 to 5 (in a scale of 0 to 8) were evaluated for Cormack & Lehane (CL) grading by Macintosh blade after standard induction. Cases with CL grade of two or more were further evaluated by Truview evo2 laryngoscope and corresponding CL grades were assigned. Intubation attempted under Truview evo2 vision and time required for each successful tracheal intubation (i.e. tracheal intubation completed within one minute) was noted. Total fifty cases were studied. The CL grades assigned by Macintosh blade correlated well with the cumulative PDI scores assigned preoperatively, confirming there predictability. Truview evo2 improved laryngeal view in 92 % cases by one or more CL grade. Intubation with Truview evo2 was possible in 88% cases within stipulated time of one minute and mean time of 28.6 seconds with SD of 11.23 was reasonably quick. No significant complication like oro- pharyngeal trauma or extreme pressor response to laryngoscopy was noticed. To conclude, Truview evo2 proved to be a better tool than conventional laryngoscope in anticipated difficult situations.

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

    Energy Technology Data Exchange (ETDEWEB)

    Chai, X; Liu, L; Xing, L [Stanford UniversitySchool of Medicine, Stanford, CA (United States)

    2014-06-01

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

  11. 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...

  12. Server-side Filtering and Aggregation within a Distributed Environment

    Science.gov (United States)

    Currey, J. C.; Bartle, A.

    2015-12-01

    Intercalibration, validation, and data mining use cases require more efficient access to the massive volumes of observation data distributed across multiple agency data centers. The traditional paradigm of downloading large volumes of data to a centralized server or desktop computer for analysis is no longer viable. More analysis should be performed within the host data centers using server-side functions. Many comparative analysis tasks require far less than 1% of the available observation data. The Multi-Instrument Intercalibration (MIIC) Framework provides web services to find, match, filter, and aggregate multi-instrument observation data. Matching measurements from separate spacecraft in time, location, wavelength, and viewing geometry is a difficult task especially when data are distributed across multiple agency data centers. Event prediction services identify near coincident measurements with matched viewing geometries near orbit crossings using complex orbit propagation and spherical geometry calculations. The number and duration of event opportunities depend on orbit inclinations, altitude differences, and requested viewing conditions (e.g., day/night). Event observation information is passed to remote server-side functions to retrieve matched data. Data may be gridded, spatially convolved onto instantaneous field-of-views, or spectrally resampled or convolved. Narrowband instruments are routinely compared to hyperspectal instruments such as AIRS and CRIS using relative spectral response (RSR) functions. Spectral convolution within server-side functions significantly reduces the amount of hyperspectral data needed by the client. This combination of intelligent selection and server-side processing significantly reduces network traffic and data to process on local servers. OPeNDAP is a mature networking middleware already deployed at many of the Earth science data centers. Custom OPeNDAP server-side functions that provide filtering, histogram analysis (1D

  13. Cinematica: a system for calibrated, Macintosh-driven displays from within Mathematica.

    Science.gov (United States)

    Solomon, J A; Watson, A B

    1996-01-01

    Cinematica is a minimal system for producing calibrated grayscale movies on an Apple Macintosh computer from within the Mathematica programming environment. It makes use of the ISR Video Attenuator and the Video Toolbox software library developed by Denis Pelli. By design, Cinematica provides a very low-level interface to the display routine. Display instructions take the form of a list of pairs (image index, colormap index). The philosophy is that programming is much easier in Mathematica than in C, so we reserve the complexity for Mathematica. A few simple examples are provided.

  14. Prevention of Cross-Site Scripting Vulnerabilities using Dynamic Hash Generation Technique on the Server Side

    Directory of Open Access Journals (Sweden)

    Shashank Gupta

    2012-09-01

    Full Text Available Cookies are a means to provide statefulcommunication over the HTTP. In the World WideWeb (WWW, once the user using web browser hasbeen successfully authenticated by the web server ofthe web application, then the web server willgenerate and transfer the cookie to the web browser.Now each time, if the user again wants to send arequest to the web server as a part of the activeconnection, the user has to include thecorresponding cookie in its request, so that the webserver associates the cookie to the correspondinguser. Cookies are the mechanisms that maintain anauthentication state between the user and webapplication. Therefore cookies are the possibletargets for the attackers. Cross Site Scripting (XSSattack is one of such attacks against the webapplications in which a user has to compromise itsbrowser’s resources (e.g. cookies etc.. In this paper,a novel technique called Dynamic Hash GenerationTechnique is introduced whose aim is to makecookies worthless for the attackers. This techniqueis implemented on the server side whose main taskis to generate a hash of the value of name attributein the cookie and send this hash value to the webbrowser. With this technique, the hash value ofname attribute in the cookie which is stored on thebrowser’s database is not valid for the attackers toexploit the vulnerabilities of XSS attacks.

  15. Modified LRU Algorithm To Implement Proxy Server With Caching Policies

    Directory of Open Access Journals (Sweden)

    Jitendra Singh Kushwah

    2011-11-01

    Full Text Available In order to produce and develop a software system, it is necessary to have a method of choosing a suitable algorithm which satisfies the required quality attributes and maintains a trade-off between sometimes conflicting ones. Proxy server is placed between the real server and clients. Proxy server uses caching policies to store web documents using algorithms. For this, different algorithms are used but drawbacks of these algorithms are that it is applicable only for the video files not for other resource types. Second drawback is that it does not tell any thing about organizing the data on the disk storage of the proxy server. Third drawback is that it is difficult to implement. Fourth drawback is that they require the knowledge about the workloads on the proxy server. Major problems in previous described algorithms is that "Cold Cache Pollution". As described in the previous description all the existing algorithms used for caching suffers from various disadvantages. This paper is proposing a technique to remove the problem of cold cache pollution which is proved mathematically that it is better than the existing LRU-Distance algorithm.

  16. GALILEE: AN INTERNET WEB BASED DISTANCE LEARNING SUPPORT SYSTEM

    Directory of Open Access Journals (Sweden)

    Arthur Budiman

    1999-01-01

    Full Text Available This paper presents a project of Web-based Distance Learning support system. The system has been built based on the Internet and World Wide Web facility. The system could be accessed with a web browser which is directed to a certain web server address so that students can do learning process just like in the real situation, such as student admissions, taking course materials, syllabus, assignments, students grades, class discussions through web, and doing online quizzes. Students could also join collaboration works by giving opinions, feedback and student produced paper/web which can be shared to the entire learning community. Therefore, it will build a collaborative learning environment where lectures together with students make constructive knowledge databases for entire learning community. This system has been developed based on Active Server Pages (ASP technology from Microsoft which is embedded in a web server. Web pages reside in a web server which is connected to an SQL Database Server. Database server is used to store structured data such as lectures/students personal information, course lists, syllabus and its descriptions, announcement texts from lecturers, commentaries for discussion forum, student's study evaluations, scores for each assignment, quizzes for each course, assignments text from lectures, assignments which are collected by students and students contribution/materials. This system has been maintained by an administrator for maintaining and developing web pages using HTML. The administrator also does ASP scripts programming to convert web pages into active server pages. Lectures and students could contribute some course materials and share their ideas through their web browser. This web-based collaborative learning system gives the students more active role in the information gathering and learning process, making the distance students feel part of a learning community, therefore increasing motivation, comprehension and

  17. Chapter 59: Web Services

    Science.gov (United States)

    Graham, M. J.

    Web services are a cornerstone of the distributed computing infrastructure that the VO is built upon yet to the newcomer, they can appear to be a black art. This perception is not helped by the miasma of technobabble that pervades the subject and the seemingly impenetrable high priesthood of actual users. In truth, however, there is nothing conceptually difficult about web services (unsurprisingly any complexities will lie in the implementation details) nor indeed anything particularly new. A web service is a piece of software available over a network with a formal description of how it is called and what it returns that a computer can understand. Note that entities such as web servers, ftp servers and database servers do not generally qualify as they lack the standardized description of their inputs and outputs. There are prior technologies, such as RMI, CORBA, and DCOM, that have employed a similar approach but the success of web services lies predominantly in its use of standardized XML to provide a language-neutral way for representing data. In fact, the standardization goes further as web services are traditionally (or as traditionally as five years will allow) tied to a specific set of technologies (WSDL and SOAP conveyed using HTTP with an XML serialization). Alternative implementations are becoming increasingly common and we will cover some of these here. One important thing to remember in all of this, though, is that web services are meant for use by computers and not humans (unlike web pages) and this is why so much of it seems incomprehensible gobbledegook. In this chapter, we will start with an overview of the web services current in the VO and present a short guide on how to use and deploy a web service. We will then review the different approaches to web services, particularly REST and SOAP, and alternatives to XML as a data format. We will consider how web services can be formally described and discuss how advanced features such as security, state

  18. Empirical study of sensor observation services server instances

    CERN Document Server

    Tamayo, Alain; Granell, Carlos; Huerta, Joaquín; 10.1007/978-3-642-19789-5_10

    2011-01-01

    The number of Sensor Observation Service (SOS) instances available online has been increasing in the last few years. The SOS specification standardises interfaces and data formats for exchanging sensor-related in-formation between information providers and consumers. SOS in conjunction with other specifications in the Sensor Web Enablement initiative, at-tempts to realise the Sensor Web vision, a worldwide system where sensor networks of any kind are interconnected. In this paper we present an empirical study of actual instances of servers implementing SOS. The study focuses mostly in which parts of the specification are more frequently included in real implementations, and how exchanged messages follows the structure defined by XML Schema files. Our findings can be of practical use when implementing servers and clients based on the SOS specification, as they can be optimized for common scenarios.

  19. A CLINICAL ASSESSMENT OF MACINTOSH BLADE, MILLER BLADE AND KING VISIONTM VIDEOLARYNGOSCOPE FOR LARYNGEAL EXPOSURE AND DIFFICULTY IN ENDOTRACHEAL INTUBATION

    Directory of Open Access Journals (Sweden)

    Apoorva Mahendera

    2016-03-01

    Full Text Available CONTEXT Previous studies suggest glottic view is better achieved with straight blades while tracheal intubation is easier with curved blades and videolaryngoscope is better than conventional laryngoscope. AIMS Comparison of conventional laryngoscope (Macintosh blade and Miller blade with channelled videolaryngoscope (King Vision TM with respect to laryngeal visualisation and difficulty in endotracheal intubation. SETTINGS AND DESIGN This prospective randomised comparative study was conducted at a tertiary care hospital (in ASA I and ASA II patients after approval from the Institutional Ethics Committee. METHODS We compared Macintosh, Miller, and the King VisionTM videolaryngoscope for glottic visualisation and ease of tracheal intubation. Patients undergoing elective surgeries under general anaesthesia requiring endotracheal intubation were randomly divided into three groups (N=180. After induction of anaesthesia, laryngoscopy was performed and trachea intubated. We recorded visualisation of glottis (Cormack-Lehane grade-CL, ease of intubation, number of attempts, need to change blade, and need for external laryngeal manipulation. STATISTICAL ANALYSIS Demographic data, Mandibular length, Mallampati classification were compared using ANOVA, Chi-square test, Kruskal-Wallis Test, where P value <0.005 is statically significant. RESULTS CL grade 1 was most often observed in King Vision -TM VL group (90% which is followed by Miller (28.33%, and Macintosh group (15%. We found intubation was to be easier (grade 1 with King Vision -TM VL group (73.33%, followed by Macintosh (38.33%, and Miller group (1.67%. External manipulation (BURP was needed more frequently in patients in Miller group (71.67%, followed by Macintosh (28.33% and in King Vision -TM VL group (6.67%. All (100% patients were intubated in the 1 st attempt with King Vision -TM VL group, followed by Macintosh group (90% and Miller group (58.33%. CONCLUSIONS In patients with normal airway

  20. Application of WebSocket in English test system

    Science.gov (United States)

    Wang, Xin; Ye, Yan; Qi, Jiahui; Wu, Min

    2017-03-01

    Due to http protocol restrictions, the traditional web real-time applications cannot push information from the server to the browser. Although it can be achieved through technical means, but there are obvious shortcomings. This paper introduces an English testing system design and development on server-side, which is based on the WebSocket protocol. Through the WebSocket, a bidirectional communication channel can be established between the browser and the server. It realizes the real-time communication in the English test system.

  1. 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

    2006-01-01

    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 L2 cache. Experiments show that under high concurrency, our optimizations improve the throughput of TUX by up to 40% and the number of requests serviced at the time of failure by 21%....

  2. The Construction and Optimization of Moodle Platform on Windows Server 2012 R2 and Wamp Server%基于Windows Server 2012 R2、WampServer环境的Moodle平台搭建及优化扩展

    Institute of Scientific and Technical Information of China (English)

    马东宇

    2014-01-01

    研究了以WampServer集成环境为Web服务器,在Windows Server 2012 R2系统下搭建Moodle平台的过程,经比较试验得出了基于 Windows 8界面操作系统的平台架设环境,并从功能扩展和性能优化等方面给出了解决方案。%A process of Moodle platform construction is researched,using WampServer integrating environment as Web server under a system of Windows Server 2012 R2.After comparable experiments,a platform construction environment on Windows 8 surface operating system is got.And a solution is given from functional expansion,performance optimization and other aspects.

  3. JWIG: Yet Another Framework for Maintainable and Secure Web Applications

    DEFF Research Database (Denmark)

    Møller, Anders; Schwarz, Mathias Romme

    2009-01-01

    Although numerous frameworks for web application programming have been developed in recent years, writing web applications remains a challenging task. Guided by a collection of classical design principles, we propose yet another framework. It is based on a simple but flexible server-oriented arch...... services.The resulting framework provides a novel foundation for developing maintainable and secure web applications.......Although numerous frameworks for web application programming have been developed in recent years, writing web applications remains a challenging task. Guided by a collection of classical design principles, we propose yet another framework. It is based on a simple but flexible server......-oriented architecture that coherently supports general aspects of modern web applications, including dynamic XML construction, session management, data persistence, caching, and authentication, but it also simplifies programming of server-push communication and integration of XHTML-based applications and XML-based web...

  4. COMPARISON BETWEEN MACINTOSH LARYNGOSCOPE AND MCGRATH VIDEO LARYNGOSCOPE FOR ENDOTRACHEAL INTUBATION IN NEUROSURGICAL PATIENTS

    Directory of Open Access Journals (Sweden)

    Aastha

    2016-03-01

    Full Text Available This study was done on sixty patients of ASA 1 and 2, undergoing elective surgery under general anaesthesia. The patients were allocated in two groups of 30 patients each. Patients selected were allocated to two groups and without risk factors. Direct laryngoscopy group (group 1 patients were intubated through direct laryngoscope. Video laryngoscopy group (group 2 patients were intubated through McGrath VLS. The distribution of patients according to age, sex and weight was comparable (p>.001 in both the two groups. The changes in heart rate, mean arterial pressure, oxygen saturation were not significant (p>.001 between the two groups after intubation at different time intervals. The number of attempts and intubation time was found to be significantly higher in McGrath VLS as compared to Macintosh laryngoscope. The increase in postoperative sore throat and hoarseness after 6 and 24 hrs following operation was found to be significant in group 1 compared to group 2. So from our study, we conclude that the use of McGrath video laryngoscope has no advantage over direct laryngoscopy in attenuating the cardiovascular responses attributed to tracheal intubation in patients with normal airway. It is also associated with greater number of attempts and longer intubation time. However, with the use of stylet, number of attempts can be reduced, although the use of stylet has its own complications. VLS has lesser incidence of post-operative sore throat and hoarseness as compared to Macintosh laryngoscopy.

  5. Tracheal intubation by inexperienced medical residents using the Airtraq and Macintosh laryngoscopes--a manikin study.

    LENUS (Irish Health Repository)

    Maharaj, Chrisen H

    2006-11-01

    The Airtraq laryngoscope is a novel intubation device that may possess advantages over conventional direct laryngoscopes for use by personnel that are infrequently required to perform tracheal intubation. We conducted a prospective study in 20 medical residents with little prior airway management experience. After brief didactic instruction, each participant took turns performing laryngoscopy and intubation using the Macintosh (Welch Allyn, Welch Allyn, NY) and Airtraq (Prodol Ltd. Vizcaya, Spain) devices, in 3 laryngoscopy scenarios in a Laerdal Intubation Trainer (Laerdal, Stavanger, Norway) and 1 scenario in a Laerdal SimMan manikin (Laerdal, Kent, UK). They then performed tracheal intubation of the normal airway a second time to characterize the learning curve. In all scenarios tested, the Airtraq decreased the duration of intubation attempts, reduced the number of optimization maneuvers required, and reduced the potential for dental trauma. The residents found the Airtraq easier to use in all scenarios compared with the Macintosh laryngoscope. The Airtraq may constitute a superior device for use by personnel infrequently required to perform tracheal intubation.

  6. Macintosh support is provided at the level of the Service Desk

    CERN Multimedia

    2011-01-01

    Since September 2010 the Apple laptops & desktops with Mac OS are recognized and supported at CERN by the IT department. Therefore, the “Macintosh support” procedure now follows the same ITIL*) schema as for all IT services, i.e.: All CERN users must address any request for support on Macintosh PCs to the Service Desk. The Service Desk will move on questions or problems they cannot solve to “IT 2nd level” support people, provided by the “computing support” contract managed by IT department. Mac OS being officially supported by the IT department, a 3rd level support is provided by CERN IT staff; they may give specialized expert assistance, within the scope described at the ITUM-2 presentation, for all incidents or requests which can be neither resolved nor fulfilled by the Service Desk (1st level) and the 2nd level support people. Therefore, users who have problems related to Mac OS should simply fill-in the appropriate form from th...

  7. Learning Curves of Macintosh Laryngoscope in Nurse Anesthetist Trainees Using Cumulative Sum Method

    Directory of Open Access Journals (Sweden)

    Panthila Rujirojindakul

    2014-01-01

    Full Text Available Background. Tracheal intubation is a potentially life-saving procedure. This skill is taught to many anesthetic healthcare professionals, including nurse anesthetists. Our goal was to evaluate the learning ability of nurse anesthetist trainees in their performance of orotracheal intubation with the Macintosh laryngoscope. Methods. Eleven nurse anesthetist trainees were enrolled in the study during the first three months of their training. All trainees attended formal lectures and practice sessions with manikins at least one time on performing successful tracheal intubation under supervision of anesthesiology staff. Learning curves for each nurse anesthetist trainee were constructed with the standard cumulative summation (cusum methods. Results. Tracheal intubation was attempted on 388 patients. Three hundred and six patients (78.9% were successfully intubated on the trainees’ first attempt and 17 patients (4.4% on the second attempt. The mean ± SD number of orotracheal intubations per trainee was 35.5 ± 5.1 (range 30–47. Ten (90.9% of 11 trainees crossed the 20% acceptable failure rate line. A median of 22 procedures was required to achieve an 80% orotracheal intubations success rate. Conclusion. At least 22 procedures were required to reach an 80% success rate for orotracheal intubation using Macintosh laryngoscope in nonexperienced nurse anesthetist trainees.

  8. Servers in SCADA applications

    Energy Technology Data Exchange (ETDEWEB)

    Marcuse, J.; Menz, B.; Payne, J.

    1995-12-31

    The rise of computerized data acquisition, storage and reporting systems has been driven by industries demand for advanced troubleshooting aids and continual, measurable process and product quality improvements. As US companies entered into global competition they discovered ever stiffer customer requirements. These requirements were especially stiff in the auto industry where the Japanese set a very high standard using SPC and other world class manufacturing methods. The architecture of these SCADA (supervisory control and data acquisition) systems has gone through several evolutionary stages over the last few years. This paper examines this evolution from the mainframe computer architecture used in the 1970`s, to the multi-tiered scheme of the 1980`s to the client-server architecture emerging today.

  9. Universal Fingerprinting Chip Server

    Science.gov (United States)

    Casique-Almazán, Janet; Larios-Serrato, Violeta; Olguín-Ruíz, Gabriela Edith; Sánchez-Vallejo, Carlos Javier; Maldonado-Rodríguez, Rogelio; Méndez-Tenorio, Alfonso

    2012-01-01

    The Virtual Hybridization approach predicts the most probable hybridization sites across a target nucleic acid of known sequence, including both perfect and mismatched pairings. Potential hybridization sites, having a user-defined minimum number of bases that are paired with the oligonucleotide probe, are first identified. Then free energy values are evaluated for each potential hybridization site, and if it has a calculated free energy of equal or higher negative value than a user-defined free energy cut-off value, it is considered as a site of high probability of hybridization. The Universal Fingerprinting Chip Applications Server contains the software for visualizing predicted hybridization patterns, which yields a simulated hybridization fingerprint that can be compared with experimentally derived fingerprints or with a virtual fingerprint arising from a different sample. Availability http://bioinformatica.homelinux.org/UFCVH/ PMID:22829736

  10. Host Integration Server 2004

    Institute of Scientific and Technical Information of China (English)

    PaulThurrott; 杨岩

    2005-01-01

    微软发布的Host Integration Server(HIS)2004,是IBM大型主机集成服务器的一个重要的更新,添加了一些重要的新特点和改进。与大多数微软公司协同工作的产品不同,HIS 2004的设计目的是为了移植,而不是纯粹的集成,事实上它将会帮助客户从现有的传统平台中得到更多的价值——在这种情况下,所指的产品就是IBM大型主机和iSeries(也就是以前的AS/400)系列机型。

  11. Autoplot and the HAPI Server

    Science.gov (United States)

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

    2016-12-01

    Autoplot was introduced in 2008 as an easy-to-use plotting tool for the space physics community. It reads data from a variety of file resources, such as CDF and HDF files, and a number of specialized data servers, such as the PDS/PPI's DIT-DOS, CDAWeb, and from the University of Iowa's RPWG Das2Server. Each of these servers have optimized methods for transmitting data to display in Autoplot, but require coordination and specialized software to work, limiting Autoplot's ability to access new servers and datasets. Likewise, groups who would like software to access their APIs must either write thier own clients, or publish a specification document in hopes that people will write clients. The HAPI specification was written so that a simple, standard API could be used by both Autoplot and server implementations, to remove these barriers to free flow of time series data. Autoplot's software for communicating with HAPI servers is presented, showing the user interface scientists will use, and how data servers might implement the HAPI specification to provide access to their data. This will also include instructions on how Autoplot is used and installed desktop computers, and used to view data from the RBSP, Juno, and other missions.

  12. Detecting and Preventing Security Threats on Servers and Browsers

    Directory of Open Access Journals (Sweden)

    Mr. Nandish. U. G Dr. Balakrishna. R Mr. Naveen. L Mr. Anand Kumar K. S

    2012-02-01

    Full Text Available Our reliance on web based services through browsers for everyday life activities has increased over the years. Everyday new vulnerabilities are found in what was previously believed to be secure applications, unlocking new risks and security hazards that can be exploited by malicious advertisers or intruders compromising the security of systems. Using cross site scripting techniques intruders can hijack web sessions and craft credible phishing sites. Similarly, intruders may harm the server by uploading malicious executables and batch files. On the other hand the java script code downloaded into browser can attack client machines to steal user’s credentials (XSS attacks and lure users into providing sensitive information to unauthorized parties (Phishing attacks. It is proposed here a model detecting and preventing malicious files and cross site scripting attacks based on monitoring JavaScript code execution and comparing the execution to high level policies, to detect malicious code behavior. The solution also protects the servers from dangerous DOS commands and executable files. The model follows an approach similar to hackers and security analyst to discover vulnerabilities in networkconnected web servers. It uses both manually and automatically generated rules to mitigate possible cross site scripting attacks. The work undertaken covers the solutions preventing client machines from stealing user’s credentials by using cookies hijacking as well as preventing the browsers from crash.

  13. LERC-SLAM - THE NASA LEWIS RESEARCH CENTER SATELLITE LINK ATTENUATION MODEL PROGRAM (MACINTOSH VERSION)

    Science.gov (United States)

    Manning, R. M.

    1994-01-01

    antenna required to establish a link with the satellite, the statistical parameters that characterize the rainrate process at the terminal site, the length of the propagation path within the potential rain region, and its projected length onto the local horizontal. The IBM PC version of LeRC-SLAM (LEW-14979) is written in Microsoft QuickBASIC for an IBM PC compatible computer with a monitor and printer capable of supporting an 80-column format. The IBM PC version is available on a 5.25 inch MS-DOS format diskette. The program requires about 30K RAM. The source code and executable are included. The Macintosh version of LeRC-SLAM (LEW-14977) is written in Microsoft Basic, Binary (b) v2.00 for Macintosh II series computers running MacOS. This version requires 400K RAM and is available on a 3.5 inch 800K Macintosh format diskette, which includes source code only. The Macintosh version was developed in 1987 and the IBM PC version was developed in 1989. IBM PC is a trademark of International Business Machines. MS-DOS is a registered trademark of Microsoft Corporation. Macintosh is a registered trademark of Apple Computer, Inc.

  14. AUTOMATED TESTING OF OPC SERVERS

    CERN Document Server

    Farnham, B

    2011-01-01

    CERN relies on OPC Server implementations from 3rd party device vendors to provide a software interface to their respective hardware. Each time a vendor releases a new OPC Server version it is regression tested internally to verify that existing functionality has not been inadvertently broken during the process of adding new features. In addition bugs and problems must be communicated to the vendors in a reliable and portable way. This presentation covers the automated test approach used at CERN to cover both cases: Scripts are written in a domain specific language specifically created for describing OPC tests and executed by a custom software engine driving the OPC Server implementation.

  15. SQL Server 2014 development essentials

    CERN Document Server

    Masood-Al-Farooq, Basit A

    2014-01-01

    This book is an easy-to-follow, comprehensive guide that is full of hands-on examples, which you can follow to successfully design, build, and deploy mission-critical database applications with SQL Server 2014. If you are a database developer, architect, or administrator who wants to learn how to design, implement, and deliver a successful database solution with SQL Server 2014, then this book is for you. Existing users of Microsoft SQL Server will also benefit from this book as they will learn what's new in the latest version.

  16. A Capacity Supply Model for Virtualized Servers

    Directory of Open Access Journals (Sweden)

    Alexander PINNOW

    2009-01-01

    Full Text Available This paper deals with determining the capacity supply for virtualized servers. First, a server is modeled as a queue based on a Markov chain. Then, the effect of server virtualization on the capacity supply will be analyzed with the distribution function of the server load.

  17. Windows Server 2012 R2 administrator cookbook

    CERN Document Server

    Krause, Jordan

    2015-01-01

    This book is intended for system administrators and IT professionals with experience in Windows Server 2008 or Windows Server 2012 environments who are looking to acquire the skills and knowledge necessary to manage and maintain the core infrastructure required for a Windows Server 2012 and Windows Server 2012 R2 environment.

  18. Mac OS X Lion Server For Dummies

    CERN Document Server

    Rizzo, John

    2011-01-01

    The perfect guide to help administrators set up Apple's Mac OS X Lion Server With the overwhelming popularity of the iPhone and iPad, more Macs are appearing in corporate settings. The newest version of Mac Server is the ideal way to administer a Mac network. This friendly guide explains to both Windows and Mac administrators how to set up and configure the server, including services such as iCal Server, Podcast Producer, Wiki Server, Spotlight Server, iChat Server, File Sharing, Mail Services, and support for iPhone and iPad. It explains how to secure, administer, and troubleshoot the networ

  19. PlanetServer: Innovative approaches for the online analysis of hyperspectral satellite data from Mars

    Science.gov (United States)

    Oosthoek, J. H. P.; Flahaut, J.; Rossi, A. P.; Baumann, P.; Misev, D.; Campalani, P.; Unnithan, V.

    2014-06-01

    PlanetServer is a WebGIS system, currently under development, enabling the online analysis of Compact Reconnaissance Imaging Spectrometer (CRISM) hyperspectral data from Mars. It is part of the EarthServer project which builds infrastructure for online access and analysis of huge Earth Science datasets. Core functionality consists of the rasdaman Array Database Management System (DBMS) for storage, and the Open Geospatial Consortium (OGC) Web Coverage Processing Service (WCPS) for data querying. Various WCPS queries have been designed to access spatial and spectral subsets of the CRISM data. The client WebGIS, consisting mainly of the OpenLayers javascript library, uses these queries to enable online spatial and spectral analysis. Currently the PlanetServer demonstration consists of two CRISM Full Resolution Target (FRT) observations, surrounding the NASA Curiosity rover landing site. A detailed analysis of one of these observations is performed in the Case Study section. The current PlanetServer functionality is described step by step, and is tested by focusing on detecting mineralogical evidence described in earlier Gale crater studies. Both the PlanetServer methodology and its possible use for mineralogical studies will be further discussed. Future work includes batch ingestion of CRISM data and further development of the WebGIS and analysis tools.

  20. Implementation of Web Usage Mining Using APRIORI and FP Growth Algorithms

    Directory of Open Access Journals (Sweden)

    B.Santhosh Kumar

    2010-05-01

    Full Text Available Web Usage Mining is the application of data mining techniques to discover interesting usage patterns from Web data, in order to understand and better serve the needs of Web-based applications. Usage data captures the identity or origin of Web users along with their browsing behavior at a Web site. Web usage mining itself can be classified further depending on the kind of usage data considered. They are web server data, application server data and application level data. Web server data correspond to the user logs that are collected at Web server. Some of the typical data collected at a Web server include IP addresses, page references, and access time of the users and is the main input to the present Research. This Research work concentrates on web usage mining and in particular focuses on discovering the web usage patterns of websites from the server log files. The comparison of memory usage and time usage is compared using Apriori algorithm and Frequent Pattern Growth algorithm.