WorldWideScience

Sample records for integrated web server

  1. Web server attack analyzer

    OpenAIRE

    Mižišin, Michal

    2013-01-01

    Web server attack analyzer - Abstract The goal of this work was to create prototype of analyzer of injection flaws attacks on web server. Proposed solution combines capabilities of web application firewall and web server log analyzer. Analysis is based on configurable signatures defined by regular expressions. This paper begins with summary of web attacks, followed by detection techniques analysis on web servers, description and justification of selected implementation. In the end are charact...

  2. Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA.

    Science.gov (United States)

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

    2010-07-01

    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.

  3. Web Server Embedded System

    Directory of Open Access Journals (Sweden)

    Adharul Muttaqin

    2014-07-01

    Full Text Available Abstrak Embedded sistem saat ini menjadi perhatian khusus pada teknologi komputer, beberapa sistem operasi linux dan web server yang beraneka ragam juga sudah dipersiapkan untuk mendukung sistem embedded, salah satu aplikasi yang dapat digunakan dalam operasi pada sistem embedded adalah web server. Pemilihan web server pada lingkungan embedded saat ini masih jarang dilakukan, oleh karena itu penelitian ini dilakukan dengan menitik beratkan pada dua buah aplikasi web server yang tergolong memiliki fitur utama yang menawarkan “keringanan” pada konsumsi CPU maupun memori seperti Light HTTPD dan Tiny HTTPD. Dengan menggunakan parameter thread (users, ramp-up periods, dan loop count pada stress test embedded system, penelitian ini menawarkan solusi web server manakah diantara Light HTTPD dan Tiny HTTPD yang memiliki kecocokan fitur dalam penggunaan embedded sistem menggunakan beagleboard ditinjau dari konsumsi CPU dan memori. Hasil penelitian menunjukkan bahwa dalam hal konsumsi CPU pada beagleboard embedded system lebih disarankan penggunaan Light HTTPD dibandingkan dengan tiny HTTPD dikarenakan terdapat perbedaan CPU load yang sangat signifikan antar kedua layanan web tersebut Kata kunci: embedded system, web server Abstract Embedded systems are currently of particular concern in computer technology, some of the linux operating system and web server variegated also prepared to support the embedded system, one of the applications that can be used in embedded systems are operating on the web server. Selection of embedded web server on the environment is still rarely done, therefore this study was conducted with a focus on two web application servers belonging to the main features that offer a "lightness" to the CPU and memory consumption as Light HTTPD and Tiny HTTPD. By using the parameters of the thread (users, ramp-up periods, and loop count on a stress test embedded systems, this study offers a solution of web server which between the Light

  4. 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/....

  5. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  7. Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.

    Science.gov (United States)

    Arneson, Douglas; Bhattacharya, Anindya; Shu, Le; Mäkinen, Ville-Petteri; Yang, Xia

    2016-09-09

    Human diseases are commonly the result of multidimensional changes at molecular, cellular, and systemic levels. Recent advances in genomic technologies have enabled an outpour of omics datasets that capture these changes. However, separate analyses of these various data only provide fragmented understanding and do not capture the holistic view of disease mechanisms. To meet the urgent needs for tools that effectively integrate multiple types of omics data to derive biological insights, we have developed Mergeomics, a computational pipeline that integrates multidimensional disease association data with functional genomics and molecular networks to retrieve biological pathways, gene networks, and central regulators critical for disease development. To make the Mergeomics pipeline available to a wider research community, we have implemented an online, user-friendly web server ( http://mergeomics. idre.ucla.edu/ ). The web server features a modular implementation of the Mergeomics pipeline with detailed tutorials. Additionally, it provides curated genomic resources including tissue-specific expression quantitative trait loci, ENCODE functional annotations, biological pathways, and molecular networks, and offers interactive visualization of analytical results. Multiple computational tools including Marker Dependency Filtering (MDF), Marker Set Enrichment Analysis (MSEA), Meta-MSEA, and Weighted Key Driver Analysis (wKDA) can be used separately or in flexible combinations. User-defined summary-level genomic association datasets (e.g., genetic, transcriptomic, epigenomic) related to a particular disease or phenotype can be uploaded and computed real-time to yield biologically interpretable results, which can be viewed online and downloaded for later use. Our Mergeomics web server offers researchers flexible and user-friendly tools to facilitate integration of multidimensional data into holistic views of disease mechanisms in the form of tissue-specific key regulators

  8. FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.

    Science.gov (United States)

    Mader, Malte; Simon, Ronald; Kurtz, Stefan

    2014-03-31

    A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells. One of the most effective ways to rapidly obtain an overview of genomic alterations in large amounts of genomic data is the integrative visualization of genomic events. We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research. A powerful search interface and a fast visualization engine provide a highly interactive visualization for such data. High quality image export enables the life scientist to easily communicate their results. A comprehensive data administration allows to keep track of the available data sets. We applied FISH Oracle 2 to published data and found evidence that, in colorectal cancer cells, the gene TTC28 may be inactivated in two different ways, a fact that has not been published before. The interactive nature of FISH Oracle 2 and the possibility to store, select and visualize large amounts of downstream processed data support life scientists in generating hypotheses. The export of high quality images supports explanatory data visualization, simplifying the communication of new biological findings. A FISH Oracle 2 demo server and the software is available at http://www.zbh.uni-hamburg.de/fishoracle.

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

    Science.gov (United States)

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

    2016-03-28

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

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

    Science.gov (United States)

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

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  11. 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.

  12. Web Server Configuration for an Academic Intranet

    National Research Council Canada - National Science Library

    Baltzis, Stamatios

    2000-01-01

    .... One of the factors that boosted this ability was the evolution of the Web Servers. Using the web server technology man can be connected and exchange information with the most remote places all over the...

  13. Implementation of SRPT Scheduling in Web Servers

    National Research Council Canada - National Science Library

    Harchol-Balter, Mor

    2000-01-01

    .... Experiments use the Linux operating system and the Flash web server. All experiments are repeated under a range of server loads and under both trace-based workloads and those generated by a Web workload generator...

  14. Web server for priority ordered multimedia services

    Science.gov (United States)

    Celenk, Mehmet; Godavari, Rakesh K.; Vetnes, Vermund

    2001-10-01

    In this work, our aim is to provide finer priority levels in the design of a general-purpose Web multimedia server with provisions of the CM services. The type of services provided include reading/writing a web page, downloading/uploading an audio/video stream, navigating the Web through browsing, and interactive video teleconferencing. The selected priority encoding levels for such operations follow the order of admin read/write, hot page CM and Web multicasting, CM read, Web read, CM write and Web write. Hot pages are the most requested CM streams (e.g., the newest movies, video clips, and HDTV channels) and Web pages (e.g., portal pages of the commercial Internet search engines). Maintaining a list of these hot Web pages and CM streams in a content addressable buffer enables a server to multicast hot streams with lower latency and higher system throughput. Cold Web pages and CM streams are treated as regular Web and CM requests. Interactive CM operations such as pause (P), resume (R), fast-forward (FF), and rewind (RW) have to be executed without allocation of extra resources. The proposed multimedia server model is a part of the distributed network with load balancing schedulers. The SM is connected to an integrated disk scheduler (IDS), which supervises an allocated disk manager. The IDS follows the same priority handling as the SM, and implements a SCAN disk-scheduling method for an improved disk access and a higher throughput. Different disks are used for the Web and CM services in order to meet the QoS requirements of CM services. The IDS ouput is forwarded to an Integrated Transmission Scheduler (ITS). The ITS creates a priority ordered buffering of the retrieved Web pages and CM data streams that are fed into an auto regressive moving average (ARMA) based traffic shaping circuitry before being transmitted through the network.

  15. Supervisory control system implemented in programmable logical controller web server

    OpenAIRE

    Milavec, Simon

    2012-01-01

    In this thesis, we study the feasibility of supervisory control and data acquisition (SCADA) system realisation in a web server of a programmable logic controller. With the introduction of Ethernet protocol to the area of process control, the more powerful programmable logic controllers obtained integrated web servers. The web server of a programmable logic controller, produced by Siemens, will also be described in this thesis. Firstly, the software and the hardware equipment used for real...

  16. 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.

  17. 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

  18. Using Web Server Logs in Evaluating Instructional Web Sites.

    Science.gov (United States)

    Ingram, Albert L.

    2000-01-01

    Web server logs contain a great deal of information about who uses a Web site and how they use it. This article discusses the analysis of Web logs for instructional Web sites; reviews the data stored in most Web server logs; demonstrates what further information can be gleaned from the logs; and discusses analyzing that information for the…

  19. 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.

  20. 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…

  1. 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/.

  2. 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)

  3. Solution for an Improved WEB Server

    Directory of Open Access Journals (Sweden)

    George PECHERLE

    2009-12-01

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

  4. Analisis Perbandingan Load Balancing Web Server Tunggal Dengan Web Server Cluster Menggunakan Linux Virtual Server

    OpenAIRE

    Lukitasari, Desy; Oklilas, Ahmad Fali

    2010-01-01

    Virtual server adalah server yang mempunyai skalabilitas dan ketersedian yang tinggi yang dibangun diatas sebuah cluster dari beberapa real server. Real server dan load balancer akan saling terkoneksi baik dalam jaringan lokal kecepatan tinggi atau yang terpisah secara geografis. Load balancer dapat mengirim permintaan-permintaan ke server yang berbeda dan membuat paralel service dari sebuah cluster pada sebuah alamat IP tunggal dan meminta pengiriman dapat menggunakan teknologi IP load...

  5. 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.

  6. A Web-Based Airborne Remote Sensing Telemetry Server, Phase I

    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,...

  7. UPGRADE OF THE CENTRAL WEB SERVERS

    CERN Multimedia

    WEB Services

    2000-01-01

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

  8. 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

    2012-07-01

    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/.

  9. 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.

  10. Amino Acid Interaction (INTAA) web server.

    Science.gov (United States)

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

    2017-07-03

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

  11. Expitope: a web server for epitope expression.

    Science.gov (United States)

    Haase, Kerstin; Raffegerst, Silke; Schendel, Dolores J; Frishman, Dmitrij

    2015-06-01

    Adoptive T cell therapies based on introduction of new T cell receptors (TCRs) into patient recipient T cells is a promising new treatment for various kinds of cancers. A major challenge, however, is the choice of target antigens. If an engineered TCR can cross-react with self-antigens in healthy tissue, the side-effects can be devastating. We present the first web server for assessing epitope sharing when designing new potential lead targets. We enable the users to find all known proteins containing their peptide of interest. The web server returns not only exact matches, but also approximate ones, allowing a number of mismatches of the users choice. For the identified candidate proteins the expression values in various healthy tissues, representing all vital human organs, are extracted from RNA Sequencing (RNA-Seq) data as well as from some cancer tissues as control. All results are returned to the user sorted by a score, which is calculated using well-established methods and tools for immunological predictions. It depends on the probability that the epitope is created by proteasomal cleavage and its affinities to the transporter associated with antigen processing and the major histocompatibility complex class I alleles. With this framework, we hope to provide a helpful tool to exclude potential cross-reactivity in the early stage of TCR selection for use in design of adoptive T cell immunotherapy. The Expitope web server can be accessed via http://webclu.bio.wzw.tum.de/expitope. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  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 (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...

  13. 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

  14. Mfold web server for nucleic acid folding and hybridization prediction.

    Science.gov (United States)

    Zuker, Michael

    2003-07-01

    The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.

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

    Science.gov (United States)

    2012-01-01

    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. PMID:23256920

  16. 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.

  17. 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.

  18. 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.

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

    Science.gov (United States)

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

    2016-07-08

    In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown 'chemical space' to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for 'chemical space', which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

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

    2016-01-01

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

  1. COMAN: a web server for comprehensive metatranscriptomics analysis.

    Science.gov (United States)

    Ni, Yueqiong; Li, Jun; Panagiotou, Gianni

    2016-08-11

    Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming. We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.

  2. 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.

  3. Dynamic thread assignment in web server performance optimization

    NARCIS (Netherlands)

    van der Weij, W.; Bhulai, S.; van der Mei, R.D.

    2009-01-01

    Popular web sites are expected to handle huge number of requests concurrently within a reasonable time frame. The performance of these web sites is largely dependent on effective thread management of their web servers. Although the implementation of static and dynamic thread policies is common

  4. Building a Library Web Server on a Budget.

    Science.gov (United States)

    Orr, Giles

    1998-01-01

    Presents a method for libraries with limited budgets to create reliable Web servers with existing hardware and free software available via the Internet. Discusses staff, hardware and software requirements, and security; outlines the assembly process. (PEN)

  5. Continuous Integration in PHP web applications development

    OpenAIRE

    Hujer, Martin

    2011-01-01

    This work deals with continuous integration of web applications, especially those in PHP language. The main objective is the selection of the server for continuous integration, its deployment and configuration for continuous integration of PHP web applications. The first chapter describes the concept of continuous integration and its individual techniques. The second chapter deals with the choice of server for continuous integration and its basic settings. The third chapter contains an overvi...

  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. 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

  8. 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

  9. 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

    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...... for a given sequence. Together with the predicted topology, the server also displays a signal peptide prediction determined with SPEP. The PONGO web server is available at http://pongo.biocomp.unibo.it/pongo .......The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes ( http://www.biosapiens.info/ ). In this context, the PONGO DAS server ( http...

  10. MultiSETTER: web server for multiple RNA structure comparison.

    Science.gov (United States)

    Čech, Petr; Hoksza, David; Svozil, Daniel

    2015-08-12

    Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

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

    Science.gov (United States)

    Umapathy, Karthikeyan; Wallace, F. Layne

    2010-01-01

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

  12. Professional Microsoft SQL Server 2012 Integration Services

    CERN Document Server

    Knight, Brian; Moss, Jessica M; Davis, Mike; Rock, Chris

    2012-01-01

    An in-depth look at the radical changes to the newest release of SISS Microsoft SQL Server 2012 Integration Services (SISS) builds on the revolutionary database product suite first introduced in 2005. With this crucial resource, you will explore how this newest release serves as a powerful tool for performing extraction, transformation, and load operations (ETL). A team of SQL Server experts deciphers this complex topic and provides detailed coverage of the new features of the 2012 product release. In addition to technical updates and additions, the authors present you with a new set of SISS b

  13. 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

  14. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

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

    Science.gov (United States)

    Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Yuhong Zhu

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

  17. PENGUKURAN KINERJA ROUND-ROBIN SCHEDULER UNTUK LINUX VIRTUAL SERVER PADA KASUS WEB SERVER

    Directory of Open Access Journals (Sweden)

    Royyana Muslim Ijtihadie

    2005-07-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Dengan meningkatnya perkembangan jumlah pengguna internet dan mulai diadopsinya penggunaan internet dalam kehidupan sehari-hari, maka lalulintas data di Internet telah meningkat secara signifikan. Sejalan dengan itu pula beban kerja server-server yang memberikan service di Internet juga mengalami kenaikan yang cukup signifikan. Hal tersebut dapat mengakibatkan suatu server mengalami kelebihan beban pada suatu saat. Untuk mengatasi hal tersebut maka diterapkan skema konfigurasi server cluster menggunakan konsep load balancing. Load balancing server menerapkan algoritma dalam melakukan pembagian tugas. Algoritma round robin telah digunakan pada Linux Virtual Server. Penelitian ini melakukan pengukuran kinerja terhadap Linux Virtual Server yang menggunakan algoritma round robin untuk melakukan penjadwalan pembagian beban terhadap server. Penelitian ini mengukur performa dari sisi client yang mencoba mengakses web server.performa yang diukur adalah jumlah request yang bisa diselesaikan perdetik (request per second, waktu untuk menyelesaikan per satu request, dan   throughput yang dihasilkan. Dari hasil percobaan didapatkan bahwa penggunaan LVS bisa meningkatkan performa, yaitu menaikkan jumlah request per detik

  18. 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

  19. PANNZER2: a rapid functional annotation web server.

    Science.gov (United States)

    Törönen, Petri; Medlar, Alan; Holm, Liisa

    2018-05-08

    The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

  20. 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.

  1. Analisis Perbandingan Unjuk Kerja Sistem Penyeimbang Beban Web Server dengan HAProxy dan Pound Links

    Directory of Open Access Journals (Sweden)

    Dite Ardian

    2013-04-01

    Full Text Available The development of internet technology has many organizations that expanded service website. Initially used single web server that is accessible to everyone through the Internet, but when the number of users that access the web server is very much the traffic load to the web server and the web server anyway. It is necessary for the optimization of web servers to cope with the overload received by the web server when traffic is high. Methodology of this final project research include the study of literature, system design, and testing of the system. Methods from the literature reference books related as well as from several sources the internet. The design of this thesis uses Haproxy and Pound Links as a load balancing web server. The end of this reaserch is testing the network system, where the system will be tested this stage so as to create a web server system that is reliable and safe. The result is a web server system that can be accessed by many user simultaneously rapidly as load balancing Haproxy and Pound Links system which is set up as front-end web server performance so as to create a web server that has performance and high availability.

  2. 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

  3. Analisis Kinerja Penerapan Container untuk Load Balancing Web Server

    Directory of Open Access Journals (Sweden)

    Muhammad Agung Nugroho

    2016-12-01

    Full Text Available Container merupakan teknologi virtualisasi terbaru. Container memudahkan system administrator dalam mengelola aplikasi pada server. Docker container dapat digunakan untuk membangun, mempersiapkan, dan menjalankan aplikasi. Dapat membuat aplikasi dari bahasa pemrograman yang berbeda pada lapisan apapun. Aplikasi dapat di bungkus dalam container, dan aplikasi dapat berjalan pada lingkungan apapun dimana saja.  Dalam perkembangannya container ini dapat digunakan untuk load balancing, dengan memanfaatkan HA Proxy. Load Balancing dapat digunakan untuk menyelesaikan permasalahan beban kinerja web server yang terlalu berat (overload terhadap permintaan. Load Balancing merupakan salah satu metode untuk meningkatkan skalabilitas web server sekaligus mengurangi beban kerja web server. Ujicoba dilakukan dengan memberikan beban request pada single container dan multi container, dan membandingkan kinerjanya. Analisis kinerja dapat dilakukan dengan menggunakan parameter performance pada processor, memori dan proses layanan. Penerapan ujicoba dilakukan pada raspberry pi. Hasil yang diperoleh multi container dapat digunakan untuk mengembangkan metode load balancing, hasil ujicoba menunjukkan performance raspberry pi dapat optimum karena pembagian beban processor.

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

  5. minepath.org: a free interactive pathway analysis web server.

    Science.gov (United States)

    Koumakis, Lefteris; Roussos, Panos; Potamias, George

    2017-07-03

    ( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. A web server for analysis, comparison and prediction of protein ligand binding sites.

    Science.gov (United States)

    Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

    2016-03-25

    One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

  7. The new protein topology graph library web server.

    Science.gov (United States)

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

    2016-02-01

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

  8. AlignMe—a membrane protein sequence alignment web server

    Science.gov (United States)

    Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

    2014-01-01

    We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

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

    OpenAIRE

    Dimnik, Tomaž

    2016-01-01

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

  10. 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/.

  11. 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

  12. 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.

  13. Penerapan Pengujian Keamanan Web Server Menggunakan Metode OWASP versi 4 (Studi Kasus Web Server Ujian Online

    Directory of Open Access Journals (Sweden)

    Mohammad Muhsin

    2016-05-01

    Full Text Available Fakultas Teknik Universitas Muhammadiyah Ponorogo telah menerapkan Ujian Tengah Semester dan Ujian Akhir Semester menggunakan aplikasi Si Ujo (Sistem Ujian Online berbasis web. Sejak tahun 2012 sampai tahun 2014, Si Ujo telah beberapa kali mengalami pengembangan baik dari sisi fitur maupun data yang disimpan. Data tersebut menyimpan data nilai matakuliah setiap mahasiswa teknik Universitas Muhammadiyah Ponorogo. Mengingat pentingnya data yang tersimpan maka perlu diterapkan pengujian keamanan dari aplikasi Si Ujo. Pengujian keamanan tersebut dilakukan untuk mengetahui tingkat kerentanan agar terhindar dari serangan dari pihak yang tidak bertanggung jawab. Salah satu metode untuk menguji aplikasi berbasis web adalah metode OWASP (Open Web Application Security Project versi 4 yang dikeluarkan oleh owasp.org sebuah organisasi non profit yang berdedikasi pada keamanan aplikasi berbasis web. Hasil pengujian menggunakan OWASP versi 4 menunjukkan bahwa manajemen otentifikasi, otorisasi dan manajemen sesi belum diimplementasikan dengan baik sehingga perlu dilakukan perbaikan lebih lanjut oleh pihak stake holder Fakul tas Teknik Universitas Muhammadiyah Ponorogo

  14. 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.

  15. WebSphere Application Server Step by Step

    CERN Document Server

    Cline, Owen; Van Sickel, Peter

    2012-01-01

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

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

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    El-Kalioby Mohamed

    2010-06-01

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

  19. COGNAT: a web server for comparative analysis of genomic neighborhoods.

    Science.gov (United States)

    Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

    2017-11-22

    In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

  20. The HMMER Web Server for Protein Sequence Similarity Search.

    Science.gov (United States)

    Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

    2017-12-08

    Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  1. StarScan: a web server for scanning small RNA targets from degradome sequencing data.

    Science.gov (United States)

    Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

    2015-07-01

    Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. 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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  4. PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

    Science.gov (United States)

    Kuzniar, Arnold; Kanaar, Roland

    2014-07-01

    We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

    Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong

    2011-09-07

    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. 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. WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.

  6. 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.

  7. TMFoldWeb: a web server for predicting transmembrane protein fold class.

    Science.gov (United States)

    Kozma, Dániel; Tusnády, Gábor E

    2015-09-17

    Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

  8. Rtools: a web server for various secondary structural analyses on single RNA sequences.

    Science.gov (United States)

    Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

    2016-07-08

    The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

    Science.gov (United States)

    Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen

    2014-07-01

    The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. 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.

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

    Science.gov (United States)

    Knudsen, Vegeir; Caetano-Anollés, Gustavo

    2008-01-01

    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. PMID:18448469

  12. Analisis Algoritma Pergantian Cache Pada Proxy Web Server Internet Dengan Simulasi

    OpenAIRE

    Nurwarsito, Heru

    2007-01-01

    Pertumbuhan jumlah client internet dari waktu ke waktu terus bertambah, maka respon akses internet menjadi semakin lambat. Untuk membantu kecepatan akses tersebut maka diperlukan cache pada Proxy Server. Penelitian ini bertujuan untuk menganalisis performansi Proxy Server pada Jaringan Internet terhadap penggunaan algoritma pergantian cache-nya.Analisis Algoritma Pergantian Cache Pada Proxy Server didesain dengan metoda pemodelan simulasi jaringan internet yang terdiri dari Web server, Proxy ...

  13. 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 RNA...... motif of limited size, or the entire sequences can be aligned locally or globally. The web server offers a graphical interface, which makes it simple to make alignments and manually browse the results. the web server can be accessed at http://foldalign.kvl.dk...

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

    Science.gov (United States)

    Coombs, Karen A.

    2005-01-01

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

  15. 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

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

    Science.gov (United States)

    York, David W.; Ponyik, Joseph G.

    2000-01-01

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

  17. 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...

  18. 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.

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

    OpenAIRE

    Dalai, Asish Kumar; Jena, Sanjay Kumar

    2017-01-01

    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 prevent...

  20. Bringing it All Together: NODC's Geoportal Server as an Integration Tool for Interoperable Data Services

    Science.gov (United States)

    Casey, K. S.; Li, Y.

    2011-12-01

    The US National Oceanographic Data Center (NODC) has implemented numerous interoperable data technologies in recent years to enhance the discovery, understanding, and use of the vast quantities of data in the NODC archives. These services include OPeNDAP's Hyrax server, Unidata's THREDDS Data Server (TDS), NOAA's Live Access Server (LAS), and most recently the ESRI ArcGIS Server. Combined, these technologies enable NODC to provide access to its data holdings and products through most of the commonly-used standardized web services like the Data Access Protocol (DAP) and the Open Geospatial Consortium suite of services such as the Web Mapping Service (WMS) and Web Coverage Service (WCS). Despite the strong demand for and use of these services, the acronym-rich environment of services can also result in confusion for producers of data to the NODC archives, for consumers of data from the NODC archives, and for the data stewards at the archives as well. The situation is further complicated by the fact that NODC also maintains some ad hoc services like WODselect, and that not all services can be applied to all of the tens of thousands of collections in the NODC archive; where once every data set was available only through FTP and HTTP servers, now many are also available from the LAS, TDS, Hyrax, and ArcGIS Server. To bring order and clarity to this potentially confusing collection of services, NODC deployed the Geoportal Server into its Archive Management System as an integrating technology that brings together its various data access, visualization, and discovery services as well as its overall metadata management workflows. While providing an enhanced web-based interface for more integrated human-to-machine discovery and access, the deployment also enables NODC for the first time to support a robust set of machine-to-machine discovery services such as the Catalog Service for the Web (CS/W), OpenSearch, and Search and Retrieval via URL (SRU) . This approach allows NODC

  1. 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…

  2. ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.

    Science.gov (United States)

    Konc, Janez; Janezic, Dusanka

    2012-07-01

    The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.

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

    NARCIS (Netherlands)

    Van Der Schot, Gijs; Bonvin, Alexandre M J J

    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

  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. A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

    Science.gov (United States)

    Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

    2012-07-01

    The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

  6. WEB-server for search of a periodicity in amino acid and nucleotide sequences

    Science.gov (United States)

    E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

    2017-12-01

    A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

  7. Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server

    Science.gov (United States)

    2016-09-01

    tool has been developed for many platforms: Android , iOS, and Windows. The Windows version has been developed as a web server that allows the...Microsoft Windows. 15. SUBJECT TERMS Applied Anomaly Detection Tool, AADT, Windows, server, web service, installation 16. SECURITY CLASSIFICATION OF: 17...instructional information about identifying them as groups and individually. The software has been developed for several different platforms: Android

  8. CentroidFold: a web server for RNA secondary structure prediction

    OpenAIRE

    Sato, Kengo; Hamada, Michiaki; Asai, Kiyoshi; Mituyama, Toutai

    2009-01-01

    The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the ser...

  9. AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

    Science.gov (United States)

    Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

    2017-01-01

    Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

  10. 3Drefine: an interactive web server for efficient protein structure refinement.

    Science.gov (United States)

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

    2016-07-08

    3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

    Science.gov (United States)

    Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

    2017-07-03

    AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

    Ochoa, David; Pazos, Florencio

    2010-05-15

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

  13. TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.

    Science.gov (United States)

    Bonnet, Eric; He, Ying; Billiau, Kenny; Van de Peer, Yves

    2010-06-15

    We present a new web server called TAPIR, designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. The TAPIR web server can be accessed at: http://bioinformatics.psb.ugent.be/webtools/tapir. Supplementary data are available at Bioinformatics online.

  14. APLIKASI PEMBELAJARAN INTEGRAL BERBASIS WEB

    Directory of Open Access Journals (Sweden)

    Juwairiah Juwairiah Juwairiah

    2015-04-01

    Full Text Available Mathematics lessons, is one lesson that is not liked by the students. Hearing the words of mathematics, will only think of the word difficult by the students. This is because the medium of learning that there are still less attractive. The material is a material that is considered integral to the most difficult of lessons. Thus the need for an application that can be used to study the material with the pattern of applied learning and interesting .. System development method used is waterfall method of analysis, design, programming, testing, and maintenance. This application uses the programming language PHP, MySql as database, Dreamweaver, Macromedia Flash for animation and Photoshop as graphic design. Web server used is Apache.

  15. GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

    Science.gov (United States)

    Chande, Aroon T; Wang, Lu; Rishishwar, Lavanya; Conley, Andrew B; Norris, Emily T; Valderrama-Aguirre, Augusto; Jordan, I King

    2018-05-18

    Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

  16. 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.

  17. DelPhiForce web server: electrostatic forces and energy calculations and visualization.

    Science.gov (United States)

    Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

    2017-11-15

    Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  18. DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

    Science.gov (United States)

    Wang, Lin; Zhang, Min; Alexov, Emil

    2016-02-15

    A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2016-06-01

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

  1. PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins.

    Science.gov (United States)

    Hussein, Hiba Abi; Borrel, Alexandre; Geneix, Colette; Petitjean, Michel; Regad, Leslie; Camproux, Anne-Claude

    2015-07-01

    Predicting protein pocket's ability to bind drug-like molecules with high affinity, i.e. druggability, is of major interest in the target identification phase of drug discovery. Therefore, pocket druggability investigations represent a key step of compound clinical progression projects. Currently computational druggability prediction models are attached to one unique pocket estimation method despite pocket estimation uncertainties. In this paper, we propose 'PockDrug-Server' to predict pocket druggability, efficient on both (i) estimated pockets guided by the ligand proximity (extracted by proximity to a ligand from a holo protein structure) and (ii) estimated pockets based solely on protein structure information (based on amino atoms that form the surface of potential binding cavities). PockDrug-Server provides consistent druggability results using different pocket estimation methods. It is robust with respect to pocket boundary and estimation uncertainties, thus efficient using apo pockets that are challenging to estimate. It clearly distinguishes druggable from less druggable pockets using different estimation methods and outperformed recent druggability models for apo pockets. It can be carried out from one or a set of apo/holo proteins using different pocket estimation methods proposed by our web server or from any pocket previously estimated by the user. PockDrug-Server is publicly available at: http://pockdrug.rpbs.univ-paris-diderot.fr. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Development of Sales and Inventory Workflow Management Information System Web Portal for Petrospan Integrated Services, Eket, Akwa Ibom State, Nigeria

    OpenAIRE

    Ezeonwumelu, Adanna Ngozi; Eunice, Akinloye Bolanle; Ezenugu, Isaac A.

    2017-01-01

    In this paper, the development of Sales and Inventory Workflow Management Information System (SIWfMS) web portal for Petrospan Integrated Services, Eket, Akwa Ibom state, Nigeria was presented. Rapid Application Development (RAP) methodology is used in the web application development. Three-tier architecture based on WAMP server configuration was adopted. The WAMP server was made up of Windows Operating system; Apache web server, MySQL database system and PHP server-side scripting langue. The...

  3. GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

    Science.gov (United States)

    Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

    2017-07-03

    Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. 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.

  5. 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.

  6. AnnoLnc: a web server for systematically annotating novel human lncRNAs.

    Science.gov (United States)

    Hou, Mei; Tang, Xing; Tian, Feng; Shi, Fangyuan; Liu, Fenglin; Gao, Ge

    2016-11-16

    Long noncoding RNAs (lncRNAs) have been shown to play essential roles in almost every important biological process through multiple mechanisms. Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive, calling for a systematic and integrative annotation tool. Here we present AnnoLnc ( http://annolnc.cbi.pku.edu.cn ), a one-stop portal for systematically annotating novel human lncRNAs. Based on more than 700 data sources and various tool chains, AnnoLnc enables a systematic annotation covering genomic location, secondary structure, expression patterns, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution. An intuitive web interface is available for interactive analysis through both desktops and mobile devices, and programmers can further integrate AnnoLnc into their pipeline through standard JSON-based Web Service APIs. To the best of our knowledge, AnnoLnc is the only web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Compared with similar tools, the annotation generated by AnnoLnc covers a much wider spectrum with intuitive visualization. Case studies demonstrate the power of AnnoLnc in not only rediscovering known functions of human lncRNAs but also inspiring novel hypotheses.

  7. MCTBI: a web server for predicting metal ion effects in RNA structures.

    Science.gov (United States)

    Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

    2017-08-01

    Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  8. CovalentDock Cloud: a web server for automated covalent docking.

    Science.gov (United States)

    Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

    2013-07-01

    Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

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

    Science.gov (United States)

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

    2000-01-01

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

  10. SQL Server 2012 data integration recipes solutions for integration services and other ETL tools

    CERN Document Server

    Aspin, Adam

    2012-01-01

    SQL Server 2012 Data Integration Recipes provides focused and practical solutions to real world problems of data integration. Need to import data into SQL Server from an outside source? Need to export data and send it to another system? SQL Server 2012 Data Integration Recipes has your back. You'll find solutions for importing from Microsoft Office data stores such as Excel and Access, from text files such as CSV files, from XML, from other database brands such as Oracle and MySQL, and even from other SQL Server databases. You'll learn techniques for managing metadata, transforming data to mee

  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. Genonets server-a web server for the construction, analysis and visualization of genotype networks.

    Science.gov (United States)

    Khalid, Fahad; Aguilar-Rodríguez, José; Wagner, Andreas; Payne, Joshua L

    2016-07-08

    A genotype network is a graph in which vertices represent genotypes that have the same phenotype. Edges connect vertices if their corresponding genotypes differ in a single small mutation. Genotype networks are used to study the organization of genotype spaces. They have shed light on the relationship between robustness and evolvability in biological systems as different as RNA macromolecules and transcriptional regulatory circuits. Despite the importance of genotype networks, no tool exists for their automatic construction, analysis and visualization. Here we fill this gap by presenting the Genonets Server, a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography and how it relates to the navigability of a genotype network via mutation and natural selection; (iii) multiple interactive visualizations that facilitate exploratory research and education. The Genonets Server is freely available at http://ieu-genonets.uzh.ch. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

    Science.gov (United States)

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

    2009-06-01

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

  15. miRNAFold: a web server for fast miRNA precursor prediction in genomes.

    Science.gov (United States)

    Tav, Christophe; Tempel, Sébastien; Poligny, Laurent; Tahi, Fariza

    2016-07-08

    Computational methods are required for prediction of non-coding RNAs (ncRNAs), which are involved in many biological processes, especially at post-transcriptional level. Among these ncRNAs, miRNAs have been largely studied and biologists need efficient and fast tools for their identification. In particular, ab initio methods are usually required when predicting novel miRNAs. Here we present a web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high sensitivity. miRNAFold is implemented as a web server with an intuitive and user-friendly interface, as well as a standalone version. The web server is freely available at: http://EvryRNA.ibisc.univ-evry.fr/miRNAFold. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. 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 .

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

    Directory of Open Access Journals (Sweden)

    Mayumbo Nyirenda

    2010-07-01

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

  18. Analisis Kelayakan Sistem Monitoring dan Kontrol Lampu Menggunakan Web Server Berbasis Raspberry Pi

    Directory of Open Access Journals (Sweden)

    Maslan - Maslan

    2017-09-01

    Full Text Available As technology develops progressively over time, system developers continue to strive to create more efficient monitoring systems. The problem that often happens is the control room and light control is currently not utilize an integrated system based web server. Room control systems still utilize large equipment such as televisions and large computers, so that every problem occurs in the room is difficult to control. From these problems then the purpose of this study to create an efficient control system that utilizes super mini-based Raspberry Pi. To create a system based on Raspberry P microcontroller then required an initial observation to perform the feasibility test on the system to be developed. The feasibility test system is the successful monitoring of the room using CCTV (Closed Circuit Television equipment and control the lamp automatically by using prototyping method. The CCTV feasibility test is viewed from the resolution while the control of room light control is seen from the success of controlling the life of the lights on the test. Based on the testing concluded that the monitoring of the room using Raspberry Pi-based web server is feasible to use, seen the test results when the light control goes smoothly, because the lights controlled through the webserver managed to live and die. Similarly, when monitoring the room with live CCTV also runs well. And while conducting Room monitoring experiments with Webcam at 800 x 600 resolution there is a lot of variation value of frame rate sometimes up and down. The up and down frame is caused by an unstable network connection.

  19. 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.

  20. SISTEM INFORMASI RUMAH SAKIT BERBASIS WEB MENGGUNAKAN JAVA SERVER PAGES

    Directory of Open Access Journals (Sweden)

    Heru Cahya Rustamaji

    2010-01-01

    Teknologi yang dipakai untuk membangun sistem informasi berbasis web ini adalah menggunakan JSP dan apache Tomcat. Tomcat merupakan servlet engine open source yang termasuk dalam proyek Jakarta yang dikerjakan oleh Apache Software Foundation.

  1. Rclick: a web server for comparison of RNA 3D structures.

    Science.gov (United States)

    Nguyen, Minh N; Verma, Chandra

    2015-03-15

    RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Web Application Design Using Server-Side JavaScript

    Energy Technology Data Exchange (ETDEWEB)

    Hampton, J.; Simons, R.

    1999-02-01

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

  3. Vfold: a web server for RNA structure and folding thermodynamics prediction.

    Science.gov (United States)

    Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

    2014-01-01

    The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

  4. DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

    Science.gov (United States)

    Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

    2012-06-15

    A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

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

    Science.gov (United States)

    Heo, Lim; Feig, Michael

    2018-03-15

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

  6. Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank

    Science.gov (United States)

    Collier, James H.; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

    2012-01-01

    Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80 500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from: http://lcb.infotech.monash.edu.au/super. PMID:22638586

  7. CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments

    OpenAIRE

    Cao, Qingyi; Ma, Jian; Chen, Chen-Hao; Xu, Han; Chen, Zhi; Li, Wei; Liu, X. Shirley

    2017-01-01

    The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioriti...

  8. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    Science.gov (United States)

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  9. 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

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

    OpenAIRE

    Iulian ILIE NEMEDI

    2007-01-01

    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

  11. 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...

  12. 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.

  13. 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.

  14. 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.

  15. Chromothripsis Detection and Characterization Using the CTLPScanner Web Server.

    Science.gov (United States)

    Yang, Jian; Liu, Bo; Cai, Haoyang

    2018-01-01

    Accurate detection of chromothripsis event is important to study the mechanisms underlying this phenomenon. CTLPScanner ( http://cgma.scu.edu.cn/CTLPScanner/ ) is a web-based tool for identification and annotation of chromothripsis-like pattern (CTLP) in genomic array data. In this chapter, we illustrate the utility of CTLPScanner for screening chromosome pulverization regions and give interpretation of the results. The web interface offers a set of parameters and thresholds for customized screening. We also provide practical recommendations for effective chromothripsis detection. In addition to the user data processing module, CTLPScanner contains more than 50,000 preprocessed oncogenomic arrays, which allow users to explore the presence of chromothripsis signatures from public data resources.

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

    Science.gov (United States)

    2016-12-01

    service is developed using Jersey framework , which is an open-source framework for developing RESTful web services in Java that provides support for...interoperability (e.g., between Java and Python or Windows and Linux applications) is due to the use of open standards. 3. Twitter API The scope of this...twitterfeeds/updateTweet. This method should call the appropriate implementation defined in TweetUsingJava. java to obtain response from Twitter API

  17. 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.

  18. Pathview Web: user friendly pathway visualization and data integration.

    Science.gov (United States)

    Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

    2017-07-03

    Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity.

    Science.gov (United States)

    Marini, Simone; Nazzicari, Nelson; Biscarini, Filippo; Wang, Guang-Zhong

    2017-06-15

    Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations. We developed Dscam1 Web Server to quickly predict Dscam1 self- and hetero- binding affinity for batches of Dscam1 isomers. The server can help the study of Dscam1 affinity and help researchers navigate through the tens of millions of possible isomer combinations to isolate the strong-binding ones. Dscam1 Web Server is freely available at: http://bioinformatics.tecnoparco.org/Dscam1-webserver . Web server code is available at https://gitlab.com/ne1s0n/Dscam1-binding . simone.marini@unipv.it or guangzhong.wang@picb.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  20. LocExpress: a web server for efficiently estimating expression of novel transcripts.

    Science.gov (United States)

    Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

    2016-12-22

    The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

  1. The pepATTRACT web server for blind, large-scale peptide-protein docking.

    Science.gov (United States)

    de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

    2017-07-03

    Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. 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.

  3. Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

    Science.gov (United States)

    Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

    2013-01-01

    The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

  4. 3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments.

    KAUST Repository

    Le Pera, Loredana; Mazzapioda, Mariagiovanna; Tramontano, Anna

    2015-01-01

    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.

  5. 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.

  6. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

    Science.gov (United States)

    Tsirigos, Konstantinos D; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

    2015-07-01

    TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. CalFitter: a web server for analysis of protein thermal denaturation data.

    Science.gov (United States)

    Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

    2018-05-14

    Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

  8. HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.

    Science.gov (United States)

    Zhou, Pei; Jin, Bowen; Li, Hao; Huang, Sheng-You

    2018-05-09

    Protein-peptide interactions are crucial in many cellular functions. Therefore, determining the structure of protein-peptide complexes is important for understanding the molecular mechanism of related biological processes and developing peptide drugs. HPEPDOCK is a novel web server for blind protein-peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a success rate of 33.3% in binding mode prediction on a benchmark of 57 unbound cases when the top 10 models were considered, compared to 21.1% for pepATTRACT server. HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions. For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top 10 predictions, compared to 45.2% for HADDOCK peptide protocol. Our HPEPDOCK server is computationally efficient and consumed an average of 29.8 mins for a global peptide docking job and 14.2 mins for a local peptide docking job. The HPEPDOCK web server is available at http://huanglab.phys.hust.edu.cn/hpepdock/.

  9. 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.

  10. TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.

    Science.gov (United States)

    Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

    2015-07-01

    This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Cyber-T web server: differential analysis of high-throughput data.

    Science.gov (United States)

    Kayala, Matthew A; Baldi, Pierre

    2012-07-01

    The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is one of the most widely validated. Cyber-T implements a t-test using a Bayesian framework to compute a regularized variance of the measurements associated with each probe under each condition. This regularized estimate is derived by flexibly combining the empirical measurements with a prior, or background, derived from pooling measurements associated with probes in the same neighborhood. This approach flexibly addresses problems associated with low replication levels and technology biases, not only for DNA microarrays, but also for other technologies, such as protein arrays, quantitative mass spectrometry and next-generation sequencing (RNA-seq). Here we present an update to the Cyber-T web server, incorporating several useful new additions and improvements. Several preprocessing data normalization options including logarithmic and (Variance Stabilizing Normalization) VSN transforms are included. To augment two-sample t-tests, a one-way analysis of variance is implemented. Several methods for multiple tests correction, including standard frequentist methods and a probabilistic mixture model treatment, are available. Diagnostic plots allow visual assessment of the results. The web server provides comprehensive documentation and example data sets. The Cyber-T web server, with R source code and data sets, is publicly available at http://cybert.ics.uci.edu/.

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

    Science.gov (United States)

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

    2010-12-01

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

  13. 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.

  14. GenProBiS: web server for mapping of sequence variants to protein binding sites.

    Science.gov (United States)

    Konc, Janez; Skrlj, Blaz; Erzen, Nika; Kunej, Tanja; Janezic, Dusanka

    2017-07-03

    Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

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

    2014-07-01

    Animal trials are currently the major method for determining the possible toxic effects of drug candidates and cosmetics. In silico prediction methods represent an alternative approach and aim to rationalize the preclinical drug development, thus enabling the reduction of the associated time, costs and animal experiments. Here, we present ProTox, a web server for the prediction of rodent oral toxicity. The prediction method is based on the analysis of the similarity of compounds with known median lethal doses (LD50) and incorporates the identification of toxic fragments, therefore representing a novel approach in toxicity prediction. In addition, the web server includes an indication of possible toxicity targets which is based on an in-house collection of protein-ligand-based pharmacophore models ('toxicophores') for targets associated with adverse drug reactions. The ProTox web server is open to all users and can be accessed without registration at: http://tox.charite.de/tox. The only requirement for the prediction is the two-dimensional structure of the input compounds. All ProTox methods have been evaluated based on a diverse external validation set and displayed strong performance (sensitivity, specificity and precision of 76, 95 and 75%, respectively) and superiority over other toxicity prediction tools, indicating their possible applicability for other compound classes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. SISTEM INFORMASI UJIAN BERBASIS WEB SERVER SMK BINA ISLAM MANDIRI (BISMA KERSANA BREBES TEGAL

    Directory of Open Access Journals (Sweden)

    M. Rifqi Tsani

    2016-09-01

    Full Text Available Seiring dengan berkembangnya kemajuan teknologi informasi, mungkin akan sangat terbantu dengan adanya internet. Dengan internet, kita akan mudah menghadirkan layanan yang dapat diakses dari manapun dan kapanpun di dunia ini. Saat ini hampir setiap orang melakukan pengaksesan informasi, salah satunya dengan situs website. SMK BISMA Kersana merupakan sekolah swasta yang cukup terkenal di daerah Kersana. Dalam tiap tahunnya selalu mengalami kesulitan dalam menyajikan soal-soal yang akan diberikan kepada murid-muridnya. Begitu juga dalam melakukan sistem pengolahan nilai, pada SMK BISMA Kersana masih begitu sederhana sehingga memerlukan waktu yang lama. Untuk mengatasi masalah tersebut, maka diperlukan suatu sistem yang terkomputerisasi untuk mendukung kemajuan dan perkembangan sekolah tersebut. Maka dirancanglah sistem ujian online dan penilaian siswa berbasis web server. Dimana para guru langsung mengolah soal-soal ujian siswa. Begitu juga para siswa setelah melakukan ujian akan bisa langsung melihat hasil ujiannya. Dalam pembuatan sistem informasi ujian berbasis web server ini metode perancangan yang digunakan adalah ADDIE (Analysis, Design, Development or Production, Implementation or Delivery and Evaluations. Dengan menggunakan sistem informasi berbasis web server ini dapat membantu guru dalam memberikan nilai pada anak didiknya yang telah melaksanakn ujian di karenakan sistem ini langsung memberikan hasil berupa nilai ujian setelah siswa melaksanakan ujian.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

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

  2. EarthServer - an FP7 project to enable the web delivery and analysis of 3D/4D models

    Science.gov (United States)

    Laxton, John; Sen, Marcus; Passmore, James

    2013-04-01

    EarthServer aims at open access and ad-hoc analytics on big Earth Science data, based on the OGC geoservice standards Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS). The WCS model defines "coverages" as a unifying paradigm for multi-dimensional raster data, point clouds, meshes, etc., thereby addressing a wide range of Earth Science data including 3D/4D models. WCPS allows declarative SQL-style queries on coverages. The project is developing a pilot implementing these standards, and will also investigate the use of GeoSciML to describe coverages. Integration of WCPS with XQuery will in turn allow coverages to be queried in combination with their metadata and GeoSciML description. The unified service will support navigation, extraction, aggregation, and ad-hoc analysis on coverage data from SQL. Clients will range from mobile devices to high-end immersive virtual reality, and will enable 3D model visualisation using web browser technology coupled with developing web standards. EarthServer is establishing open-source client and server technology intended to be scalable to Petabyte/Exabyte volumes, based on distributed processing, supercomputing, and cloud virtualization. Implementation will be based on the existing rasdaman server technology developed. Services using rasdaman technology are being installed serving the atmospheric, oceanographic, geological, cryospheric, planetary and general earth observation communities. The geology service (http://earthserver.bgs.ac.uk/) is being provided by BGS and at present includes satellite imagery, superficial thickness data, onshore DTMs and 3D models for the Glasgow area. It is intended to extend the data sets available to include 3D voxel models. Use of the WCPS standard allows queries to be constructed against single or multiple coverages. For example on a single coverage data for a particular area can be selected or data with a particular range of pixel values. Queries on multiple surfaces can be

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

  4. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

    Science.gov (United States)

    Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

    2013-07-01

    The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

  5. Analysis of Web Server Log Files: Website of Information Management Department of Hacettepe University

    Directory of Open Access Journals (Sweden)

    Mandana Mir Moftakhari

    2015-09-01

    Full Text Available Over the last decade, the importance of analysing information management systems logs has grown, because it has proved that results of the analysing log data can help developing in information system design, interface and architecture of websites. Log file analysis is one of the best ways in order to understand information-searching process of online searchers, users’ needs, interests, knowledge, and prejudices. The utilization of data collected in transaction logs of web search engines helps designers, researchers and web site managers to find complex interactions of users’ goals and behaviours to increase efficiency and effectiveness of websites. Before starting any analysis it should be observed that the log file of the web site contain enough information, otherwise analyser wouldn’t be able to create complete report. In this study we evaluate the website of Information Management Department of Hacettepe University by analysing the server log files. Results show that there is not adequate amount of information in log files which are provided by web site server. The reports which we have created have some information about users’ behaviour and need but they are not sufficient for taking ideal decisions about contents & hyperlink structure of website. It also provides that creating an extended log file is essential for the website. Finally we believe that results can be helpful to improve, redesign and create better website.

  6. 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/.

  7. 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.

  8. 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

  9. LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

    Science.gov (United States)

    Dodda, Leela S.

    2017-01-01

    Abstract The accurate calculation of protein/nucleic acid–ligand interactions or condensed phase properties by force field-based methods require a precise description of the energetics of intermolecular interactions. Despite the progress made in force fields, small molecule parameterization remains an open problem due to the magnitude of the chemical space; the most critical issue is the estimation of a balanced set of atomic charges with the ability to reproduce experimental properties. The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte Carlo simulation packages. This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations. It is free and open to all at jorgensenresearch.com/ligpargen, and has no login requirements. PMID:28444340

  10. FireProt: web server for automated design of thermostable proteins

    Science.gov (United States)

    Musil, Milos; Stourac, Jan; Brezovsky, Jan; Prokop, Zbynek; Zendulka, Jaroslav; Martinek, Tomas

    2017-01-01

    Abstract There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot. PMID:28449074

  11. The UMLS Knowledge Source Server: an experience in Web 2.0 technologies.

    Science.gov (United States)

    Thorn, Karen E; Bangalore, Anantha K; Browne, Allen C

    2007-10-11

    The UMLS Knowledge Source Server (UMLSKS), developed at the National Library of Medicine (NLM), makes the knowledge sources of the Unified Medical Language System (UMLS) available to the research community over the Internet. In 2003, the UMLSKS was redesigned utilizing state-of-the-art technologies available at that time. That design offered a significant improvement over the prior version but presented a set of technology-dependent issues that limited its functionality and usability. Four areas of desired improvement were identified: software interfaces, web interface content, system maintenance/deployment, and user authentication. By employing next generation web technologies, newer authentication paradigms and further refinements in modular design methods, these areas could be addressed and corrected to meet the ever increasing needs of UMLSKS developers. In this paper we detail the issues present with the existing system and describe the new system's design using new technologies considered entrants in the Web 2.0 development era.

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

    Science.gov (United States)

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

    1999-01-01

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

  13. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

    Science.gov (United States)

    Konc, Janez; Janežič, Dušanka

    2014-07-01

    The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. 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.

  15. The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

    Science.gov (United States)

    Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

    2018-04-01

    The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https

  16. 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

  17. DEVELOPING WEB MAPPING APPLICATION USING ARCGIS SERVER WEB APPLICATION DEVELOPMEN FRAMEWORK (ADF FOR GEOSPATIAL DATA GENERATED DURING REHABILITATION AND RECONSTRUCTION PROCESS OF POST-TSUNAMI 2004 DISASTER IN ACEH

    Directory of Open Access Journals (Sweden)

    Nizamuddin Nizamuddin

    2014-04-01

    Full Text Available ESRI ArcGIS Server is equipped with ArcGIS Server Web Application Development Framework (ADF and ArcGIS Web Controls integration for Visual Studio.NET. Both the ArcGIS Server Manager for .NET and ArcGIS Web Controls can be easily utilized for developing the ASP.NET based ESRI Web mapping application. In  this study we implemented both tools for developing the ASP.NET based ESRI Web mapping application for geospatial data generated dring rehabilitation and reconstruction process of post-tsunami 2004 disaster in Aceh province. Rehabilitation and reconstruction process has produced a tremendous amount of geospatial data. This method was chosen in this study because in the process of developing  a web mapping application, one can easily and quickly create Mapping Services of huge geospatial data and also develop Web mapping application without writing any code. However, when utilizing Visual Studio.NET 2008, one needs to have some coding ability.

  18. An Integrated Library System on the CERN Document Server

    CERN Document Server

    Rodrigues Silvestre, Joaquim Jorge; Le Meur, Jean-Yves; Šimko, Tibor

    2010-01-01

    CERN – The European Organization for Nuclear Research – is one of the largest research centres worldwide, responsible for several discoveries in physics as well as in computer science. The CERN Document Server, also known as CDS Invenio, is a software developed at CERN, which aims to provide a set of tools for managing digital libraries. In order to improve the functionalities of CDS Invenio a new module was developed , called BibCirculation, to manage books (and other items) from the CERN library, and working as an Integrated Library System. This thesis shows the steps that have been done to achieve the several goals of this project, explaining, among others aspects, the process of integration with other existing modules as well as the way to associate the information about books with the metadata from CDS Invenio. You can also find a detailed explanation of the entire implementation process and testing. Finally, there are presented the conclusions of this project and ideas for future development.

  19. dAPE: a web server to detect homorepeats and follow their evolution.

    Science.gov (United States)

    Mier, Pablo; Andrade-Navarro, Miguel A

    2017-04-15

    Homorepeats are low complexity regions consisting of repetitions of a single amino acid residue. There is no current consensus on the minimum number of residues needed to define a functional homorepeat, nor even if mismatches are allowed. Here we present dAPE, a web server that helps following the evolution of homorepeats based on orthology information, using a sensitive but tunable cutoff to help in the identification of emerging homorepeats. dAPE can be accessed from http://cbdm-01.zdv.uni-mainz.de/∼munoz/polyx . munoz@uni-mainz.de. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  20. 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.

  1. Transitioning to Intel-based Linux Servers in the Payload Operations Integration Center

    Science.gov (United States)

    Guillebeau, P. L.

    2004-01-01

    The MSFC Payload Operations Integration Center (POIC) is the focal point for International Space Station (ISS) payload operations. The POIC contains the facilities, hardware, software and communication interface necessary to support payload operations. ISS ground system support for processing and display of real-time spacecraft and telemetry and command data has been operational for several years. The hardware components were reaching end of life and vendor costs were increasing while ISS budgets were becoming severely constrained. Therefore it has been necessary to migrate the Unix portions of our ground systems to commodity priced Intel-based Linux servers. hardware architecture including networks, data storage, and highly available resources. This paper will concentrate on the Linux migration implementation for the software portion of our ground system. The migration began with 3.5 million lines of code running on Unix platforms with separate servers for telemetry, command, Payload information management systems, web, system control, remote server interface and databases. The Intel-based system is scheduled to be available for initial operational use by August 2004 The overall migration to Intel-based Linux servers in the control center involves changes to the This paper will address the Linux migration study approach including the proof of concept, criticality of customer buy-in and importance of beginning with POSlX compliant code. It will focus on the development approach explaining the software lifecycle. Other aspects of development will be covered including phased implementation, interim milestones and metrics measurements and reporting mechanisms. This paper will also address the testing approach covering all levels of testing including development, development integration, IV&V, user beta testing and acceptance testing. Test results including performance numbers compared with Unix servers will be included. need for a smooth transition while maintaining

  2. WEBnm@ v2.0: Web server and services for comparing protein flexibility.

    Science.gov (United States)

    Tiwari, Sandhya P; Fuglebakk, Edvin; Hollup, Siv M; Skjærven, Lars; Cragnolini, Tristan; Grindhaug, Svenn H; Tekle, Kidane M; Reuter, Nathalie

    2014-12-30

    Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

  3. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    Science.gov (United States)

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

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

    Science.gov (United States)

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

    2016-01-01

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

  5. PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

    Science.gov (United States)

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

    2012-07-01

    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.

  6. Web Services Integration on the Fly

    National Research Council Canada - National Science Library

    Leong, Hoe W

    2008-01-01

    .... Given data, software agents and supporting software infrastructure, web services integration on the fly means that human coding is not required to integrate web services into a Web Service Architecture...

  7. CSAR-web: a web server of contig scaffolding using algebraic rearrangements.

    Science.gov (United States)

    Chen, Kun-Tze; Lu, Chin Lung

    2018-05-04

    CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism. It takes as input a target genome in multi-FASTA format and a reference genome in FASTA or multi-FASTA format, depending on whether the reference genome is complete or incomplete, respectively. In addition, it requires the users to choose either 'NUCmer on nucleotides' or 'PROmer on translated amino acids' for CSAR-web to identify conserved genomic markers (i.e. matched sequence regions) between the target and reference genomes, which are used by the rearrangement-based scaffolding algorithm in CSAR-web to order and orient the contigs of the target genome based on the reference genome. In the output page, CSAR-web displays its scaffolding result in a graphical mode (i.e. scalable dotplot) allowing the users to visually validate the correctness of scaffolded contigs and in a tabular mode allowing the users to view the details of scaffolds. CSAR-web is available online at http://genome.cs.nthu.edu.tw/CSAR-web.

  8. COGcollator: a web server for analysis of distant relationships between homologous protein families.

    Science.gov (United States)

    Dibrova, Daria V; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Mulkidjanian, Armen Y

    2017-11-29

    The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs. We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. Here we introduce the COGcollator, a web tool for identification of evolutionarily related COGs and their further analysis. We demonstrate the utility of this tool by identifying the COGs that contain distant homologs of (i) the catalytic subunit of bacterial rotary membrane ATP synthases and (ii) the DNA/RNA helicases of the superfamily 1. This article was reviewed by Drs. Igor N. Berezovsky, Igor Zhulin and Yuri Wolf.

  9. HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

    2017-01-01

    Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

  10. 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.

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

    International Nuclear Information System (INIS)

    Maizura Ibrahim; Rosnah Shariff; Ahmad Bazlie Abdul Kadir; John Konsoh Sangau; Mohd Amin Sharifuldin Salleh; Taiman Kadni; Noriah Mod Ali

    2007-01-01

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

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

  13. Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

    Science.gov (United States)

    Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

    2018-01-01

    The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

  14. 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

    2014-01-01

    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. PMID:24379047

  15. 3dRPC: a web server for 3D RNA-protein structure prediction.

    Science.gov (United States)

    Huang, Yangyu; Li, Haotian; Xiao, Yi

    2018-04-01

    RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

  16. 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

    2009-01-01

    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/. PMID:19531740

  17. 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

    2016-01-01

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

  18. SeMPI: a genome-based secondary metabolite prediction and identification web server.

    Science.gov (United States)

    Zierep, Paul F; Padilla, Natàlia; Yonchev, Dimitar G; Telukunta, Kiran K; Klementz, Dennis; Günther, Stefan

    2017-07-03

    The secondary metabolism of bacteria, fungi and plants yields a vast number of bioactive substances. The constantly increasing amount of published genomic data provides the opportunity for an efficient identification of gene clusters by genome mining. Conversely, for many natural products with resolved structures, the encoding gene clusters have not been identified yet. Even though genome mining tools have become significantly more efficient in the identification of biosynthetic gene clusters, structural elucidation of the actual secondary metabolite is still challenging, especially due to as yet unpredictable post-modifications. Here, we introduce SeMPI, a web server providing a prediction and identification pipeline for natural products synthesized by polyketide synthases of type I modular. In order to limit the possible structures of PKS products and to include putative tailoring reactions, a structural comparison with annotated natural products was introduced. Furthermore, a benchmark was designed based on 40 gene clusters with annotated PKS products. The web server of the pipeline (SeMPI) is freely available at: http://www.pharmaceutical-bioinformatics.de/sempi. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets.

    Science.gov (United States)

    Dozmorov, Mikhail G; Cara, Lukas R; Giles, Cory B; Wren, Jonathan D

    2016-08-01

    The growing amount of regulatory data from the ENCODE, Roadmap Epigenomics and other consortia provides a wealth of opportunities to investigate the functional impact of single nucleotide polymorphisms (SNPs). Yet, given the large number of regulatory datasets, researchers are posed with a challenge of how to efficiently utilize them to interpret the functional impact of SNP sets. We developed the GenomeRunner web server to automate systematic statistical analysis of SNP sets within a regulatory context. Besides defining the functional impact of SNP sets, GenomeRunner implements novel regulatory similarity/differential analyses, and cell type-specific regulatory enrichment analysis. Validated against literature- and disease ontology-based approaches, analysis of 39 disease/trait-associated SNP sets demonstrated that the functional impact of SNP sets corresponds to known disease relationships. We identified a group of autoimmune diseases with SNPs distinctly enriched in the enhancers of T helper cell subpopulations, and demonstrated relevant cell type-specificity of the functional impact of other SNP sets. In summary, we show how systematic analysis of genomic data within a regulatory context can help interpreting the functional impact of SNP sets. GenomeRunner web server is freely available at http://www.integrativegenomics.org/ mikhail.dozmorov@gmail.com 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.

  20. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.

    Science.gov (United States)

    Parca, Luca; Ferré, Fabrizio; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2013-07-01

    Nucleos is a web server for the identification of nucleotide-binding sites in protein structures. Nucleos compares the structure of a query protein against a set of known template 3D binding sites representing nucleotide modules, namely the nucleobase, carbohydrate and phosphate. Structural features, clustering and conservation are used to filter and score the predictions. The predicted nucleotide modules are then joined to build whole nucleotide-binding sites, which are ranked by their score. The server takes as input either the PDB code of the query protein structure or a user-submitted structure in PDB format. The output of Nucleos is composed of ranked lists of predicted nucleotide-binding sites divided by nucleotide type (e.g. ATP-like). For each ranked prediction, Nucleos provides detailed information about the score, the template structure and the structural match for each nucleotide module composing the nucleotide-binding site. The predictions on the query structure and the template-binding sites can be viewed directly on the web through a graphical applet. In 98% of the cases, the modules composing correct predictions belong to proteins with no homology relationship between each other, meaning that the identification of brand-new nucleotide-binding sites is possible using information from non-homologous proteins. Nucleos is available at http://nucleos.bio.uniroma2.it/nucleos/.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. iPhone with Microsoft Exchange Server 2010 Business Integration and Deployment

    CERN Document Server

    Goodman, Steve

    2012-01-01

    iPhone with Microsoft Exchange Server 2010 - Business Integration and Deployment is a practical, step-by-step tutorial on planning, installing and configuring Exchange Server to deploy iPhones into your business. This book is aimed at system administrators who don't necessarily know about Exchange Server 2010 or ActiveSync-based mobile devices. A basic level of knowledge around Windows Servers is expected, and knowledge of smartphones and email systems in general will make some topics a little easier.

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

    Science.gov (United States)

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

    2011-01-01

    APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of 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 electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

  8. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

    Science.gov (United States)

    Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

    2018-05-14

    Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

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

    Energy Technology Data Exchange (ETDEWEB)

    Beer, Tjaart A. P. de; Laskowski, Roman A. [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom); Duban, Mark-Eugene [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Chan, A. W. Edith [University College London, London WC1E 6BT (United Kingdom); Anderson, Wayne F. [Northwestern University Feinberg School of Medicine, Chicago, Illinois (United States); Thornton, Janet M., E-mail: thornton@ebi.ac.uk [European Bioinformatics Institute (EMBL–EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD (United Kingdom)

    2013-12-01

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

  10. iELM—a web server to explore short linear motif-mediated interactions

    Science.gov (United States)

    Weatheritt, Robert J.; Jehl, Peter; Dinkel, Holger; Gibson, Toby J.

    2012-01-01

    The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org. PMID:22638578

  11. 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/.

  12. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

    Science.gov (United States)

    van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

    2018-05-21

    Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

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

    International Nuclear Information System (INIS)

    Neri, Emanuele; Bargellini, Irene; Vignali, Claudio; Bartolozzi, Carlo; Rieger, Michael; Jaschke, Werner; Giachetti, Andrea; Tuveri, Massimiliano

    2005-01-01

    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.)

  14. 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.

  15. ComplexContact: a web server for inter-protein contact prediction using deep learning

    KAUST Repository

    Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

    2018-01-01

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  16. GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome.

    Science.gov (United States)

    Deng, Feilong; Chen, Shi-Yi; Wu, Zhou-Lin; Hu, Yongsong; Jia, Xianbo; Lai, Song-Jia

    2017-10-01

    Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization. GFFview is very useful for investigating quality and difference of the de novo assembled transcriptome in RNA-seq studies.

  17. Computational resources for ribosome profiling: from database to Web server and software.

    Science.gov (United States)

    Wang, Hongwei; Wang, Yan; Xie, Zhi

    2017-08-14

    Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation. This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. At present, however, a comprehensive review on these resources is still lacking. Here, we survey the recent computational advances guided by ribosome profiling, with a focus on databases, Web servers and software tools for storing, visualizing and analyzing ribosome profiling data. This review is intended to provide experimental and computational biologists with a reference to make appropriate choices among existing resources for the question at hand. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. ComplexContact: a web server for inter-protein contact prediction using deep learning

    KAUST Repository

    Zeng, Hong

    2018-05-20

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  19. InterProSurf: a web server for predicting interacting sites on protein surfaces

    Science.gov (United States)

    Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

    2009-01-01

    Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

  20. ComplexContact: a web server for inter-protein contact prediction using deep learning.

    Science.gov (United States)

    Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

    2018-05-22

    ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

    Science.gov (United States)

    Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

    2017-07-03

    The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

    Davis, Michael J.; And Others

    1997-01-01

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

  7. WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results.

    Science.gov (United States)

    Joshi, Vineet K; Freudenberg, Johannes M; Hu, Zhen; Medvedovic, Mario

    2011-01-17

    Cluster analysis methods have been extensively researched, but the adoption of new methods is often hindered by technical barriers in their implementation and use. WebGimm is a free cluster analysis web-service, and an open source general purpose clustering web-server infrastructure designed to facilitate easy deployment of integrated cluster analysis servers based on clustering and functional annotation algorithms implemented in R. Integrated functional analyses and interactive browsing of both, clustering structure and functional annotations provides a complete analytical environment for cluster analysis and interpretation of results. The Java Web Start client-based interface is modeled after the familiar cluster/treeview packages making its use intuitive to a wide array of biomedical researchers. For biomedical researchers, WebGimm provides an avenue to access state of the art clustering procedures. For Bioinformatics methods developers, WebGimm offers a convenient avenue to deploy their newly developed clustering methods. WebGimm server, software and manuals can be freely accessed at http://ClusterAnalysis.org/.

  8. 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/.

  9. 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)

  10. RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

    Science.gov (United States)

    Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

    2017-01-21

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA

  11. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

    Science.gov (United States)

    Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

    2011-01-01

    Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

  12. Analisis Perbandingan Antara Colocation Server Dengan Amazon Web Services (Cloud Untuk Usabilitas Portal Swa.co.id Di PT. Swa Media Bisnis

    Directory of Open Access Journals (Sweden)

    Lipur Sugiyanta

    2017-06-01

    Full Text Available Untuk mendukung usabilitas web portal nya, SWA Media Online menggunakan layanan web hosting Colocation Server dari Wowrack. Layanan Colocation Server dari Wowrack ini memiliki lokasi server fisik atau pusat data di Surabaya, Indonesia. Seiring berjalannya waktu, penggunaan Colocation Server dirasa semakin menghambat perkembangan perusahaan, terbukti dengan melambatnya akses ke web portal swa.co.id. Untuk itu, pada bulan Mei - Juni 2015 SWA Media Online memutuskan berpaling dari Colocation Server ke teknologi cloud terbaru. Pada akhir bulan Juni 2015, SWA Media Online resmi bermigrasi dari colocation ke Amazon Web Services. Dimana server fisik nya berada di Singapura (untuk pelanggan ASEAN. Untuk fitur yang digunakan, hampir sama seperti saat menggunakan colocation yaitu yang sesuai dengan kebutuhan perusahaan. Namun, pada Amazon Web Services memberikan service atau fitur tambahan berupa adanya load balancer, auto scaling, dan bucket atau media penyimpanan. Metodologi yang peneliti terapkan dalam penelitian ini adalah metodologi analisis secara kualitatif. Berdasarkan hasil penelitian, didapatkan hasil bahwa fitur tambahan yang diberikan Amazon Web Services mampu meningkatkan usabilitas portal dalam segi kemudahan dalam kecepatan akses portal. Kecepatan akses web portal meningkat lebih baik dibandingkan saat menggunakan Colocation Server.

  13. 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.

  14. 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.

  15. osFP: a web server for predicting the oligomeric states of fluorescent proteins.

    Science.gov (United States)

    Simeon, Saw; Shoombuatong, Watshara; Anuwongcharoen, Nuttapat; Preeyanon, Likit; Prachayasittikul, Virapong; Wikberg, Jarl E S; Nantasenamat, Chanin

    2016-01-01

    Currently, monomeric fluorescent proteins (FP) are ideal markers for protein tagging. The prediction of oligomeric states is helpful for enhancing live biomedical imaging. Computational prediction of FP oligomeric states can accelerate the effort of protein engineering efforts of creating monomeric FPs. To the best of our knowledge, this study represents the first computational model for predicting and analyzing FP oligomerization directly from the amino acid sequence. After data curation, an exhaustive data set consisting of 397 non-redundant FP oligomeric states was compiled from the literature. Results from benchmarking of the protein descriptors revealed that the model built with amino acid composition descriptors was the top performing model with accuracy, sensitivity and specificity in excess of 80% and MCC greater than 0.6 for all three data subsets (e.g. training, tenfold cross-validation and external sets). The model provided insights on the important residues governing the oligomerization of FP. To maximize the benefit of the generated predictive model, it was implemented as a web server under the R programming environment. osFP affords a user-friendly interface that can be used to predict the oligomeric state of FP using the protein sequence. The advantage of osFP is that it is platform-independent meaning that it can be accessed via a web browser on any operating system and device. osFP is freely accessible at http://codes.bio/osfp/ while the source code and data set is provided on GitHub at https://github.com/chaninn/osFP/.Graphical Abstract.

  16. kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

    Science.gov (United States)

    Fletez-Brant, Christopher; Lee, Dongwon; McCallion, Andrew S.; Beer, Michael A.

    2013-01-01

    Massively parallel sequencing technologies have made the generation of genomic data sets a routine component of many biological investigations. For example, Chromatin immunoprecipitation followed by sequence assays detect genomic regions bound (directly or indirectly) by specific factors, and DNase-seq identifies regions of open chromatin. A major bottleneck in the interpretation of these data is the identification of the underlying DNA sequence code that defines, and ultimately facilitates prediction of, these transcription factor (TF) bound or open chromatin regions. We have recently developed a novel computational methodology, which uses a support vector machine (SVM) with kmer sequence features (kmer-SVM) to identify predictive combinations of short transcription factor-binding sites, which determine the tissue specificity of these genomic assays (Lee, Karchin and Beer, Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21:2167–80). This regulatory information can (i) give confidence in genomic experiments by recovering previously known binding sites, and (ii) reveal novel sequence features for subsequent experimental testing of cooperative mechanisms. Here, we describe the development and implementation of a web server to allow the broader research community to independently apply our kmer-SVM to analyze and interpret their genomic datasets. We analyze five recently published data sets and demonstrate how this tool identifies accessory factors and repressive sequence elements. kmer-SVM is available at http://kmersvm.beerlab.org. PMID:23771147

  17. QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

    Science.gov (United States)

    Dhapola, Parashar; Chowdhury, Shantanu

    2016-01-01

    DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

  18. 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%.

  19. 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.

  20. MORPH-PRO: a novel algorithm and web server for protein morphing.

    Science.gov (United States)

    Castellana, Natalie E; Lushnikov, Andrey; Rotkiewicz, Piotr; Sefcovic, Natasha; Pevzner, Pavel A; Godzik, Adam; Vyatkina, Kira

    2013-07-11

    Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations. We present a novel, efficient morphing algorithm, Morph-Pro based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts. Visualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. The Morph-Pro web server can be accessed at http://morph-pro.bioinf.spbau.ru.

  1. AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins.

    Science.gov (United States)

    Zhang, Zong Hong; Koh, Judice L Y; Zhang, Guang Lan; Choo, Khar Heng; Tammi, Martti T; Tong, Joo Chuan

    2007-02-15

    Assessment of potential allergenicity and patterns of cross-reactivity is necessary whenever novel proteins are introduced into human food chain. Current bioinformatic methods in allergology focus mainly on the prediction of allergenic proteins, with no information on cross-reactivity patterns among known allergens. In this study, we present AllerTool, a web server with essential tools for the assessment of predicted as well as published cross-reactivity patterns of allergens. The analysis tools include graphical representation of allergen cross-reactivity information; a local sequence comparison tool that displays information of known cross-reactive allergens; a sequence similarity search tool for assessment of cross-reactivity in accordance to FAO/WHO Codex alimentarius guidelines; and a method based on support vector machine (SVM). A 10-fold cross-validation results showed that the area under the receiver operating curve (A(ROC)) of SVM models is 0.90 with 86.00% sensitivity (SE) at specificity (SP) of 86.00%. AllerTool is freely available at http://research.i2r.a-star.edu.sg/AllerTool/.

  2. 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

  3. Development of web-based integrity evaluation system for primary components in a nuclear power plant

    International Nuclear Information System (INIS)

    Lee, S.M.; Kim, J.C.; Choi, J.B.; Kim, Y.J.; Choi, S.N.; Jang, K.S.; Hong, S.Y.

    2004-01-01

    A nuclear power plant is composed of a number of primary components. Maintaining the integrity of these components is one of the most critical issues in nuclear industry. In order to maintain the integrity of these primary components, a complicated procedure is required including periodical in-service inspection, failure assessment, fracture mechanics analysis, etc. Also, experts in different fields have to co-operate to resolve the integrity issues on the basis of inspection results. This integrity evaluation process usually takes long, and thus, is detrimental for the plant productivity. Therefore, an effective safety evaluation system is essential to manage integrity issues on a nuclear power plant. In this paper, a web-based integrity evaluation system for primary components in a nuclear power plant is proposed. The proposed system, which is named as WEBIES (web-based integrity evaluation system), has been developed in the form of 3-tier system architecture. The system consists of three servers; application program server, user interface program server and data warehouse server. The application program server includes the defect acceptance analysis module and the fracture mechanics analysis module which are programmed on the basis of ASME sec. XI, appendix A. The data warehouse server provides data for the integrity evaluation including material properties, geometry information, inspection data and stress data. The user interface program server provides information to all co- workers in the field of integrity evaluation. The developed system provides engineering knowledge-based information and concurrent and collaborative working environment through internet, and thus, is expected to raise the efficiency of integrity evaluation procedures on primary components of a nuclear power plant. (orig.)

  4. Development of web-based integrity evaluation system for primary components in a nuclear power plant

    Energy Technology Data Exchange (ETDEWEB)

    Lee, S.M.; Kim, J.C.; Choi, J.B.; Kim, Y.J. [SAFE Research Center, Sungkyunkwan Univ., Suwon (Korea); Choi, S.N.; Jang, K.S.; Hong, S.Y. [Korea Electronic Power Research Inst., Daejeon (Korea)

    2004-07-01

    A nuclear power plant is composed of a number of primary components. Maintaining the integrity of these components is one of the most critical issues in nuclear industry. In order to maintain the integrity of these primary components, a complicated procedure is required including periodical in-service inspection, failure assessment, fracture mechanics analysis, etc. Also, experts in different fields have to co-operate to resolve the integrity issues on the basis of inspection results. This integrity evaluation process usually takes long, and thus, is detrimental for the plant productivity. Therefore, an effective safety evaluation system is essential to manage integrity issues on a nuclear power plant. In this paper, a web-based integrity evaluation system for primary components in a nuclear power plant is proposed. The proposed system, which is named as WEBIES (web-based integrity evaluation system), has been developed in the form of 3-tier system architecture. The system consists of three servers; application program server, user interface program server and data warehouse server. The application program server includes the defect acceptance analysis module and the fracture mechanics analysis module which are programmed on the basis of ASME sec. XI, appendix A. The data warehouse server provides data for the integrity evaluation including material properties, geometry information, inspection data and stress data. The user interface program server provides information to all co- workers in the field of integrity evaluation. The developed system provides engineering knowledge-based information and concurrent and collaborative working environment through internet, and thus, is expected to raise the efficiency of integrity evaluation procedures on primary components of a nuclear power plant. (orig.)

  5. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

    Science.gov (United States)

    Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

    2017-07-03

    Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Integrating Web Services into Map Image Applications

    National Research Council Canada - National Science Library

    Tu, Shengru

    2003-01-01

    Web services have been opening a wide avenue for software integration. In this paper, we have reported our experiments with three applications that are built by utilizing and providing web services for Geographic Information Systems (GIS...

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

    International Nuclear Information System (INIS)

    Suarez, Patricia M.; Pepe, Maria E.; Sbaffoni, Maria M.

    2000-01-01

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

  8. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

    Science.gov (United States)

    Maghrabi, Ali H A; McGuffin, Liam J

    2017-07-03

    Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    Yan-Lin Liu

    2014-01-01

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

  11. mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications.

    Science.gov (United States)

    Li, Zhongshan; Liu, Zhenwei; Jiang, Yi; Chen, Denghui; Ran, Xia; Sun, Zhong Sheng; Wu, Jinyu

    2017-01-01

    Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/. © 2016 WILEY PERIODICALS, INC.

  12. 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,…

  13. 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. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

  14. GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.

    Science.gov (United States)

    Baek, Minkyung; Park, Taeyong; Heo, Lim; Park, Chiwook; Seok, Chaok

    2017-07-03

    Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure database or by ab initio docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, ab initio docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. 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

  16. SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

    Science.gov (United States)

    Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

    2016-01-01

    To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial

  17. 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.

  18. 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…

  19. CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction.

    Science.gov (United States)

    Xu, Youjun; Wang, Shiwei; Hu, Qiwan; Gao, Shuaishi; Ma, Xiaomin; Zhang, Weilin; Shen, Yihang; Chen, Fangjin; Lai, Luhua; Pei, Jianfeng

    2018-05-10

    CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

  20. Integrating Data Warehouses with Web Data

    DEFF Research Database (Denmark)

    Perez, Juan Manuel; Berlanga, Rafael; Aramburu, Maria Jose

    This paper surveys the most relevant research on combining Data Warehouse (DW) and Web data. It studies the XML technologies that are currently being used to integrate, store, query and retrieve web data, and their application to data warehouses. The paper addresses the problem of integrating...

  1. 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.

  2. 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

    2015-01-01

    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. PMID:25940619

  3. PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition.

    Science.gov (United States)

    Zuo, Yongchun; Li, Yuan; Chen, Yingli; Li, Guangpeng; Yan, Zhenhe; Yang, Lei

    2017-01-01

    The reduced amino acids perform powerful ability for both simplifying protein complexity and identifying functional conserved regions. However, dealing with different protein problems may need different kinds of cluster methods. Encouraged by the success of pseudo-amino acid composition algorithm, we developed a freely available web server, called PseKRAAC (the pseudo K-tuple reduced amino acids composition). By implementing reduced amino acid alphabets, the protein complexity can be significantly simplified, which leads to decrease chance of overfitting, lower computational handicap and reduce information redundancy. PseKRAAC delivers more capability for protein research by incorporating three crucial parameters that describes protein composition. Users can easily generate many different modes of PseKRAAC tailored to their needs by selecting various reduced amino acids alphabets and other characteristic parameters. It is anticipated that the PseKRAAC web server will become a very useful tool in computational proteomics and protein sequence analysis. Freely available on the web at http://bigdata.imu.edu.cn/psekraac CONTACTS: yczuo@imu.edu.cn or imu.hema@foxmail.com or yanglei_hmu@163.comSupplementary information: 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.

  4. CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

    International Nuclear Information System (INIS)

    Tyagi, Sonika; Vaz, Candida; Gupta, Vipin; Bhatia, Rohit; Maheshwari, Sachin; Srinivasan, Ashwin; Bhattacharya, Alok

    2008-01-01

    microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filtering systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Science.gov (United States)

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

    2017-01-04

    Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.

    Science.gov (United States)

    Ghosh, Pritha; Mathew, Oommen K; Sowdhamini, Ramanathan

    2016-10-07

    RNA-binding proteins (RBPs) interact with their cognate RNA(s) to form large biomolecular assemblies. They are versatile in their functionality and are involved in a myriad of processes inside the cell. RBPs with similar structural features and common biological functions are grouped together into families and superfamilies. It will be useful to obtain an early understanding and association of RNA-binding property of sequences of gene products. Here, we report a web server, RStrucFam, to predict the structure, type of cognate RNA(s) and function(s) of proteins, where possible, from mere sequence information. The web server employs Hidden Markov Model scan (hmmscan) to enable association to a back-end database of structural and sequence families. The database (HMMRBP) comprises of 437 HMMs of RBP families of known structure that have been generated using structure-based sequence alignments and 746 sequence-centric RBP family HMMs. The input protein sequence is associated with structural or sequence domain families, if structure or sequence signatures exist. In case of association of the protein with a family of known structures, output features like, multiple structure-based sequence alignment (MSSA) of the query with all others members of that family is provided. Further, cognate RNA partner(s) for that protein, Gene Ontology (GO) annotations, if any and a homology model of the protein can be obtained. The users can also browse through the database for details pertaining to each family, protein or RNA and their related information based on keyword search or RNA motif search. RStrucFam is a web server that exploits structurally conserved features of RBPs, derived from known family members and imprinted in mathematical profiles, to predict putative RBPs from sequence information. Proteins that fail to associate with such structure-centric families are further queried against the sequence-centric RBP family HMMs in the HMMRBP database. Further, all other essential

  8. ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins.

    Science.gov (United States)

    Konc, Janez; Janežič, Dušanka

    2017-09-01

    ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis.nih.gov. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. 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

    2017-04-15

    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. The service is available for free at http://www.combio.pl/orcan/ . wmk@amu.edu.pl. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  10. 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.

  11. 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. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

  12. COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures.

    Science.gov (United States)

    Firdaus-Raih, Mohd; Hamdani, Hazrina Yusof; Nadzirin, Nurul; Ramlan, Effirul Ikhwan; Willett, Peter; Artymiuk, Peter J

    2014-07-01

    Hydrogen bonds are crucial factors that stabilize a complex ribonucleic acid (RNA) molecule's three-dimensional (3D) structure. Minute conformational changes can result in variations in the hydrogen bond interactions in a particular structure. Furthermore, networks of hydrogen bonds, especially those found in tight clusters, may be important elements in structure stabilization or function and can therefore be regarded as potential tertiary motifs. In this paper, we describe a graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. This server, COGNAC (COnnection tables Graphs for Nucleic ACids), is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events. The COGNAC server can be accessed at http://mfrlab.org/grafss/cognac. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Implementation and Evaluation of a JSON Binding for Mobile Web Services with IMS Integration Support

    OpenAIRE

    Murtaza, Shahid

    2012-01-01

    Service Oriented Architecture SOA is a well recognized and immensely applied reference model for service oriented computing, both in industry and research. Because of its fastidious features, such as reusability, interoperability, scalability and flexibility a Web Based SOA is adopted, in the areas like Enterprise Application Integration EAI. These days the Web Based Services, such as XML Web Services are not limited to fixed servers but can also be deployed on mobile devices in order to enha...

  14. Information Interpretation Code For Providing Secure Data Integrity On Multi-Server Cloud Infrastructure

    OpenAIRE

    Sathiya Moorthy Srinivsan; Chandrasekar Chaillah

    2014-01-01

    Data security is one of the biggest concerns in cloud computing environment. Although the advantages of storing data in cloud computing environment is extremely high, there arises a problem related to data missing. CyberLiveApp (CLA) supports secure application development between multiple users, even though cloud users distinguish their vision privileges during storing of data. But CyberLiveApp failed to integrate the system with certain cloud-based computing environments on multi-server. En...

  15. 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…

  16. 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.

  17. GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.

    Science.gov (United States)

    Wang, Jia-Hong; Zhao, Ling-Feng; Lin, Pei; Su, Xiao-Rong; Chen, Shi-Jun; Huang, Li-Qiang; Wang, Hua-Feng; Zhang, Hai; Hu, Zhen-Fu; Yao, Kai-Tai; Huang, Zhong-Xi

    2014-09-01

    Identifying biological functions and molecular networks in a gene list and how the genes may relate to various topics is of considerable value to biomedical researchers. Here, we present a web-based text-mining server, GenCLiP 2.0, which can analyze human genes with enriched keywords and molecular interactions. Compared with other similar tools, GenCLiP 2.0 offers two unique features: (i) analysis of gene functions with free terms (i.e. any terms in the literature) generated by literature mining or provided by the user and (ii) accurate identification and integration of comprehensive molecular interactions from Medline abstracts, to construct molecular networks and subnetworks related to the free terms. http://ci.smu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

    Science.gov (United States)

    Condie, Brian G; Urbanski, William M

    2014-01-01

    Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

  19. Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

    Science.gov (United States)

    Capuzzi, Stephen J; Thornton, Thomas E; Liu, Kammy; Baker, Nancy; Lam, Wai In; O'Banion, Colin P; Muratov, Eugene N; Pozefsky, Diane; Tropsha, Alexander

    2018-02-26

    Elucidation of the mechanistic relationships between drugs, their targets, and diseases is at the core of modern drug discovery research. Thousands of studies relevant to the drug-target-disease (DTD) triangle have been published and annotated in the Medline/PubMed database. Mining this database affords rapid identification of all published studies that confirm connections between vertices of this triangle or enable new inferences of such connections. To this end, we describe the development of Chemotext, a publicly available Web server that mines the entire compendium of published literature in PubMed annotated by Medline Subject Heading (MeSH) terms. The goal of Chemotext is to identify all known DTD relationships and infer missing links between vertices of the DTD triangle. As a proof-of-concept, we show that Chemotext could be instrumental in generating new drug repurposing hypotheses or annotating clinical outcomes pathways for known drugs. The Chemotext Web server is freely available at http://chemotext.mml.unc.edu .

  20. PROFEAT Update: A Protein Features Web Server with Added Facility to Compute Network Descriptors for Studying Omics-Derived Networks.

    Science.gov (United States)

    Zhang, P; Tao, L; Zeng, X; Qin, C; Chen, S Y; Zhu, F; Yang, S Y; Li, Z R; Chen, W P; Chen, Y Z

    2017-02-03

    The studies of biological, disease, and pharmacological networks are facilitated by the systems-level investigations using computational tools. In particular, the network descriptors developed in other disciplines have found increasing applications in the study of the protein, gene regulatory, metabolic, disease, and drug-targeted networks. Facilities are provided by the public web servers for computing network descriptors, but many descriptors are not covered, including those used or useful for biological studies. We upgraded the PROFEAT web server http://bidd2.nus.edu.sg/cgi-bin/profeat2016/main.cgi for computing up to 329 network descriptors and protein-protein interaction descriptors. PROFEAT network descriptors comprehensively describe the topological and connectivity characteristics of unweighted (uniform binding constants and molecular levels), edge-weighted (varying binding constants), node-weighted (varying molecular levels), edge-node-weighted (varying binding constants and molecular levels), and directed (oriented processes) networks. The usefulness of the network descriptors is illustrated by the literature-reported studies of the biological networks derived from the genome, interactome, transcriptome, metabolome, and diseasome profiles. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. 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.

  2. The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

    Science.gov (United States)

    Olechnovič, Kliment; Venclovas, Ceslovas

    2014-07-01

    The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Lum Karl

    2011-03-01

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

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

    Science.gov (United States)

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

    2011-03-09

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

  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. StructRNAfinder: an automated pipeline and web server for RNA families prediction.

    Science.gov (United States)

    Arias-Carrasco, Raúl; Vásquez-Morán, Yessenia; Nakaya, Helder I; Maracaja-Coutinho, Vinicius

    2018-02-17

    The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills. We present an automated pipeline named StructRNAfinder that predicts and annotates RNA families in transcript or genome sequences. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Moreover, we implemented a user-friendly web service that allows researchers to upload their own nucleotide sequences in order to perform the whole analysis. Finally, we provided a stand-alone version of StructRNAfinder to be used in large-scale projects. The tool was developed under GNU General Public License (GPLv3) and is freely available at http://structrnafinder.integrativebioinformatics.me . The main advantage of StructRNAfinder relies on the large-scale processing and integrating the data obtained by each tool and database employed along the workflow, of which several files are generated and displayed in user-friendly reports, useful for downstream analyses and data exploration.

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

  9. Forecasting of interaction between bee propolis and protective antigenic domain in anthrax using the software and bioinformatics web servers

    Directory of Open Access Journals (Sweden)

    Elmira Mohammadi

    2017-01-01

    Full Text Available Background: Protective antigen of anthrax toxin, after touching the cell receptors, plays an important role in the pathogenesis of toxin. The purpose of this study was to investigate the interaction of anthrax toxin protective antigen and four great combination propolis included caffeic acid, benzyl caffeate, cinnamic acid and kaempferol using the softwares and bioinformatics web servers. Methods: Three-dimensional structure of protective antigen (receptor obtains from Protein Data Bank (PDB. Four of the main components from propolis were selected          as ligand and their 3D-structures were obtained from ChemSpider and ZINC     compound database. The interaction of each ligand and receptor was assessed                   by SwissDock server (http://www.swissdock.ch/ and BSP-SLIM server (http://zhanglab.ccmb.med.umich.edu/BSP-SLIM. Docking results appears with Fullfitness numbers (in kcal/mol. Identification of amino acids involved in ligand and receptor interaction, was performed using the Chimera software; UCSF Chimera program (http://www.cgl.ucsf.edu/. Results: The results of interaction between propolis components and protective antigen by BSP-SLIM server showed that the most interaction was related with benzyl caffeate, caffeic acid, kaempferol and cinnamic acid, respectively. Results for the desired ligand Interaction with protective antigen genes using SwissDock server showed that the caffeic acid had ΔG equals -9.10 kcal/mol and FullFitness equal to -993.16 kcal/mol respectively. The analysis of interaction between ligands with amino-acids of protective antigen indicated that the interaction of Caffeic acid whit Glutamic acid 117 had energy -15.5429 kcal/mol. Conclusion: Finding strong and safe inhibitors for anthrax toxin is very useful method for inhibiting its toxicity to cell. In this study the binding ability of four flavonoids to protective antigen was studied. Glutamic acid 117 is very effective

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

    Science.gov (United States)

    Breeding, Marshall

    2005-01-01

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

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

    DEFF Research Database (Denmark)

    Nitsch, Daniela; Tranchevent, Léon-Charles; Goncalves, Joana P.

    2011-01-01

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

  12. Spliceman2: a computational web server that predicts defects in pre-mRNA splicing.

    Science.gov (United States)

    Cygan, Kamil Jan; Sanford, Clayton Hendrick; Fairbrother, William Guy

    2017-09-15

    Most pre-mRNA transcripts in eukaryotic cells must undergo splicing to remove introns and join exons, and splicing elements present a large mutational target for disease-causing mutations. Splicing elements are strongly position dependent with respect to the transcript annotations. In 2012, we presented Spliceman, an online tool that used positional dependence to predict how likely distant mutations around annotated splice sites were to disrupt splicing. Here, we present an improved version of the previous tool that will be more useful for predicting the likelihood of splicing mutations. We have added industry-standard input options (i.e. Spliceman now accepts variant call format files), which allow much larger inputs than previously available. The tool also can visualize the locations-within exons and introns-of sequence variants to be analyzed and the predicted effects on splicing of the pre-mRNA transcript. In addition, Spliceman2 integrates with RNAcompete motif libraries to provide a prediction of which trans -acting factors binding sites are disrupted/created and links out to the UCSC genome browser. In summary, the new features in Spliceman2 will allow scientists and physicians to better understand the effects of single nucleotide variations on splicing. Freely available on the web at http://fairbrother.biomed.brown.edu/spliceman2 . Website implemented in PHP framework-Laravel 5, PostgreSQL, Apache, and Perl, with all major browsers supported. william_fairbrother@brown.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  13. AMPA: an automated web server for prediction of protein antimicrobial regions.

    Science.gov (United States)

    Torrent, Marc; Di Tommaso, Paolo; Pulido, David; Nogués, M Victòria; Notredame, Cedric; Boix, Ester; Andreu, David

    2012-01-01

    AMPA is a web application for assessing the antimicrobial domains of proteins, with a focus on the design on new antimicrobial drugs. The application provides fast discovery of antimicrobial patterns in proteins that can be used to develop new peptide-based drugs against pathogens. Results are shown in a user-friendly graphical interface and can be downloaded as raw data for later examination. AMPA is freely available on the web at http://tcoffee.crg.cat/apps/ampa. The source code is also available in the web. marc.torrent@upf.edu; david.andreu@upf.edu Supplementary data are available at Bioinformatics online.

  14. SAS Enterprise Data Integration Server - A Complete Solution Designed To Meet the Full Spectrum of Enterprise Data Integration Needs

    Directory of Open Access Journals (Sweden)

    Silvia BOLOHAN

    2012-05-01

    Full Text Available This paper is about why is Data Integration important for organisations around the world. Organizations struggle daily with the challenges of large distributed data volumes, inconsistently defined data across disparate systems and the high expectations of data consumers who depend on information to be correct, complete and available when they need it. SAS Enterprise Data Integration Server provides a comprehensive solution that enables organizations to solve these challenges in a timely, cost-effective manner with the ability to efficiently manage data integration projects on an enterprise scale, increasing overall productivity and reducing the total cost of ownership.

  15. FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.

    Science.gov (United States)

    Mader, Malte; Simon, Ronald; Steinbiss, Sascha; Kurtz, Stefan

    2011-07-28

    The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle.

  16. Web Server Berbasis ATmega 128 Untuk Monitoring dan Kontrol Peralatan Rumah

    Directory of Open Access Journals (Sweden)

    Sigit Pramono

    2015-05-01

    Full Text Available Penggunaan mikropengendali untuk mengendalikan perangkat yang ada di rumah tentu menjadi salah satu penerapan prinsip kerja yang praktis dan fleksibel.Mikropengendali dapat digunakan untuk memudahkan dalam mengendalikan lampu ruangan, pemantauan suhu, dan pengendalian sistem penggerak tirai.Dengan memanfaatkan modul jaringanNM7010A TCP/IP Starter Kit maka aplikasi rumah tersebut dapat dikendalikan melalui jaringan intranet. Pada mikropengendali ATmega128, data akan diproses dan dieksekusi untuk mengendalikan sistem kerja keseluruhan rangkaian. Dari hasil pengujian membuktikan bahwa mikropengendali dapat berperan sebagai Embedded Server untuk mengendalikan lampu, pengaktifan kanal Analog to Digital Converter (ADC yang digunakan untuk memantau suhu.Hasil pengujian terhadap LM35 menunjukan bahwa rata-rata error konversi sebesar 0,64%. Untuk mengeksekusi sistem melalui jaringan TCP/IP diperlukan waktu tunda antara 0,5 sampai 1,2 detik.

  17. The anisotropic network model web server at 2015 (ANM 2.0).

    Science.gov (United States)

    Eyal, Eran; Lum, Gengkon; Bahar, Ivet

    2015-05-01

    The anisotropic network model (ANM) is one of the simplest yet powerful tools for exploring protein dynamics. Its main utility is to predict and visualize the collective motions of large complexes and assemblies near their equilibrium structures. The ANM server, introduced by us in 2006 helped making this tool more accessible to non-sophisticated users. We now provide a new version (ANM 2.0), which allows inclusion of nucleic acids and ligands in the network model and thus enables the investigation of the collective motions of protein-DNA/RNA and -ligand systems. The new version offers the flexibility of defining the system nodes and the interaction types and cutoffs. It also includes extensive improvements in hardware, software and graphical interfaces. ANM 2.0 is available at http://anm.csb.pitt.edu eran.eyal@sheba.health.gov.il, eyal.eran@gmail.com. © The Author 2015. Published by Oxford University Press.

  18. Deep web query interface understanding and integration

    CERN Document Server

    Dragut, Eduard C; Yu, Clement T

    2012-01-01

    There are millions of searchable data sources on the Web and to a large extent their contents can only be reached through their own query interfaces. There is an enormous interest in making the data in these sources easily accessible. There are primarily two general approaches to achieve this objective. The first is to surface the contents of these sources from the deep Web and add the contents to the index of regular search engines. The second is to integrate the searching capabilities of these sources and support integrated access to them. In this book, we introduce the state-of-the-art tech

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

    Energy Technology Data Exchange (ETDEWEB)

    Boboshin, I N; Varlamov, A V; Varlamov, V V; Rudenko, D S; Stepanov, M E [D.V. Skobel' tsyn Scientific Research Institute for Nuclear Physics, M.V. Lomonosov Moscow State University, Centre for Photonuclear Experiments Data (Russian Federation)

    2001-02-01

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

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

    International Nuclear Information System (INIS)

    Boboshin, I.N.; Varlamov, A.V.; Varlamov, V.V.; Rudenko, D.S.; Stepanov, M.E.

    2001-01-01

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

  1. Semantic Web meets Integrative Biology: a survey.

    Science.gov (United States)

    Chen, Huajun; Yu, Tong; Chen, Jake Y

    2013-01-01

    Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

  2. EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures.

    Science.gov (United States)

    Reynolds, Christopher R; Islam, Suhail A; Sternberg, Michael J E

    2018-01-31

    EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images. Copyright © 2018. Published by Elsevier Ltd.

  3. PIQMIe: A web server for semi-quantitative proteomics data management and analysis

    NARCIS (Netherlands)

    A. Kuzniar (Arnold); R. Kanaar (Roland)

    2014-01-01

    textabstractWe present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates

  4. Analisis dan Perancangan Aplikasi Administrasi User Pada Server Radius Berbasis Web (Studi Kasus Binus@Ccess

    Directory of Open Access Journals (Sweden)

    Rony Baskoro Lukito

    2010-12-01

    Full Text Available Bina Nusantara University as one of the information technology-based educational institutions in Indonesia have used the Internet in learning activities. To meet the needs of Internet access, Binus provides students with BiNus@ccess Premium service. BiNus@ccess Premium already have an application to help admin to user management with the help of a centralized accounting system (which is provided by the RADIUS server. However, applications that use is still limited in some ways so that there are still many manual processes. Therefore we need an application that serves to replace the existing application but still supports the existing system. The methodology used to admin consists of interviews, questionnaires to users, observation to analyze the problem, designing application solutions, and evaluation by distributing questionnaires to the admin. With the RSIM applications, manual administrative processes can be eliminated because the user can perform the registration process and the addition of its own loans through the application by themselves. RSIM Applications can also provide solutions for prepaid voucher sales system because it provides the ability to generate a voucher, print vouchers, and see the voucher reports, list payment, and the sale report. Suggestions for further development is to create applications for the sale of voucher system with e-commerce or SMSgateway.. 

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

    OpenAIRE

    Fisseha, Frehiwot; Hagedorn, Kat; Keizer, Johannes

    2002-01-01

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

  6. pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

    Science.gov (United States)

    Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

    2014-07-01

    The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. 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/.

  8. AthMethPre: a web server for the prediction and query of mRNA m6A 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 .

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

    Science.gov (United States)

    Pulsani, B. R.

    2017-11-01

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

  10. 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/.

  11. TANK INFORMATION SYSTEM (TIS: A CASE STUDY IN MIGRATING WEB MAPPING APPLICATION FROM FLEX TO DOJO FOR ARCGIS SERVER AND THEN TO OPEN SOURCE

    Directory of Open Access Journals (Sweden)

    B. R. Pulsani

    2017-11-01

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

  12. MOWServ: a web client for integration of bioinformatic resources

    Science.gov (United States)

    Ramírez, Sergio; Muñoz-Mérida, Antonio; Karlsson, Johan; García, Maximiliano; Pérez-Pulido, Antonio J.; Claros, M. Gonzalo; Trelles, Oswaldo

    2010-01-01

    The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user’s tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. PMID:20525794

  13. 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

    . 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......When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all...

  14. Nebula--a web-server for advanced ChIP-seq data analysis.

    Science.gov (United States)

    Boeva, Valentina; Lermine, Alban; Barette, Camille; Guillouf, Christel; Barillot, Emmanuel

    2012-10-01

    ChIP-seq consists of chromatin immunoprecipitation and deep sequencing of the extracted DNA fragments. It is the technique of choice for accurate characterization of the binding sites of transcription factors and other DNA-associated proteins. We present a web service, Nebula, which allows inexperienced users to perform a complete bioinformatics analysis of ChIP-seq data. Nebula was designed for both bioinformaticians and biologists. It is based on the Galaxy open source framework. Galaxy already includes a large number of functionalities for mapping reads and peak calling. We added the following to Galaxy: (i) peak calling with FindPeaks and a module for immunoprecipitation quality control, (ii) de novo motif discovery with ChIPMunk, (iii) calculation of the density and the cumulative distribution of peak locations relative to gene transcription start sites, (iv) annotation of peaks with genomic features and (v) annotation of genes with peak information. Nebula generates the graphs and the enrichment statistics at each step of the process. During Steps 3-5, Nebula optionally repeats the analysis on a control dataset and compares these results with those from the main dataset. Nebula can also incorporate gene expression (or gene modulation) data during these steps. In summary, Nebula is an innovative web service that provides an advanced ChIP-seq analysis pipeline providing ready-to-publish results. Nebula is available at http://nebula.curie.fr/ Supplementary data are available at Bioinformatics online.

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

    International Nuclear Information System (INIS)

    Blaylock, R.E.; Martin, F.D.; Emery, R.

    1996-01-01

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

  16. 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.

  17. FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures.

    Science.gov (United States)

    Huang, Yi-Fei; Golding, G Brian

    2015-02-15

    A number of statistical phylogenetic methods have been developed to infer conserved functional sites or regions in proteins. Many methods, e.g. Rate4Site, apply the standard phylogenetic models to infer site-specific substitution rates and totally ignore the spatial correlation of substitution rates in protein tertiary structures, which may reduce their power to identify conserved functional patches in protein tertiary structures when the sequences used in the analysis are highly similar. The 3D sliding window method has been proposed to infer conserved functional patches in protein tertiary structures, but the window size, which reflects the strength of the spatial correlation, must be predefined and is not inferred from data. We recently developed GP4Rate to solve these problems under the Bayesian framework. Unfortunately, GP4Rate is computationally slow. Here, we present an intuitive web server, FuncPatch, to perform a fast approximate Bayesian inference of conserved functional patches in protein tertiary structures. Both simulations and four case studies based on empirical data suggest that FuncPatch is a good approximation to GP4Rate. However, FuncPatch is orders of magnitudes faster than GP4Rate. In addition, simulations suggest that FuncPatch is potentially a useful tool complementary to Rate4Site, but the 3D sliding window method is less powerful than FuncPatch and Rate4Site. The functional patches predicted by FuncPatch in the four case studies are supported by experimental evidence, which corroborates the usefulness of FuncPatch. The software FuncPatch is freely available at the web site, http://info.mcmaster.ca/yifei/FuncPatch golding@mcmaster.ca Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules.

    Science.gov (United States)

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

    2015-07-01

    Several algorithms for RNA inverse folding have been used to design synthetic riboswitches, ribozymes and thermoswitches, whose activity has been experimentally validated. The RNAiFold software is unique among approaches for inverse folding in that (exhaustive) constraint programming is used instead of heuristic methods. For that reason, RNAiFold can generate all sequences that fold into the target structure or determine that there is no solution. RNAiFold 2.0 is a complete overhaul of RNAiFold 1.0, rewritten from the now defunct COMET language to C++. The new code properly extends the capabilities of its predecessor by providing a user-friendly pipeline to design synthetic constructs having the functionality of given Rfam families. In addition, the new software supports amino acid constraints, even for proteins translated in different reading frames from overlapping coding sequences; moreover, structure compatibility/incompatibility constraints have been expanded. With these features, RNAiFold 2.0 allows the user to design single RNA molecules as well as hybridization complexes of two RNA molecules. the web server, source code and linux binaries are publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold2.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

    Science.gov (United States)

    Poitevin, Frédéric; Orland, Henri; Doniach, Sebastian; Koehl, Patrice; Delarue, Marc

    2011-01-01

    Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php). PMID:21665925

  20. 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/

  1. ProSeeK: a web server for MLPA probe design.

    Science.gov (United States)

    Pantano, Lorena; Armengol, Lluís; Villatoro, Sergi; Estivill, Xavier

    2008-11-28

    The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susceptibility. Multiplex Ligation-dependent Probe Amplification (MLPA) is a targeted method to assess copy number differences for up to 40 genomic loci in one single experiment. Although specific MLPA assays can be ordered from MRC-Holland (the proprietary company of the MLPA technology), custom designs are also developed in many laboratories worldwide. After our own experience, an important drawback of custom MLPA assays is the time spent during the design of the specific oligonucleotides that are used as probes. Due to the large number of probes included in a single assay, a number of restrictions need to be met in order to maximize specificity and to increase success likelihood. We have developed a web tool for facilitating and optimising custom probe design for MLPA experiments. The algorithm only requires the target sequence in FASTA format and a set of parameters, that are provided by the user according to each specific MLPA assay, to identify the best probes inside the given region. To our knowledge, this is the first available tool for optimizing custom probe design of MLPA assays. The ease-of-use and speed of the algorithm dramatically reduces the turn around time of probe design. ProSeeK will become a useful tool for all laboratories that are currently using MLPA in their research projects for CNV studies.

  2. ProSeeK: A web server for MLPA probe design

    Directory of Open Access Journals (Sweden)

    Villatoro Sergi

    2008-11-01

    Full Text Available Abstract Background The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susceptibility. Multiplex Ligation-dependent Probe Amplification (MLPA is a targeted method to assess copy number differences for up to 40 genomic loci in one single experiment. Although specific MLPA assays can be ordered from MRC-Holland (the proprietary company of the MLPA technology, custom designs are also developed in many laboratories worldwide. After our own experience, an important drawback of custom MLPA assays is the time spent during the design of the specific oligonucleotides that are used as probes. Due to the large number of probes included in a single assay, a number of restrictions need to be met in order to maximize specificity and to increase success likelihood. Results We have developed a web tool for facilitating and optimising custom probe design for MLPA experiments. The algorithm only requires the target sequence in FASTA format and a set of parameters, that are provided by the user according to each specific MLPA assay, to identify the best probes inside the given region. Conclusion To our knowledge, this is the first available tool for optimizing custom probe design of MLPA assays. The ease-of-use and speed of the algorithm dramatically reduces the turn around time of probe design. ProSeeK will become a useful tool for all laboratories that are currently using MLPA in their research projects for CNV studies.

  3. 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.

  4. A WEB-based integrated data processing system for the TRIAM-1M

    International Nuclear Information System (INIS)

    Hasegawa, M.; Higashijima, A.; Nakamura, K.; Hanada, K.; Sato, K.N.; Sakamoto, M.; Idei, H.; Kawasaki, S.; Nakashima, H.

    2008-01-01

    In TRIAM-1M, plasma discharge can be sustained for over five hours [H. Zushi, et al., Steady-state tokamak operation, ITB transition and sustainment and ECCD experiments in TRIAM-1M, Nucl. Fusion 45 (2005) S142-S156]. In order to avoid sitting in front of one console for the purpose of monitoring the plasma discharge, it is recommended that the experimental information be accessible from any location at any time. In addition, simple services to access experimental information are required in order to promote the participation of multiple researchers in the TRIAM-1M experiment. Thus, A WEB-based integrated data processing system that provides management for experiment planning, an experimental log, numerical data, and plasma supervision has been installed in the TRIAM-1M. These services are composed primarily of an Apache WEB server, a Tomcat JSP/Servlet container, and a MySQL relational database. This system is constructed using the object-oriented Java language, which is easy to maintain and develop because of the intrinsic characteristics of the Java language. When participating in experiments, researchers are required only to prepare a WEB browser on any platform and are no longer required to memorize complex operations because all services are provided with a uniform user interface through a WEB browser. Furthermore, with the integration of these services, the required information and numerical data can be provided promptly by tracing HTML links that are created dynamically by server applications

  5. A WEB-based integrated data processing system for the TRIAM-1M

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, M. [Advanced Fusion Research Center, Research Institute for Applied Mechanics, Kyushu University, Fukuoka 816-8580 (Japan)], E-mail: hasegawa@triam.kyushu-u.ac.jp; Higashijima, A; Nakamura, K; Hanada, K; Sato, K N; Sakamoto, M; Idei, H; Kawasaki, S; Nakashima, H [Advanced Fusion Research Center, Research Institute for Applied Mechanics, Kyushu University, Fukuoka 816-8580 (Japan)

    2008-05-15

    In TRIAM-1M, plasma discharge can be sustained for over five hours [H. Zushi, et al., Steady-state tokamak operation, ITB transition and sustainment and ECCD experiments in TRIAM-1M, Nucl. Fusion 45 (2005) S142-S156]. In order to avoid sitting in front of one console for the purpose of monitoring the plasma discharge, it is recommended that the experimental information be accessible from any location at any time. In addition, simple services to access experimental information are required in order to promote the participation of multiple researchers in the TRIAM-1M experiment. Thus, A WEB-based integrated data processing system that provides management for experiment planning, an experimental log, numerical data, and plasma supervision has been installed in the TRIAM-1M. These services are composed primarily of an Apache WEB server, a Tomcat JSP/Servlet container, and a MySQL relational database. This system is constructed using the object-oriented Java language, which is easy to maintain and develop because of the intrinsic characteristics of the Java language. When participating in experiments, researchers are required only to prepare a WEB browser on any platform and are no longer required to memorize complex operations because all services are provided with a uniform user interface through a WEB browser. Furthermore, with the integration of these services, the required information and numerical data can be provided promptly by tracing HTML links that are created dynamically by server applications.

  6. MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics.

    Science.gov (United States)

    Zhou, Zhiwei; Xiong, Xin; Zhu, Zheng-Jiang

    2017-07-15

    In metabolomics, rigorous structural identification of metabolites presents a challenge for bioinformatics. The use of collision cross-section (CCS) values of metabolites derived from ion mobility-mass spectrometry effectively increases the confidence of metabolite identification, but this technique suffers from the limit number of available CCS values. Currently, there is no software available for rapidly generating the metabolites' CCS values. Here, we developed the first web server, namely, MetCCS Predictor, for predicting CCS values. It can predict the CCS values of metabolites using molecular descriptors within a few seconds. Common users with limited background on bioinformatics can benefit from this software and effectively improve the metabolite identification in metabolomics. The web server is freely available at: http://www.metabolomics-shanghai.org/MetCCS/ . jiangzhu@sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  8. Flexible Web services integration: a novel personalised social approach

    Science.gov (United States)

    Metrouh, Abdelmalek; Mokhati, Farid

    2018-05-01

    Dynamic composition or integration remains one of the key objectives of Web services technology. This paper aims to propose an innovative approach of dynamic Web services composition based on functional and non-functional attributes and individual preferences. In this approach, social networks of Web services are used to maintain interactions between Web services in order to select and compose Web services that are more tightly related to user's preferences. We use the concept of Web services community in a social network of Web services to reduce considerably their search space. These communities are created by the direct involvement of Web services providers.

  9. iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

    Science.gov (United States)

    Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

    2016-08-12

    Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the

  10. Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

    Science.gov (United States)

    Duncan, R G; Saperia, D; Dulbandzhyan, R; Shabot, M M; Polaschek, J X; Jones, D T

    2001-01-01

    The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

  11. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

    Science.gov (United States)

    Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

    2016-11-18

    ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

  12. 4DGeoBrowser: A Web-Based Data Browser and Server for Accessing and Analyzing Multi-Disciplinary Data

    National Research Council Canada - National Science Library

    Lerner, Steven

    2001-01-01

    .... Once the information is loaded onto a Geobrowser server the investigator-user is able to login to the website and use a set of data access and analysis tools to search, plot, and display this information...

  13. NExT server

    CERN Document Server

    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.

  14. A web GIS based integrated flood assessment modeling tool for coastal urban watersheds

    Science.gov (United States)

    Kulkarni, A. T.; Mohanty, J.; Eldho, T. I.; Rao, E. P.; Mohan, B. K.

    2014-03-01

    Urban flooding has become an increasingly important issue in many parts of the world. In this study, an integrated flood assessment model (IFAM) is presented for the coastal urban flood simulation. A web based GIS framework has been adopted to organize the spatial datasets for the study area considered and to run the model within this framework. The integrated flood model consists of a mass balance based 1-D overland flow model, 1-D finite element based channel flow model based on diffusion wave approximation and a quasi 2-D raster flood inundation model based on the continuity equation. The model code is written in MATLAB and the application is integrated within a web GIS server product viz: Web Gram Server™ (WGS), developed at IIT Bombay, using Java, JSP and JQuery technologies. Its user interface is developed using open layers and the attribute data are stored in MySQL open source DBMS. The model is integrated within WGS and is called via Java script. The application has been demonstrated for two coastal urban watersheds of Navi Mumbai, India. Simulated flood extents for extreme rainfall event of 26 July, 2005 in the two urban watersheds of Navi Mumbai city are presented and discussed. The study demonstrates the effectiveness of the flood simulation tool in a web GIS environment to facilitate data access and visualization of GIS datasets and simulation results.

  15. Usability as the Key Factor to the Design of a Web Server for the CReF Protein Structure Predictor: The wCReF

    Directory of Open Access Journals (Sweden)

    Vanessa Stangherlin Machado Paixão-Cortes

    2018-01-01

    Full Text Available Protein structure prediction servers use various computational methods to predict the three-dimensional structure of proteins from their amino acid sequence. Predicted models are used to infer protein function and guide experimental efforts. This can contribute to solving the problem of predicting tertiary protein structures, one of the main unsolved problems in bioinformatics. The challenge is to understand the relationship between the amino acid sequence of a protein and its three-dimensional structure, which is related to the function of these macromolecules. This article is an extended version of the article wCReF: The Web Server for the Central Residue Fragment-based Method (CReF Protein Structure Predictor, published in the 14th International Conference on Information Technology: New Generations. In the first version, we presented the wCReF, a protein structure prediction server for the central residue fragment-based method. The wCReF interface was developed with a focus on usability and user interaction. With this tool, users can enter the amino acid sequence of their target protein and obtain its approximate 3D structure without the need to install all the multitude of necessary tools. In this extended version, we present the design process of the prediction server in detail, which includes: (A identification of user needs: aiming at understanding the features of a protein structure prediction server, the end user profiles and the commonly-performed tasks; (B server usability inspection: in order to define wCReF’s requirements and features, we have used heuristic evaluation guided by experts in both the human-computer interaction and bioinformatics domain areas, applied to the protein structure prediction servers I-TASSER, QUARK and Robetta; as a result, changes were found in all heuristics resulting in 89 usability problems; (C software requirements document and prototype: assessment results guiding the key features that wCReF must

  16. Linux Server Security

    CERN Document Server

    Bauer, Michael D

    2005-01-01

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

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

    International Nuclear Information System (INIS)

    Nomura, Yukihiro; Hayashi, Naoto; Masutani, Yoshitaka; Yoshikawa, Takeharu; Nemoto, Mitsutaka; Hanaoka, Shouhei; Maeda, Eriko; Ohtomo, Kuni; Miki, Soichiro

    2010-01-01

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

  18. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

    Science.gov (United States)

    Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

    2008-01-01

    The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

  19. 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。

  20. 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 .

  1. Integrating WebQuests in Preservice Teacher Education

    Science.gov (United States)

    Wang, Feng; Hannafin, Michael J.

    2008-01-01

    During the past decade, WebQuests have been widely used by teachers to integrate technology into teaching and learning. Recently, teacher educators have applied the WebQuest model with preservice teachers in order to develop technology integration skills akin to those used in everyday schools. Scaffolding, used to support the gradual acquisition…

  2. 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

  3. 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.

  4. 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.

  5. 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. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Integrating ecosystem engineering and food webs

    NARCIS (Netherlands)

    Sanders, Dirk; Jones, Clive G.; Thebault, Elisa; Bouma, Tjeerd J.; van der Heide, Tjisse; van Belzen, Jim; Barot, Sebastien

    Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non-trophic interactions, we

  7. Integrating ecosystem engineering and food webs

    NARCIS (Netherlands)

    Sanders, D.; Jones, C.G.; Thébault, E.; Bouma, T.J.; van der Heide, T.; van Belzen, J.; Barot, S.

    2014-01-01

    Ecosystem engineering, the physical modification of the environment by organisms, is a common and often influential process whose significance to food web structure and dynamics is largely unknown. In the light of recent calls to expand food web studies to include non-trophic interactions, we

  8. Semantic web for integrated network analysis in biomedicine.

    Science.gov (United States)

    Chen, Huajun; Ding, Li; Wu, Zhaohui; Yu, Tong; Dhanapalan, Lavanya; Chen, Jake Y

    2009-03-01

    The Semantic Web technology enables integration of heterogeneous data on the World Wide Web by making the semantics of data explicit through formal ontologies. In this article, we survey the feasibility and state of the art of utilizing the Semantic Web technology to represent, integrate and analyze the knowledge in various biomedical networks. We introduce a new conceptual framework, semantic graph mining, to enable researchers to integrate graph mining with ontology reasoning in network data analysis. Through four case studies, we demonstrate how semantic graph mining can be applied to the analysis of disease-causal genes, Gene Ontology category cross-talks, drug efficacy analysis and herb-drug interactions analysis.

  9. Development of an Web Service Architecture for Enterprise Application Integration

    International Nuclear Information System (INIS)

    Kim, Ji-Hyeon; Jung, Jae-Cheon; Chang, Young-Woo; Chang, Hoon-Seon; Kim, Jae-Cheol; Kim, Hang-Bae; Kim, Kyu-Ho; Lee, Dong-Chul

    2007-01-01

    The purpose of Enterprise Application Integration (EAI) is to enable the interoperability between two or more enterprise software systems. These systems, for example, can be an Enterprise Resource Planning (ERP) system, an Enterprise Asset Management (EAM) system or a Condition Monitoring system. Traditional EAI approach, based on point-to-point connection, is expensive, vendor specific with limited modules and restricted interoperability with other ERPs and applications. To overcome these drawbacks, the Web Service based EAI has emerged. It allows the integration without point to point linking and with less costs. Many approaches of Web service based EAI are combined with ORACLE, SAP, PeopleSoft, WebSphere, SIEBEL etc. as a system integration platform. The approach still has the restriction that only predefined clients can access the services. This means clients must know exactly the protocol for calling the services and if they don't have the access information they never can get the services. This is because these Web services are based on syntactic service description. In this paper, a semantic based EAI approach, that allows the uninformed clients to access the services, is introduced. The semantic EAI is designed with the Web services that have semantic service descriptions. The Semantic Web Services(SWS) are described in Web Ontology Language for Services(OWL-S), a semantic service ontology language, and advertised in Universal Description, Discovery and Integration (UDDI). Clients find desired services through the UDDI and get services from service providers through Web Service Description Language(WSDL)

  10. Development of an Web Service Architecture for Enterprise Application Integration

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji-Hyeon; Jung, Jae-Cheon; Chang, Young-Woo; Chang, Hoon-Seon; Kim, Jae-Cheol; Kim, Hang-Bae [Korea Power Engineering Company, Daejeon (Korea, Republic of); Kim, Kyu-Ho; Lee, Dong-Chul [Korea Electric Power Data Network, Daejeon (Korea, Republic of)

    2007-07-01

    The purpose of Enterprise Application Integration (EAI) is to enable the interoperability between two or more enterprise software systems. These systems, for example, can be an Enterprise Resource Planning (ERP) system, an Enterprise Asset Management (EAM) system or a Condition Monitoring system. Traditional EAI approach, based on point-to-point connection, is expensive, vendor specific with limited modules and restricted interoperability with other ERPs and applications. To overcome these drawbacks, the Web Service based EAI has emerged. It allows the integration without point to point linking and with less costs. Many approaches of Web service based EAI are combined with ORACLE, SAP, PeopleSoft, WebSphere, SIEBEL etc. as a system integration platform. The approach still has the restriction that only predefined clients can access the services. This means clients must know exactly the protocol for calling the services and if they don't have the access information they never can get the services. This is because these Web services are based on syntactic service description. In this paper, a semantic based EAI approach, that allows the uninformed clients to access the services, is introduced. The semantic EAI is designed with the Web services that have semantic service descriptions. The Semantic Web Services(SWS) are described in Web Ontology Language for Services(OWL-S), a semantic service ontology language, and advertised in Universal Description, Discovery and Integration (UDDI). Clients find desired services through the UDDI and get services from service providers through Web Service Description Language(WSDL)

  11. PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids.

    Science.gov (United States)

    Kuznetsov, Igor B; McDuffie, Michael

    2015-05-07

    Alignment of amino acid sequences is the main sequence comparison method used in computational molecular biology. The selection of the amino acid substitution matrix best suitable for a given alignment problem is one of the most important decisions the user has to make. In a conventional amino acid substitution matrix all elements are fixed and their values cannot be easily adjusted. Moreover, most existing amino acid substitution matrices account for the average (dis)similarities between amino acid types and do not distinguish the contribution of a specific biochemical property to these (dis)similarities. PR2ALIGN is a stand-alone software program and a web-server that provide the functionality for implementing flexible user-specified alignment scoring functions and aligning pairs of amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike the conventional sequence alignment methods that use 20x20 fixed amino acid substitution matrices, PR2ALIGN uses a set of weighted biochemical properties of amino acids to measure the distance between pairs of aligned residues and to find an optimal minimal distance global alignment. The user can provide any number of amino acid properties and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. We show that in many cases the approach implemented in PR2ALIGN produces better quality pair-wise alignments than the conventional matrix-based approach. PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix. To the best of the authors' knowledge, there are no existing stand-alone software programs or web-servers analogous to PR2ALIGN. The software is freely available from http://pr2align.rit.albany.edu.

  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

    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...... 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. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can...

  13. 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

  14. Web-Ice: Integrated Data Collection and Analysis for Macromolecular Crystallography

    International Nuclear Information System (INIS)

    Gonzalez, Ana; Gonzalez, Ana; Moorhead, Penjit; McPhillips, Scott E.; Song, Jinhu; Sharp, Ken; Taylor, John R.; Adams, Paul D.; Sauter, Nicholas K.; Soltis, S. Michael

    2007-01-01

    New software tools are introduced to facilitate diffraction experiments involving large numbers of crystals. While existing programs have long provided a framework for lattice indexing, Bragg spot integration, and symmetry determination, these initial data processing steps often require significant manual effort. This limits the timely availability of data analysis needed for high-throughput procedures, including the selection of the best crystals from a large sample pool, and the calculation of optimal data collection parameters to assure complete spot coverage with minimal radiation damage. To make these protocols more efficient, we developed a network of software applications and application servers, collectively known as Web-Ice. When the package is installed at a crystallography beamline, a programming interface allows the beamline control software (e.g., Blu-Ice/DCSS) to trigger data analysis automatically. Results are organized based on a list of samples that the user provides, and are examined within a Web page, accessible both locally at the beamline or remotely. Optional programming interfaces permit the user to control data acquisition through the Web browser. The system as a whole is implemented to support multiple users and multiple processors, and can be expanded to provide additional scientific functionality. Web-Ice has a distributed architecture consisting of several stand-alone software components working together via a well defined interface. Other synchrotrons or institutions may integrate selected components or the whole of Web-Ice with their own data acquisition software. Updated information about current developments may be obtained at http://smb.slac.stanford.edu/research/developments/webice

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

    Science.gov (United States)

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

  16. The NIF DISCO Framework: facilitating automated integration of neuroscience content on the web.

    Science.gov (United States)

    Marenco, Luis; Wang, Rixin; Shepherd, Gordon M; Miller, Perry L

    2010-06-01

    This paper describes the capabilities of DISCO, an extensible approach that supports integrative Web-based information dissemination. DISCO is a component of the Neuroscience Information Framework (NIF), an NIH Neuroscience Blueprint initiative that facilitates integrated access to diverse neuroscience resources via the Internet. DISCO facilitates the automated maintenance of several distinct capabilities using a collection of files 1) that are maintained locally by the developers of participating neuroscience resources and 2) that are "harvested" on a regular basis by a central DISCO server. This approach allows central NIF capabilities to be updated as each resource's content changes over time. DISCO currently supports the following capabilities: 1) resource descriptions, 2) "LinkOut" to a resource's data items from NCBI Entrez resources such as PubMed, 3) Web-based interoperation with a resource, 4) sharing a resource's lexicon and ontology, 5) sharing a resource's database schema, and 6) participation by the resource in neuroscience-related RSS news dissemination. The developers of a resource are free to choose which DISCO capabilities their resource will participate in. Although DISCO is used by NIF to facilitate neuroscience data integration, its capabilities have general applicability to other areas of research.

  17. GDR (Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research

    Directory of Open Access Journals (Sweden)

    Ficklin Stephen

    2004-09-01

    Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  18. GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.

    Science.gov (United States)

    Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

    2004-09-09

    Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

  19. Developing a Web-based system by integrating VGI and SDI for real estate management and marketing

    Directory of Open Access Journals (Sweden)

    J. Salajegheh

    2014-10-01

    Full Text Available Property importance of various aspects, especially the impact on various sectors of the economy and the country's macroeconomic is clear. Because of the real, multi-dimensional and heterogeneous nature of housing as a commodity, the lack of an integrated system includes comprehensive information of property, the lack of awareness of some actors in this field about comprehensive information about property and the lack of clear and comprehensive rules and regulations for the trading and pricing, several problems arise for the people involved in this field. In this research implementation of a crowd-sourced Web-based real estate support system is desired. Creating a Spatial Data Infrastructure (SDI in this system for collecting, updating and integrating all official data about property is also desired in this study. In this system a Web2.0 broker and technologies such as Web services and service composition has been used. This work aims to provide comprehensive and diverse information about property from different sources. For this purpose five-level real estate support system architecture is used. PostgreSql DBMS is used to implement the desired system. Geoserver software is also used as map server and reference implementation of OGC (Open Geospatial Consortium standards. And Apache server is used to run web pages and user interfaces. Integration introduced methods and technologies provide a proper environment for various users to use the system and share their information. This goal is only achieved by cooperation between all involved organizations in real estate with implementation their required infrastructures in interoperability Web services format.

  20. Developing a Web-based system by integrating VGI and SDI for real estate management and marketing

    Science.gov (United States)

    Salajegheh, J.; Hakimpour, F.; Esmaeily, A.

    2014-10-01

    Property importance of various aspects, especially the impact on various sectors of the economy and the country's macroeconomic is clear. Because of the real, multi-dimensional and heterogeneous nature of housing as a commodity, the lack of an integrated system includes comprehensive information of property, the lack of awareness of some actors in this field about comprehensive information about property and the lack of clear and comprehensive rules and regulations for the trading and pricing, several problems arise for the people involved in this field. In this research implementation of a crowd-sourced Web-based real estate support system is desired. Creating a Spatial Data Infrastructure (SDI) in this system for collecting, updating and integrating all official data about property is also desired in this study. In this system a Web2.0 broker and technologies such as Web services and service composition has been used. This work aims to provide comprehensive and diverse information about property from different sources. For this purpose five-level real estate support system architecture is used. PostgreSql DBMS is used to implement the desired system. Geoserver software is also used as map server and reference implementation of OGC (Open Geospatial Consortium) standards. And Apache server is used to run web pages and user interfaces. Integration introduced methods and technologies provide a proper environment for various users to use the system and share their information. This goal is only achieved by cooperation between all involved organizations in real estate with implementation their required infrastructures in interoperability Web services format.

  1. SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

    Science.gov (United States)

    Ramu, Chenna

    2003-07-01

    SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

  2. Integrating Thematic Web Portal Capabilities into the NASA Earthdata Web Infrastructure

    Science.gov (United States)

    Wong, Minnie; Baynes, Kathleen E.; Huang, Thomas; McLaughlin, Brett

    2015-01-01

    This poster will present the process of integrating thematic web portal capabilities into the NASA Earth data web infrastructure, with examples from the Sea Level Change Portal. The Sea Level Change Portal will be a source of current NASA research, data and information regarding sea level change. The portal will provide sea level change information through articles, graphics, videos and animations, an interactive tool to view and access sea level change data and a dashboard showing sea level change indicators.

  3. Integrated Propulsion Data System Public Web Site

    Science.gov (United States)

    Hamilton, Kimberly

    2001-01-01

    The Integrated Propulsion Data System's (IPDS) focus is to provide technologically-advanced philosophies of doing business at SSC that will enhance the existing operations, engineering and management strategies and provide insight and metrics to assess their daily impacts, especially as related to the Propulsion Test Directorate testing scenarios for the 21st Century.

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

    Science.gov (United States)

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

    2015-05-01

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

  5. Integrating Space Communication Network Capabilities via Web Portal Technologies

    Science.gov (United States)

    Johnston, Mark D.; Lee, Carlyn-Ann; Lau, Chi-Wung; Cheung, Kar-Ming; Levesque, Michael; Carruth, Butch; Coffman, Adam; Wallace, Mike

    2014-01-01

    We have developed a service portal prototype as part of an investigation into the feasibility of using Java portlet technology as a means of providing integrated access to NASA communications network services. Portal servers provide an attractive platform for this role due to the various built-in collaboration applications they can provide, combined with the possibility to develop custom inter-operating portlets to extent their functionality while preserving common presentation and behavior. This paper describes various options for integration of network services related to planning and scheduling, and results based on use of a popular open-source portal framework. Plans are underway to develop an operational SCaN Service Portal, building on the experiences reported here.

  6. Legacy system integration using web technology

    Science.gov (United States)

    Kennedy, Richard L.; Seibert, James A.; Hughes, Chris J.

    2000-05-01

    As healthcare moves towards a completely digital, multimedia environment there is an opportunity to provide for cost- effective, highly distributed physician access to clinical information including radiology-based imaging. In order to address this opportunity a Universal Clinical Desktop (UCD) system was developed. A UCD provides a single point of entry into an integrated view of all types of clinical data available within a network of disparate healthcare information systems. In order to explore the application of a UCD in a hospital environment, a pilot study was established with the University of California Davis Medical Center using technology from Trilix Information Systems. Within this pilot environment the information systems integrated under the UCD include a radiology information system (RIS), a picture archive and communication system (PACS) and a laboratory information system (LIS).

  7. River food webs: an integrative approach to bottom-up flow webs, top-down impact webs, and trophic position.

    Science.gov (United States)

    Benke, Arthur C

    2018-03-31

    The majority of food web studies are based on connectivity, top-down impacts, bottom-up flows, or trophic position (TP), and ecologists have argued for decades which is best. Rarely have any two been considered simultaneously. The present study uses a procedure that integrates the last three approaches based on taxon-specific secondary production and gut analyses. Ingestion flows are quantified to create a flow web and the same data are used to quantify TP for all taxa. An individual predator's impacts also are estimated using the ratio of its ingestion (I) of each prey to prey production (P) to create an I/P web. This procedure was applied to 41 invertebrate taxa inhabiting submerged woody habitat in a southeastern U.S. river. A complex flow web starting with five basal food resources had 462 flows >1 mg·m -2 ·yr -1 , providing far more information than a connectivity web. Total flows from basal resources to primary consumers/omnivores were dominated by allochthonous amorphous detritus and ranged from 1 to >50,000 mg·m -2 ·yr -1 . Most predator-prey flows were much lower (1,000  mg·m -2 ·yr -1 . The I/P web showed that 83% of individual predator impacts were weak (90%). Quantitative estimates of TP ranged from 2 to 3.7, contrasting sharply with seven integer-based trophic levels based on longest feeding chain. Traditional omnivores (TP = 2.4-2.9) played an important role by consuming more prey and exerting higher impacts on primary consumers than strict predators (TP ≥ 3). This study illustrates how simultaneous quantification of flow pathways, predator impacts, and TP together provide an integrated characterization of natural food webs. © 2018 by the Ecological Society of America.

  8. Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Kerem [Environmental; Li, Da-Wei; Zhang, Bo; Brüschweiler, Rafael

    2016-12-06

    Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the co-analysis of up to three 2D NMR spectra, namely 13C-1H HSQC, 1H-1H TOCSY, and 13C-1H HSQC-TOCSY for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.

  9. 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/.

  10. 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.

  11. HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.

    Science.gov (United States)

    Sumbalova, Lenka; Stourac, Jan; Martinek, Tomas; Bednar, David; Damborsky, Jiri

    2018-05-23

    HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity. Since there are three orders of magnitude fewer protein structures than sequences in bioinformatic databases, the major limitation to the usability of previous versions was the requirement for the protein structure to be a compulsory input for the calculation. HotSpot Wizard 3.0 now accepts the protein sequence as input data. The protein structure for the query sequence is obtained either from eight repositories of homology models or is modeled using Modeller and I-Tasser. The quality of the models is then evaluated using three quality assessment tools-WHAT_CHECK, PROCHECK and MolProbity. During follow-up analyses, the system automatically warns the users whenever they attempt to redesign poorly predicted parts of their homology models. The second main limitation of HotSpot Wizard's predictions is that it identifies suitable positions for mutagenesis, but does not provide any reliable advice on particular substitutions. A new module for the estimation of thermodynamic stabilities using the Rosetta and FoldX suites has been introduced which prevents destabilizing mutations among pre-selected variants entering experimental testing. HotSpot Wizard is freely available at http://loschmidt.chemi.muni.cz/hotspotwizard.

  12. Home e-health system integration in the Smart Home through a common media server.

    Science.gov (United States)

    Pau, I; Seoane, F; Lindecrantz, K; Valero, M A; Carracedo, J

    2009-01-01

    Home e-health systems and services are revealed as one of the most important challenges to promote Quality of Life related to Health in the Information Society. Leading companies have worked on e-health systems although the majority of them are addressed to hospital or primary care settings. The solution detailed in this paper offers a personal health system to be integrated with Smart Home services platform to support home based e-care. Thus, the home e-health system and architecture detailed in this research work is ready to supply a seamless personal care solution both from the biomedical data analysis, service provision, security guarantee and information management s point of view. The solution is ready to be integrated within the Accessible Digital Home, a living lab managed by Universidad Politécnica de Madrid for R&D activities.

  13. 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.

  14. jORCA: easily integrating bioinformatics Web Services.

    Science.gov (United States)

    Martín-Requena, Victoria; Ríos, Javier; García, Maximiliano; Ramírez, Sergio; Trelles, Oswaldo

    2010-02-15

    Web services technology is becoming the option of choice to deploy bioinformatics tools that are universally available. One of the major strengths of this approach is that it supports machine-to-machine interoperability over a network. However, a weakness of this approach is that various Web Services differ in their definition and invocation protocols, as well as their communication and data formats-and this presents a barrier to service interoperability. jORCA is a desktop client aimed at facilitating seamless integration of Web Services. It does so by making a uniform representation of the different web resources, supporting scalable service discovery, and automatic composition of workflows. Usability is at the top of the jORCA agenda; thus it is a highly customizable and extensible application that accommodates a broad range of user skills featuring double-click invocation of services in conjunction with advanced execution-control, on the fly data standardization, extensibility of viewer plug-ins, drag-and-drop editing capabilities, plus a file-based browsing style and organization of favourite tools. The integration of bioinformatics Web Services is made easier to support a wider range of users. .

  15. New nuclear data service at CNEA: retrieval of the update libraries from a local Web-Server; Nuevo servicio de datos nucleares en CNEA: obtencion de bibliotecas actualizadas desde un Servidor Local

    Energy Technology Data Exchange (ETDEWEB)

    Suarez, Patricia M [Comision Nacional de Energia Atomica, Ezeiza (Argentina). Centro Atomico Ezeiza; Pepe, Maria E [Comision Nacional de Energia Atomica, General San Martin (Argentina). Centro Atomico Constituyentes; Sbaffoni, Maria M [Comision Nacional de Energia Atomica, Buenos Aires (Argentina). Gerencia de Tecnologia

    2000-07-01

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

  16. Personalized Pseudonyms for Servers in the Cloud

    Directory of Open Access Journals (Sweden)

    Xiao Qiuyu

    2017-10-01

    Full Text Available A considerable and growing fraction of servers, especially of web servers, is hosted in compute clouds. In this paper we opportunistically leverage this trend to improve privacy of clients from network attackers residing between the clients and the cloud: We design a system that can be deployed by the cloud operator to prevent a network adversary from determining which of the cloud’s tenant servers a client is accessing. The core innovation in our design is a PoPSiCl (pronounced “popsicle”, a persistent pseudonym for a tenant server that can be used by a single client to access the server, whose real identity is protected by the cloud from both passive and active network attackers. When instantiated for TLS-based access to web servers, our design works with all major browsers and requires no additional client-side software and minimal changes to the client user experience. Moreover, changes to tenant servers can be hidden in supporting software (operating systems and web-programming frameworks without imposing on web-content development. Perhaps most notably, our system boosts privacy with minimal impact to web-browsing performance, after some initial setup during a user’s first access to each web server.

  17. 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

  18. MAPI: towards the integrated exploitation of bioinformatics Web Services.

    Science.gov (United States)

    Ramirez, Sergio; Karlsson, Johan; Trelles, Oswaldo

    2011-10-27

    Bioinformatics is commonly featured as a well assorted list of available web resources. Although diversity of services is positive in general, the proliferation of tools, their dispersion and heterogeneity complicate the integrated exploitation of such data processing capacity. To facilitate the construction of software clients and make integrated use of this variety of tools, we present a modular programmatic application interface (MAPI) that provides the necessary functionality for uniform representation of Web Services metadata descriptors including their management and invocation protocols of the services which they represent. This document describes the main functionality of the framework and how it can be used to facilitate the deployment of new software under a unified structure of bioinformatics Web Services. A notable feature of MAPI is the modular organization of the functionality into different modules associated with specific tasks. This means that only the modules needed for the client have to be installed, and that the module functionality can be extended without the need for re-writing the software client. The potential utility and versatility of the software library has been demonstrated by the implementation of several currently available clients that cover different aspects of integrated data processing, ranging from service discovery to service invocation with advanced features such as workflows composition and asynchronous services calls to multiple types of Web Services including those registered in repositories (e.g. GRID-based, SOAP, BioMOBY, R-bioconductor, and others).

  19. Bridging UX and web development better results through team integration

    CERN Document Server

    Moffett, Jack

    2014-01-01

    The divide between UX and Web development can be stifling. Bridging UX and Web Development prepares you to break down those walls by teaching you how to integrate with your team's developers. You examine the process from their perspective, discovering tools and coding principles that will help you bridge the gap between design and implementation. With these tried and true approaches, you'll be able to capitalize on a more productive work environment. Whether you're a novice UX professional finding your place in the software industry and looking to nail down your technical skills, or a seasone

  20. [A web-based integrated clinical database for laryngeal cancer].

    Science.gov (United States)

    E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

    2014-08-01

    To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

  1. 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.

  2. 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.

  3. Learning SQL Server Reporting Services 2012

    CERN Document Server

    Krishnaswamy, Jayaram

    2013-01-01

    The book is packed with clear instructions and plenty of screenshots, providing all the support and guidance you will need as you begin to generate reports with SQL Server 2012 Reporting Services.This book is for those who are new to SQL Server Reporting Services 2012 and aspiring to create and deploy cutting edge reports. This book is for report developers, report authors, ad-hoc report authors and model developers, and Report Server and SharePoint Server Integrated Report Server administrators. Minimal knowledge of SQL Server is assumed and SharePoint experience would be helpful.

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

  5. Enabling collaboration on semiformal mathematical knowledge by semantic web integration

    CERN Document Server

    Lange, C

    2011-01-01

    Mathematics is becoming increasingly collaborative, but software does not sufficiently support that: Social Web applications do not currently make mathematical knowledge accessible to automated agents that have a deeper understanding of mathematical structures. Such agents exist but focus on individual research tasks, such as authoring, publishing, peer-review, or verification, instead of complex collaboration workflows. This work effectively enables their integration by bridging the document-oriented perspective of mathematical authoring and publishing, and the network perspective of threaded

  6. 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 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...... services.The resulting framework provides a novel foundation for developing maintainable and secure web applications....

  7. SCALEUS: Semantic Web Services Integration for Biomedical Applications.

    Science.gov (United States)

    Sernadela, Pedro; González-Castro, Lorena; Oliveira, José Luís

    2017-04-01

    In recent years, we have witnessed an explosion of biological data resulting largely from the demands of life science research. The vast majority of these data are freely available via diverse bioinformatics platforms, including relational databases and conventional keyword search applications. This type of approach has achieved great results in the last few years, but proved to be unfeasible when information needs to be combined or shared among different and scattered sources. During recent years, many of these data distribution challenges have been solved with the adoption of semantic web. Despite the evident benefits of this technology, its adoption introduced new challenges related with the migration process, from existent systems to the semantic level. To facilitate this transition, we have developed Scaleus, a semantic web migration tool that can be deployed on top of traditional systems in order to bring knowledge, inference rules, and query federation to the existent data. Targeted at the biomedical domain, this web-based platform offers, in a single package, straightforward data integration and semantic web services that help developers and researchers in the creation process of new semantically enhanced information systems. SCALEUS is available as open source at http://bioinformatics-ua.github.io/scaleus/ .

  8. Ontology alignment architecture for semantic sensor Web integration.

    Science.gov (United States)

    Fernandez, Susel; Marsa-Maestre, Ivan; Velasco, Juan R; Alarcos, Bernardo

    2013-09-18

    Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity). Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity's names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI) tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

  9. Ontology Alignment Architecture for Semantic Sensor Web Integration

    Directory of Open Access Journals (Sweden)

    Bernardo Alarcos

    2013-09-01

    Full Text Available Sensor networks are a concept that has become very popular in data acquisition and processing for multiple applications in different fields such as industrial, medicine, home automation, environmental detection, etc. Today, with the proliferation of small communication devices with sensors that collect environmental data, semantic Web technologies are becoming closely related with sensor networks. The linking of elements from Semantic Web technologies with sensor networks has been called Semantic Sensor Web and has among its main features the use of ontologies. One of the key challenges of using ontologies in sensor networks is to provide mechanisms to integrate and exchange knowledge from heterogeneous sources (that is, dealing with semantic heterogeneity. Ontology alignment is the process of bringing ontologies into mutual agreement by the automatic discovery of mappings between related concepts. This paper presents a system for ontology alignment in the Semantic Sensor Web which uses fuzzy logic techniques to combine similarity measures between entities of different ontologies. The proposed approach focuses on two key elements: the terminological similarity, which takes into account the linguistic and semantic information of the context of the entity’s names, and the structural similarity, based on both the internal and relational structure of the concepts. This work has been validated using sensor network ontologies and the Ontology Alignment Evaluation Initiative (OAEI tests. The results show that the proposed techniques outperform previous approaches in terms of precision and recall.

  10. Seamless Integration of RESTful Services into the Web of Data

    Directory of Open Access Journals (Sweden)

    Markus Lanthaler

    2012-01-01

    Full Text Available We live in an era of ever-increasing abundance of data. To cope with the information overload we suffer from every single day, more sophisticated methods are required to access, manipulate, and analyze these humongous amounts of data. By embracing the heterogeneity, which is unavoidable at such a scale, and accepting the fact that the data quality and meaning are fuzzy, more adaptable, flexible, and extensible systems can be built. RESTful services combined with Semantic Web technologies could prove to be a viable path to achieve that. Their combination allows data integration on an unprecedented scale and solves some of the problems Web developers are continuously struggling with. This paper introduces a novel approach to create machine-readable descriptions for RESTful services as a first step towards this ambitious goal. It also shows how these descriptions along with an algorithm to translate SPARQL queries to HTTP requests can be used to integrate RESTful services into a global read-write Web of Data.

  11. Integrated Patient Education on U.S. Hospital Web Sites.

    Science.gov (United States)

    Huang, Edgar; Wu, Kerong; Edwards, Kelsey

    2016-01-01

    Based on a census of the 2015 Most Wired Hospitals, this content analysis aimed to find out how patient education has been integrated on these best IT hospitals' Web sites to serve the purposes of marketing and meeting online visitors' needs. This study will help hospitals to understand where the weaknesses are in their interactive patient education implementation and come up with a smart integration strategy. The study found that 70% of these hospitals had adopted interactive patient education contents, 76.6% of such contents were from a third-party developer, and only 20% of the hospitals linked their patient education contents to one or more of the hospital's resources while 26% cross-references such contents. The authors concluded that more hospitals should take advantage of modern information communication technology to cross-reference their patient education contents and to integrate such contents into their overall online marketing strategy to benefit patients and themselves.

  12. Integration of Web mining and web crawler: Relevance and State of Art

    OpenAIRE

    Subhendu kumar pani; Deepak Mohapatra,; Bikram Keshari Ratha

    2010-01-01

    This study presents the role of web crawler in web mining environment. As the growth of the World Wide Web exceeded all expectations,the research on Web mining is growing more and more.web mining research topic which combines two of the activated research areas: Data Mining and World Wide Web .So, the World Wide Web is a very advanced area for data mining research. Search engines that are based on web crawling framework also used in web mining to find theinteracted web pages. This paper discu...

  13. A Web Based Approach to Integrate Space Culture and Education

    Science.gov (United States)

    Gerla, F.

    2002-01-01

    , who can use it to prepare their lessons, retrieve information and organize the didactic material in order to support their lessons. We think it important to use a user centered "psychology" based on UM: we have to know the needs and expectations of the students. Our intent is to use usability tests not just to prove the site effectiveness and clearness, but also to investigate aesthetical preferences of children and young people. Physics, mathematics, chemistry are just some of the difficult learning fields connected with space technologies. Space culture is a potentially never-ending field, and our scope will be to lead students by hand in this universe of knowledge. This paper will present MARS activities in the framework of the above methodologies aimed at implementing a web based approach to integrate space culture and education. The activities are already in progress and some results will be presented in the final paper.

  14. Integrating Mathematics, Science, and Language Arts Instruction Using the World Wide Web.

    Science.gov (United States)

    Clark, Kenneth; Hosticka, Alice; Kent, Judi; Browne, Ron

    1998-01-01

    Addresses issues of access to World Wide Web sites, mathematics and science content-resources available on the Web, and methods for integrating mathematics, science, and language arts instruction. (Author/ASK)

  15. Integrating thematic web portal capabilities into the NASA Earthdata Web Infrastructure

    Science.gov (United States)

    Wong, M. M.; McLaughlin, B. D.; Huang, T.; Baynes, K.

    2015-12-01

    The National Aeronautics and Space Administration (NASA) acquires and distributes an abundance of Earth science data on a daily basis to a diverse user community worldwide. To assist the scientific community and general public in achieving a greater understanding of the interdisciplinary nature of Earth science and of key environmental and climate change topics, the NASA Earthdata web infrastructure is integrating new methods of presenting and providing access to Earth science information, data, research and results. This poster will present the process of integrating thematic web portal capabilities into the NASA Earthdata web infrastructure, with examples from the Sea Level Change Portal. The Sea Level Change Portal will be a source of current NASA research, data and information regarding sea level change. The portal will provide sea level change information through articles, graphics, videos and animations, an interactive tool to view and access sea level change data and a dashboard showing sea level change indicators. Earthdata is a part of the Earth Observing System Data and Information System (EOSDIS) project. EOSDIS is a key core capability in NASA's Earth Science Data Systems Program. It provides end-to-end capabilities for managing NASA's Earth science data from various sources - satellites, aircraft, field measurements, and various other programs. It is comprised of twelve Distributed Active Archive Centers (DAACs), Science Computing Facilities (SCFs), data discovery and service access client (Reverb and Earthdata Search), dataset directory (Global Change Master Directory - GCMD), near real-time data (Land Atmosphere Near real-time Capability for EOS - LANCE), Worldview (an imagery visualization interface), Global Imagery Browse Services, the Earthdata Code Collaborative and a host of other discipline specific data discovery, data access, data subsetting and visualization tools.

  16. 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.

  17. Integrated web system of geospatial data services for climate research

    Science.gov (United States)

    Okladnikov, Igor; Gordov, Evgeny; Titov, Alexander

    2016-04-01

    Georeferenced datasets are currently actively used for modeling, interpretation and forecasting of climatic and ecosystem changes on different spatial and temporal scales. Due to inherent heterogeneity of environmental datasets as well as their huge size (up to tens terabytes for a single dataset) a special software supporting studies in the climate and environmental change areas is required. An approach for integrated analysis of georefernced climatological data sets based on combination of web and GIS technologies in the framework of spatial data infrastructure paradigm is presented. According to this approach a dedicated data-processing web system for integrated analysis of heterogeneous georeferenced climatological and meteorological data is being developed. It is based on Open Geospatial Consortium (OGC) standards and involves many modern solutions such as object-oriented programming model, modular composition, and JavaScript libraries based on GeoExt library, ExtJS Framework and OpenLayers software. This work is supported by the Ministry of Education and Science of the Russian Federation, Agreement #14.613.21.0037.

  18. Semantic Web integration of Cheminformatics resources with the SADI framework

    Directory of Open Access Journals (Sweden)

    Chepelev Leonid L

    2011-05-01

    Full Text Available Abstract Background The diversity and the largely independent nature of chemical research efforts over the past half century are, most likely, the major contributors to the current poor state of chemical computational resource and database interoperability. While open software for chemical format interconversion and database entry cross-linking have partially addressed database interoperability, computational resource integration is hindered by the great diversity of software interfaces, languages, access methods, and platforms, among others. This has, in turn, translated into limited reproducibility of computational experiments and the need for application-specific computational workflow construction and semi-automated enactment by human experts, especially where emerging interdisciplinary fields, such as systems chemistry, are pursued. Fortunately, the advent of the Semantic Web, and the very recent introduction of RESTful Semantic Web Services (SWS may present an opportunity to integrate all of the existing computational and database resources in chemistry into a machine-understandable, unified system that draws on the entirety of the Semantic Web. Results We have created a prototype framework of Semantic Automated Discovery and Integration (SADI framework SWS that exposes the QSAR descriptor functionality of the Chemistry Development Kit. Since each of these services has formal ontology-defined input and output classes, and each service consumes and produces RDF graphs, clients can automatically reason about the services and available reference information necessary to complete a given overall computational task specified through a simple SPARQL query. We demonstrate this capability by carrying out QSAR analysis backed by a simple formal ontology to determine whether a given molecule is drug-like. Further, we discuss parameter-based control over the execution of SADI SWS. Finally, we demonstrate the value of computational resource

  19. canEvolve: a web portal for integrative oncogenomics.

    Directory of Open Access Journals (Sweden)

    Mehmet Kemal Samur

    Full Text Available BACKGROUND & OBJECTIVE: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects such as the Cancer Genome Atlas (TCGA and the International Cancer Genome Consortium. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to biomedical researchers in a user-friendly manner. We have built the canEvolve web portal to meet this need. RESULTS: canEvolve query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. canEvolve stores gene, microRNA (miRNA and protein expression profiles, copy number alterations for multiple cancer types, and protein-protein interaction information. canEvolve allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. canEvolve provides results of integrative analysis of gene expression profiles with copy number alterations and with miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, canEvolve provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis. CONCLUSION: At present canEvolve provides different types of information extracted from 90 cancer genomics studies comprising of more than 10,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network

  20. Design and implementation of space physics multi-model application integration based on web

    Science.gov (United States)

    Jiang, Wenping; Zou, Ziming

    independent modules according to different business needs is applied to solve the problem of the independence of the physical space between multiple models. The classic MVC(Model View Controller) software design pattern is concerned to build the architecture of space physics multi-model application integrated system. The JSP+servlet+javabean technology is used to integrate the web application programs of space physics multi-model. It solves the problem of multi-user requesting the same job of model computing and effectively balances each server computing tasks. In addition, we also complete follow tasks: establishing standard graphical user interface based on Java Applet application program; Designing the interface between model computing and model computing results visualization; Realizing three-dimensional network visualization without plug-ins; Using Java3D technology to achieve a three-dimensional network scene interaction; Improved ability to interact with web pages and dynamic execution capabilities, including rendering three-dimensional graphics, fonts and color control. Through the design and implementation of the SPMAIS based on Web, we provide an online computing and application runtime environment of space physics multi-model. The practical application improves that researchers could be benefit from our system in space physics research and engineering applications.

  1. Mastering Microsoft Windows Small Business Server 2008

    CERN Document Server

    Johnson, Steven

    2010-01-01

    A complete, winning approach to the number one small business solution. Do you have 75 or fewer users or devices on your small-business network? Find out how to integrate everything you need for your mini-enterprise with Microsoft's new Windows Server 2008 Small Business Server, a custom collection of server and management technologies designed to help small operations run smoothly without a giant IT department. This comprehensive guide shows you how to master all SBS components as well as handle integration with other Microsoft technologies.: Focuses on Windows Server 2008 Small Business Serv

  2. A Semantic Web management model for integrative biomedical informatics.

    Directory of Open Access Journals (Sweden)

    Helena F Deus

    2008-08-01

    Full Text Available Data, data everywhere. The diversity and magnitude of the data generated in the Life Sciences defies automated articulation among complementary efforts. The additional need in this field for managing property and access permissions compounds the difficulty very significantly. This is particularly the case when the integration involves multiple domains and disciplines, even more so when it includes clinical and high throughput molecular data.The emergence of Semantic Web technologies brings the promise of meaningful interoperation between data and analysis resources. In this report we identify a core model for biomedical Knowledge Engineering applications and demonstrate how this new technology can be used to weave a management model where multiple intertwined data structures can be hosted and managed by multiple authorities in a distributed management infrastructure. Specifically, the demonstration is performed by linking data sources associated with the Lung Cancer SPORE awarded to The University of Texas MD Anderson Cancer Center at Houston and the Southwestern Medical Center at Dallas. A software prototype, available with open source at www.s3db.org, was developed and its proposed design has been made publicly available as an open source instrument for shared, distributed data management.The Semantic Web technologies have the potential to addresses the need for distributed and evolvable representations that are critical for systems Biology and translational biomedical research. As this technology is incorporated into application development we can expect that both general purpose productivity software and domain specific software installed on our personal computers will become increasingly integrated with the relevant remote resources. In this scenario, the acquisition of a new dataset should automatically trigger the delegation of its analysis.

  3. 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....

  4. Enterprise Application Integration Using Java Technologies

    Directory of Open Access Journals (Sweden)

    Alexandru BARBULESCU

    2006-01-01

    Full Text Available The current article points out some of the tasks and challenges companies must face in order to integrate their computerized systems and applications and then to place them on the Web. Also, the article shows how the Java 2 Enterprise Edition Platform and architecture helps the Web integration of applications. By offering standardized integration contracts, J2EE Platform allows application servers to play a key role in the process of Web integration of the applications.

  5. The digital Dalton Plan: Progressive education as integral part of web-based learning environments

    Directory of Open Access Journals (Sweden)

    Georg Weichhart

    2018-03-01

    Full Text Available e-Learning systems increasingly support learning management and self-organized learning processes. Since the latter have been studied in the field of progressive education extensively, it is worthwhile to consider them for developing digital learning environments to support self-regulated learning processes. In this paper we aim at transforming one of the most prominent and sustainable approaches to self-organized learning, the “Dalton Plan” as proposed by Helen Parkhurst. Its assignment structure supports learners when managing their learning tasks, thus triggering self-organized acquisition of knowledge, and its feedback graphs enable transparent learning processes. Since e-learning environments have become common use, rather than creating another system, we propose a modular approach that can be used for extending existing e-learning environments. In order to design a respective component, we interviewed experts in self-organized e-learning. Their input facilitated integrating the Dalton Plan with existing features of e-learning environments. After representing each interview in concept maps, we were able to aggregate them for deriving e-learning requirements conform to the Dalton Plan instruments. In the course of implementing them, particular attention had to be paid to the asynchrony of interaction during runtime. Java Server Faces technology enable the Dalton Plan component to be migrated into existing web 2.0 e-learning platforms. The result was evaluated based on the acquired concept maps, as they also captured the transformation process of the Dalton Plan to e-learning features. The findings encourage embodying further progressive education approaches in this way, since the structured (concept mapping of the Dalton Plan to e-learning features turned out to be accurate. The experts were able to recognize the potential of the approach both in terms of structuring the knowledge acquisition process, and in terms of developing

  6. SMART CITIES INTELLIGENCE SYSTEM (SMACiSYS) INTEGRATING SENSOR WEB WITH SPATIAL DATA INFRASTRUCTURES (SENSDI)

    OpenAIRE

    D. Bhattacharya; M. Painho

    2017-01-01

    The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists...

  7. Gclust Server: 25795 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 25795 HSA_89056940 Cluster Sequences Related Sequences(5) 233 XP_209187.4 PREDICTED: similar to fasting...tative annotation XP_209187.4 PREDICTED: similar to fasting-inducible integral membrane protein TM6P1 isofor

  8. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

    DEFF Research Database (Denmark)

    Zhang, Han; Yohe, Tanner; Huang, Le

    2018-01-01

    of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes. Here, dbCAN2...... (http://cys.bios.niu.edu/dbCAN2) is presented as an updated meta server, which integrates three state-of-the-art tools for CAZome (all CAZymes of a genome) annotation: (i) HMMER search against the dbCAN HMM (hidden Markov model) database; (ii) DIAMOND search against the CAZy pre-annotated CAZyme...

  9. Personalized Pseudonyms for Servers in the Cloud

    OpenAIRE

    Xiao Qiuyu; Reiter Michael K.; Zhang Yinqian

    2017-01-01

    A considerable and growing fraction of servers, especially of web servers, is hosted in compute clouds. In this paper we opportunistically leverage this trend to improve privacy of clients from network attackers residing between the clients and the cloud: We design a system that can be deployed by the cloud operator to prevent a network adversary from determining which of the cloud’s tenant servers a client is accessing. The core innovation in our design is a PoPSiCl (pronounced “popsicle”), ...

  10. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro

    2016-01-01

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  11. TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

    KAUST Repository

    Kudo, Toru

    2016-11-29

    Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.

  12. Multimedia medical data archive and retrieval server on the Internet

    Science.gov (United States)

    Komo, Darmadi; Levine, Betty A.; Freedman, Matthew T.; Mun, Seong K.; Tang, Y. K.; Chiang, Ted T.

    1997-05-01

    The Multimedia Medical Data Archive and Retrieval Server has been installed at the imaging science and information systems (ISIS) center in Georgetown University Medical Center to provide medical data archive and retrieval support for medical researchers. The medical data includes text, images, sound, and video. All medical data is keyword indexed using a database management system and placed temporarily in a staging area and then transferred to a StorageTek one terabyte tape library system with a robotic arm for permanent archive. There are two methods of interaction with the system. The first method is to use a web browser with HTML functions to perform insert, query, update, and retrieve operations. These generate dynamic SQL calls to the database and produce StorageTek API calls to the tape library. The HTML functions consist of a database, StorageTek interface, HTTP server, common gateway interface, and Java programs. The second method is to issue a DICOM store command, which is translated by the system's DICOM server to SQL calls and then produce StorageTek API calls to the tape library. The system performs as both an Internet and a DICOM server using standard protocols such as HTTP, HTML, Java, and DICOM. Users with proper authentication can log on to the server from anywhere on the Internet using a standard web browser resulting in a user-friendly, open environment, and platform independent solution for archiving multimedia medical data. It represents a complex integration of different components including a robotic tape storage system, database, user-interface, WWW protocols, and TCP/IP networking. The user will only deal with the WWW and DICOM server components of the system, the database and robotic tape library system are transparent and the user will not know that the medical data is stored on magnetic tapes. The server provides the researchers a cost-effective tool for archiving and retrieving medical data across a TCP/IP network environment. It will

  13. "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.

  14. Конструктор служб SQL Server Integration Services

    OpenAIRE

    ОХОТНИКОВ В.А.; МОРГУНОВ Е.П.

    2012-01-01

    Рассматривается использование конструктора служб SQL Server Integration Services для переноса информации из различных источников в БД. Описываются результаты применения указанной технологии.

  15. Customer Decision Making in Web Services with an Integrated P6 Model

    Science.gov (United States)

    Sun, Zhaohao; Sun, Junqing; Meredith, Grant

    Customer decision making (CDM) is an indispensable factor for web services. This article examines CDM in web services with a novel P6 model, which consists of the 6 Ps: privacy, perception, propensity, preference, personalization and promised experience. This model integrates the existing 6 P elements of marketing mix as the system environment of CDM in web services. The new integrated P6 model deals with the inner world of the customer and incorporates what the customer think during the DM process. The proposed approach will facilitate the research and development of web services and decision support systems.

  16. TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Degrave Wim

    1997-01-01

    Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

  17. 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.

  18. A web-based system for the integrated water management

    Science.gov (United States)

    Giordano, R.; Passarella, G.; Uricchio, V. F.; Lopez, N.

    2003-04-01

    The success of complexity theory has posed new challenges also in the environmental resources management. From the complexity point of view, in fact, the environment has to be considered as a system with numerous parts interrelated each other by strongly and no-linear feedback relationships. In this perspective, when an action is performed its results become difficult to control. Therefore, to construct and to select the most suitable alternatives for environmental resources management, an holistic approach has to be adopted. In water resources management domain, increasing interest is posed to the integrated management, in which the total system of biotic and a-biotic elements of certain water environment is taken into account. Our contribution moves from the idea that the term integrated has to be referred also to human agents which take decisions influencing the water environment. In other words, Integrated Water Management (IWM) considers how different action affect, and can reinforce, each other and it promotes the coordinated development and management of water, land and related resources. The IWM stresses the interrelationships among the actions at different types, working at different levels of influence, coordinating stakeholders' actions. The coordination requires an appropriate information level about the strategies used by each stakeholder. To improve the information flow inside a watershed and therefore the coordination among agents, a web-based system is proposed. It could be defined as an electronic agora where a set of stakeholders can be involved both in information exchange and in conflicts resolution. More in detail, to improve the coordination process, the proposed system allows the stakeholders to find someone with similar or conflicting interests to collaborate with; to make contact with selected people; to build a common understanding (that is the identification of a common goal, the negotiation about the way this goal should be reached); to

  19. Context mining and integration into predictive web analytics

    NARCIS (Netherlands)

    Kiseleva, Y.

    2013-01-01

    Predictive Web Analytics is aimed at understanding behavioural patterns of users of various web-based applications: e-commerce, ubiquitous and mobile computing, and computational advertising. Within these applications business decisions often rely on two types of predictions: an overall or

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

    Science.gov (United States)

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

    2014-05-01

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

  1. 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

  2. Integration of RFID and web service for assisted living.

    Science.gov (United States)

    Unluturk, Mehmet S; Kurtel, Kaan

    2012-08-01

    The number of people over 65 years old throughout most stable and prosperous countries in the world is increasing. Availability of their care in their own homes is imperative because of the economic reasons and their choices where to live (World Health Organization, Definition of an older or elderly person. http://www.who.int/healthinfo/survey/ageingdefnolder/en/ ; EQUIP-European Framework for Qualifications in Home Care Services for Older People, http://www.equip-project.com ; Salonen, 2009). "Recent advancement in wireless communications and electronics has enabled the development of low-cost sensor networks. The sensor networks can be utilized in various application areas." (Akyildiz, et al. 2002) These two statements show that there is a great promise in wireless technology and utilizing it in assisted living might be very beneficial to the elderly people. In this paper, we propose software architecture called Location Windows Service (LWS) which integrates the Radio Frequency Identification (RFID) technology and the web service to build an assisted living system for elderly people at home. This architecture monitors the location of elderly people without interfering in their daily activities. Location information messages that are generated as the elderly move from room to room indicate that the elderly person is fit and healthy and going about their normal life. The communication must be timely enough to follow elderly people as they move from room to room without missing a location. Unacknowledged publishing, subscription filtering and short location change messages are also included in this software model to reduce the network traffic in large homes. We propose some defense schemes being applied to the network environment of the assisted living system to prevent any external attacks.

  3. ProFASTA: a pipeline web server for fungal protein scanning with integration of cell surface prediction software

    NARCIS (Netherlands)

    de Groot, P.W.J.; Brandt, B.W.

    2012-01-01

    Surface proteins, such as those located in the cell wall of fungi, play an important role in the interaction with the surrounding environment. For instance, they mediate primary host-pathogen interactions and are crucial to the establishment of biofilms and fungal infections. Surface localization of

  4. SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

    Science.gov (United States)

    Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines

    2017-06-24

    Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.

  5. Motivating Pre-Service Teachers in Technology Integration of Web 2.0 for Teaching Internships

    Science.gov (United States)

    Kim, Hye Jeong; Jang, Hwan Young

    2015-01-01

    The aim of this study was to examine the predictors of pre-service teachers' use of Web 2.0 tools during a teaching internship, after a course that emphasized the use of the tools for instructional activities. Results revealed that integrating Web 2.0 tools during their teaching internship was strongly predicted by participants' perceived…

  6. Integration of Web 2.0 Tools in Learning a Programming Course

    Science.gov (United States)

    Majid, Nazatul Aini Abd

    2014-01-01

    Web 2.0 tools are expected to assist students to acquire knowledge effectively in their university environment. However, the lack of effort from lecturers in planning the learning process can make it difficult for the students to optimize their learning experiences. The aim of this paper is to integrate Web 2.0 tools with learning strategy in…

  7. Integrating Web 2.0-Based Informal Learning with Workplace Training

    Science.gov (United States)

    Zhao, Fang; Kemp, Linzi J.

    2012-01-01

    Informal learning takes place in the workplace through connection and collaboration mediated by Web 2.0 applications. However, little research has yet been published that explores informal learning and how to integrate it with workplace training. We aim to address this research gap by developing a conceptual Web 2.0-based workplace learning and…

  8. ArcGIS Server per la distribuzione delle informazioni del Trasporto Pubblico

    Directory of Open Access Journals (Sweden)

    Flaminia Leggeri

    2012-06-01

    ArcGIS Server for public transportation info service in Rome One goal of ATAC, the public transport operator of the Municipality of Rome, is to provide information the the daily users of the transportation network. In recent years the efforts to improve both the quantity and quality of information have reached a high level of integration in order to provide the end user with good web mapping systems available on the Internet.

  9. Reference framework for integrating web resources as e-learning services in .LRN

    Directory of Open Access Journals (Sweden)

    Fabinton Sotelo Gómez

    2015-11-01

    Full Text Available The learning management platforms (LMS as Dot LRN (.LRN have been widely disseminated and used as a teaching tool. However, despite its great potential, most of these platforms do not allow easy integration of common services on the Web. Integration of external resources in LMS is critical to extend the quantity and quality of educational services LMS. This article presents a set of criteria and architectural guidelines for the integration of Web resources for e-learning in the LRN platform. To this end, three steps are performed: first; the possible integration technologies to be used are described, second; the Web resources that provide educational services and can be integrated into LMS platforms are analyzed, finally; some architectural aspects of the relevant platform are identified for integration. The main contributions of this paper are: a characterization of Web resources and educational services available today on the Web; and the definition of criteria and guidelines for the integration of Web resources to .LRN.

  10. LearnWeb 2.0. Integrating Social Software for Lifelong Learning.

    NARCIS (Netherlands)

    Marenzi, Ivana; Demidova, Elena; Nejdl, Wolfgang

    2008-01-01

    Marenzi, I., Demidova, E., & Nejdl, W. (2008). LearnWeb 2.0. Integrating Social Software for Lifelong Learning. Proceedings of the ED-Media 2008. World Conference on Educational Multimedia, Hypermedia & Telecommunications. June, 30 - July, 4, 2008, Austria, Vienna.

  11. Interoperative fundus image and report sharing in compliance with integrating the healthcare enterprise conformance and web access todigital imaging and communication in medicinepersistent object protocol

    Directory of Open Access Journals (Sweden)

    Hui-Qun Wu

    2013-12-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  13. CACHING DATA STORED IN SQL SERVER FOR OPTIMIZING THE PERFORMANCE

    Directory of Open Access Journals (Sweden)

    Demian Horia

    2016-12-01

    Full Text Available This paper present the architecture of web site with different techniques used for optimize the performance of loading the web content. The architecture presented here is for e-commerce site developed on windows with MVC, IIS and Micosoft SQL Server. Caching the data is one technique used by the browsers, by the web servers itself or by proxy servers. Caching the data is made without the knowledge of users and need to provide to user the more recent information from the server. This means that caching mechanism has to be aware of any modification of data on the server. There are different information’s presented in e-commerce site related to products like images, code of product, description, properties or stock

  14. Server virtualization solutions

    OpenAIRE

    Jonasts, Gusts

    2012-01-01

    Currently in the information technology sector that is responsible for a server infrastructure is a huge development in the field of server virtualization on x86 computer architecture. As a prerequisite for such a virtualization development is growth in server productivity and underutilization of available computing power. Several companies in the market are working on two virtualization architectures – hypervizor and hosting. In this paper several of virtualization products that use host...

  15. 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.

  16. Group-Server Queues

    OpenAIRE

    Li, Quan-Lin; Ma, Jing-Yu; Xie, Mingzhou; Xia, Li

    2017-01-01

    By analyzing energy-efficient management of data centers, this paper proposes and develops a class of interesting {\\it Group-Server Queues}, and establishes two representative group-server queues through loss networks and impatient customers, respectively. Furthermore, such two group-server queues are given model descriptions and necessary interpretation. Also, simple mathematical discussion is provided, and simulations are made to study the expected queue lengths, the expected sojourn times ...

  17. Performance Characteristics of Mirror Servers on the Internet

    National Research Council Canada - National Science Library

    Meyers, Andy

    1998-01-01

    ... retrieved. In this paper we present findings from measuring 9 clients scattered throughout the United States retrieving over 490,000 documents from 45 production web servers which mirror three different sites...

  18. 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

  19. 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.

  20. Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data.

    Science.gov (United States)

    Tian, Tze-Feng; Wang, San-Yuan; Kuo, Tien-Chueh; Tan, Cheng-En; Chen, Guan-Yuan; Kuo, Ching-Hua; Chen, Chi-Hsin Sally; Chan, Chang-Chuan; Lin, Olivia A; Tseng, Y Jane

    2016-11-01

    Two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC 2 MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC 2 MS consists of blob/peak detection, baseline correction, and blob alignment. GC 2 MS treats GC×GC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC 2 MS then aligns the blobs of two GC×GC/TOF-MS data sets according to their distance and similarity. The blob distance and similarity are the Euclidean distance of the first and second retention times of two blobs and the Pearson's correlation coefficient of the two mass spectra, respectively. GC 2 MS also directly corrects the raw data baseline. The analytical performance of GC 2 MS was evaluated using GC×GC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC 2 MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC 2 MS is able to align GC×GC/TOF-MS data sets acquired under different experimental conditions. GC 2 MS is freely accessible at http://gc2ms.web.cmdm.tw .

  1. Advanced 3-D analysis, client-server systems, and cloud computing-Integration of cardiovascular imaging data into clinical workflows of transcatheter aortic valve replacement.

    Science.gov (United States)

    Schoenhagen, Paul; Zimmermann, Mathis; Falkner, Juergen

    2013-06-01

    Degenerative aortic stenosis is highly prevalent in the aging populations of industrialized countries and is associated with poor prognosis. Surgical valve replacement has been the only established treatment with documented improvement of long-term outcome. However, many of the older patients with aortic stenosis (AS) are high-risk or ineligible for surgery. For these patients, transcatheter aortic valve replacement (TAVR) has emerged as a treatment alternative. The TAVR procedure is characterized by a lack of visualization of the operative field. Therefore, pre- and intra-procedural imaging is critical for patient selection, pre-procedural planning, and intra-operative decision-making. Incremental to conventional angiography and 2-D echocardiography, multidetector computed tomography (CT) has assumed an important role before TAVR. The analysis of 3-D CT data requires extensive post-processing during direct interaction with the dataset, using advance analysis software. Organization and storage of the data according to complex clinical workflows and sharing of image information have become a critical part of these novel treatment approaches. Optimally, the data are integrated into a comprehensive image data file accessible to multiple groups of practitioners across the hospital. This creates new challenges for data management requiring a complex IT infrastructure, spanning across multiple locations, but is increasingly achieved with client-server solutions and private cloud technology. This article describes the challenges and opportunities created by the increased amount of patient-specific imaging data in the context of TAVR.

  2. Interim policy on establishment and operation of internet open, anonymous information servers and services

    OpenAIRE

    Acting Dean of Computer and Information Services

    1995-01-01

    Purpose. To establish interim NPS general policy regarding establishment and operation of Open, Anonymous Information Servers and Services, such as World Wide Web (http), Gopher, Anonymous FTP, etc...

  3. A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data.

    NARCIS (Netherlands)

    Post, L.J.G.; Roos, M.; Marshall, M.S.; van Driel, R.; Breit, T.M.

    2007-01-01

    The numerous public data resources make integrative bioinformatics experimentation increasingly important in life sciences research. However, it is severely hampered by the way the data and information are made available. The semantic web approach enhances data exchange and integration by providing

  4. Inquiry of Pre-Service Teachers' Concern about Integrating Web 2.0 into Instruction

    Science.gov (United States)

    Hao, Yungwei; Lee, Kathryn S.

    2017-01-01

    To promote technology integration, it is essential to address pre-service teacher (PST) concerns about facilitating technology-enhanced learning environments. This study adopted the Concerns-Based Adoption Model to investigate PST concern on Web 2.0 integration. Four hundred and eighty-nine PSTs in a teacher education university in north Taiwan…

  5. An integrable, web-based solution for easy assessment of video-recorded performances

    DEFF Research Database (Denmark)

    Subhi, Yousif; Todsen, Tobias; Konge, Lars

    2014-01-01

    , and access to this information should be restricted to select personnel. A local software solution may also ease the need for customization to local needs and integration into existing user databases or project management software. We developed an integrable web-based solution for easy assessment of video...

  6. Review of Theoretical Prediction Models for Organic Extract Metabolites, Effect of Drying Temperature on Smooth Muscle Relaxing Activity Induced by Organic Extracts Specially Cecropia Obtusifolia Portal and Web Server Predictors of Drug-Protein Interaction.

    Science.gov (United States)

    Aguirre-Crespo, Francisco; García-Mera, Xerardo; Guillén-Poot, Mónica Anahi; May-Díaz, Héctor Fernado; Tun-Suárez, Adrián; Aguirre-Crespo, A; Hernández-Rodríguez, J; Vergara-Galicia, Jorge; Rodríguez-López, V; Prado-Prado, Francisco J

    2015-02-19

    Cecropia obtusifolia bertol is medicinal specie used in the treatment of diabetes mellitus and hypertension and it has scientific studies that support the traditional use. However, it is required to understand the influence of drying temperature on the yield and pharmacological activity. Drying rate, extraction efficiency, changes in the UV-Vis spectrum and estimating chlorophylls were stimulated with the increasing temperature. Finally, relaxant activity of vascular smooth muscle is increased by 70ºC and reducing ability by the method of CARF increases with temperature. Analytical studies are required to identify changes in the metabolic content and those that ensure the safety and efficacy for human consumption. In this sense, bioinformatic studies may be helpful. Studies such as QSAR can help us to study these metabolites derived from natural products. MIND-BETS model and NL MIND-BETS model to predict DPIs was introduced using MARCH-INSIDE (MI) software to calculate structural parameters for drugs and enzymes respectively. We firstly revised the state-of-art on the design with review of previous works with hypertension activity based on theoretical studies. A study, evaluating the effect of drying temperature of leaves of C. obtusifolia on the relaxing of vascular smooth muscle, antioxidant activity and the presence of chlorophylls, with a focus on Cecropia metabolites. Last, we carried out QSAR studies using MIND-BEST and NL MIND-BEST web servers in order to understand the essential metabolites structural requirement for binding with receptors for FDA proteins.

  7. Microsoft SQL Server OLAP Solution - A Survey

    OpenAIRE

    Badiozamany, Sobhan

    2010-01-01

    Microsoft SQL Server 2008 offers technologies for performing On-Line Analytical Processing (OLAP), directly on data stored in data warehouses, instead of moving the data into some offline OLAP tool. This brings certain benefits, such as elimination of data copying and better integration with the DBMS compared with off-line OLAP tools. This report reviews SQL Server support for OLAP, solution architectures, tools and components involved. Standard storage options are discussed but the focus of ...

  8. Web-Scale Search-Based Data Extraction and Integration

    Science.gov (United States)

    2011-10-17

    Garage band / danceteria. Piscina adulto des coberta Sala de leitura, Spa Figure 107: An apartment feature from OLX. The expected neighborhood is...11 I lon.nin - 23 I lon.bem - E I postal.code - 6010-6080 I area.code - 0612 I licence - I I mayor - Hilde Zach I website - (nttp...km’ Elevation 574 m Coordinates ’ •’:3 i * Postal cod* 6010-6060 Area code 05i: Licence plate code i Mayor Hild# Zath Web s-ie • • . . ittf

  9. Integrated bird conservation web site in the United States

    Science.gov (United States)

    Roxanne Bogart; Chris Eberly; Elizabeth Martin

    2005-01-01

    In working towards a vision of integrated bird conservation, scientists, conservationists, land managers, and administrators are faced with a variety of scientific, managerial, administrative, and logistical challenges and complexities. The broad scope of integrated bird conservation requires organizations to work together to conserve birds across taxonomic groups,...

  10. SMART CITIES INTELLIGENCE SYSTEM (SMACiSYS INTEGRATING SENSOR WEB WITH SPATIAL DATA INFRASTRUCTURES (SENSDI

    Directory of Open Access Journals (Sweden)

    D. Bhattacharya

    2017-09-01

    Full Text Available The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS with sensor-web access (SENSDI utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

  11. Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

    Science.gov (United States)

    Bhattacharya, D.; Painho, M.

    2017-09-01

    The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

  12. A Framework for Sharing and Integrating Remote Sensing and GIS Models Based on Web Service

    Science.gov (United States)

    Chen, Zeqiang; Lin, Hui; Chen, Min; Liu, Deer; Bao, Ying; Ding, Yulin

    2014-01-01

    Sharing and integrating Remote Sensing (RS) and Geographic Information System/Science (GIS) models are critical for developing practical application systems. Facilitating model sharing and model integration is a problem for model publishers and model users, respectively. To address this problem, a framework based on a Web service for sharing and integrating RS and GIS models is proposed in this paper. The fundamental idea of the framework is to publish heterogeneous RS and GIS models into standard Web services for sharing and interoperation and then to integrate the RS and GIS models using Web services. For the former, a “black box” and a visual method are employed to facilitate the publishing of the models as Web services. For the latter, model integration based on the geospatial workflow and semantic supported marching method is introduced. Under this framework, model sharing and integration is applied for developing the Pearl River Delta water environment monitoring system. The results show that the framework can facilitate model sharing and model integration for model publishers and model users. PMID:24901016

  13. A framework for sharing and integrating remote sensing and GIS models based on Web service.

    Science.gov (United States)

    Chen, Zeqiang; Lin, Hui; Chen, Min; Liu, Deer; Bao, Ying; Ding, Yulin

    2014-01-01

    Sharing and integrating Remote Sensing (RS) and Geographic Information System/Science (GIS) models are critical for developing practical application systems. Facilitating model sharing and model integration is a problem for model publishers and model users, respectively. To address this problem, a framework based on a Web service for sharing and integrating RS and GIS models is proposed in this paper. The fundamental idea of the framework is to publish heterogeneous RS and GIS models into standard Web services for sharing and interoperation and then to integrate the RS and GIS models using Web services. For the former, a "black box" and a visual method are employed to facilitate the publishing of the models as Web services. For the latter, model integration based on the geospatial workflow and semantic supported marching method is introduced. Under this framework, model sharing and integration is applied for developing the Pearl River Delta water environment monitoring system. The results show that the framework can facilitate model sharing and model integration for model publishers and model users.

  14. Integration of Web Technologies in Software Applications. Is Web 2.0 a Solution?

    Directory of Open Access Journals (Sweden)

    Cezar Liviu CERVINSCHI

    2010-12-01

    Full Text Available Starting from the idea that Web 2.0 represents “the era of dynamic web”, the paper proposes to provide arguments (demonstrated by physical results regarding the question that is at the foundation if this article. Due to the findings we can definitely affirm that Web 2.0 is a solution to building powerful and robust software, since the Internet has become more than just a simple presence on the users’ desktop that develops easy access to information, services, entertainment, online transactions, e-commerce, e-learning and so on, but basically every kind of human or institutional interaction can happen online. This paper seeks to study the impact of two of these braches upon the user – e-commerce and e-testing. The statistic reports will be made on different sets of people, while the conclusions are the results of a detailed research and study of the applications’ behaviour in the actual operating environment.

  15. Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP for bioinformatics resource discovery and disparate data and service integration

    Directory of Open Access Journals (Sweden)

    Nelson Rex T

    2010-06-01

    Full Text Available Abstract Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap" offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS] used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL, genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL, Resource Description Framework (RDF and eXtensible Markup Language (XML documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST. Conclusions The need for semantic integration technologies has preceded

  16. Sharing human-generated observations by integrating HMI and the Semantic Sensor Web.

    Science.gov (United States)

    Sigüenza, Alvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

    2012-01-01

    Current "Internet of Things" concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound.

  17. A Web-Based Integration Procedure for the Development of Reconfigurable Robotic Work-Cells

    OpenAIRE

    Paulo Ferreira; Victoria Reyes; João Mestre

    2013-01-01

    Concepts related to the development of reconfigurable manufacturing systems (RMS) and methodologies to provide the best practices in the processing industry and factory automation, such as system integration and web-based technology, are major issues in designing next-generation manufacturing systems (NGMS). Adaptable and integrable devices are crucial for the success of NGMS. In robotic cells the integration of manufacturing components is essential to accelerate system adaptability. Sensors,...

  18. 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.

  19. Web-based approach to the INTEGRAL data

    Czech Academy of Sciences Publication Activity Database

    Münz, F.; Kocka, Matúš

    2009-01-01

    Roč. 18, 3-4 (2009), s. 379-382 ISSN 1392-0049. [INTEGRAL/BART workshop 2009. Karlovy Vary, 26.03.2009-29.03.2009] R&D Projects: GA AV ČR IAA3003206 Grant - others:ESA(XE) ESA-PECS project No. 98023 Institutional research plan: CEZ:AV0Z10030501 Keywords : gamma rays * gursts * INTEGRAL Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 1.032, year: 2009

  20. The Semantic Automated Discovery and Integration (SADI Web service Design-Pattern, API and Reference Implementation

    Directory of Open Access Journals (Sweden)

    Wilkinson Mark D

    2011-10-01

    Full Text Available Abstract Background The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services

  1. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

    Science.gov (United States)

    2011-01-01

    Background The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. Description SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner

  2. The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation.

    Science.gov (United States)

    Wilkinson, Mark D; Vandervalk, Benjamin; McCarthy, Luke

    2011-10-24

    The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community. SADI - Semantic Automated Discovery and Integration - is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services "stack", SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behaviour we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in

  3. Utilization of a Web-Based vs Integrated Phone/Web Cessation Program Among 140,000 Tobacco Users: An Evaluation Across 10 Free State Quitlines

    Science.gov (United States)

    Vickerman, Katrina A; Kellogg, Elizabeth S; Zbikowski, Susan M

    2015-01-01

    Background Phone-based tobacco cessation program effectiveness has been established and randomized controlled trials have provided some support for Web-based services. Relatively little is known about who selects different treatment modalities and how they engage with treatments in a real-world setting. Objective This paper describes the characteristics, Web utilization patterns, and return rates of tobacco users who self-selected into a Web-based (Web-Only) versus integrated phone/Web (Phone/Web) cessation program. Methods We examined the demographics, baseline tobacco use, Web utilization patterns, and return rates of 141,429 adult tobacco users who self-selected into a Web-Only or integrated Phone/Web cessation program through 1 of 10 state quitlines from August 2012 through July 2013. For each state, registrants were only included from the timeframe in which both programs were offered to all enrollees. Utilization data were limited to site interactions occurring within 6 months after registration. Results Most participants selected the Phone/Web program (113,019/141,429, 79.91%). After enrollment in Web services, Web-Only were more likely to log in compared to Phone/Web (21,832/28,410, 76.85% vs 23,920/56,892, 42.04%; PPhone/Web were also more likely to return if they had completed a coaching call, identified as white non-Hispanic or “other” race, or were commercially insured (all Pphone. The interactive Tobacco Tracker, Cost Savings Calculator, and Quitting Plan were the most widely used features overall. Web-Only were more likely than Phone/Web to use most key features (all PPhone/Web and Web-Only, Web-Only were less likely to have received quitline NRT. Conclusions This paper adds to our understanding of who selects different cessation treatment modalities and how they engage with the program in a real-world setting. Web-Only were younger, healthier smokers of higher socioeconomic status who interacted more intensely with services in a single session

  4. Server hardware trends

    CERN Multimedia

    CERN. Geneva

    2014-01-01

    This talk will cover the status of the current and upcoming offers on server platforms, focusing mainly on the processing and storage parts. Alternative solutions like Open Compute (OCP) will be quickly covered.

  5. Locating Hidden Servers

    National Research Council Canada - National Science Library

    Oeverlier, Lasse; Syverson, Paul F

    2006-01-01

    .... Announced properties include server resistance to distributed DoS. Both the EFF and Reporters Without Borders have issued guides that describe using hidden services via Tor to protect the safety of dissidents as well as to resist censorship...

  6. Web Based Database Processing for Turkish Navy Officers in USA

    National Research Council Canada - National Science Library

    Ozkan, Gokhan

    2002-01-01

    ...) and details the supporting web server and database server choices, It then presents a prototype of a web-based database system to speed and simplify tracking of academic and personal information...

  7. 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.

  8. Welcome to Our Web: Integrating Subjects through Entomology.

    Science.gov (United States)

    Tevebaugh, Tara

    2001-01-01

    Shares how the study of insects became a focal point for cross-curricular convergence in the author's classroom. Describes the design of a unit of study that focused on entomology but integrated academic areas, especially language arts. Concludes that students must develop a sense of interdependence and an understanding of possible relationships…

  9. Deploying web-based visual exploration tools on the grid

    Energy Technology Data Exchange (ETDEWEB)

    Jankun-Kelly, T.J.; Kreylos, Oliver; Shalf, John; Ma, Kwan-Liu; Hamann, Bernd; Joy, Kenneth; Bethel, E. Wes

    2002-02-01

    We discuss a web-based portal for the exploration, encapsulation, and dissemination of visualization results over the Grid. This portal integrates three components: an interface client for structured visualization exploration, a visualization web application to manage the generation and capture of the visualization results, and a centralized portal application server to access and manage grid resources. We demonstrate the usefulness of the developed system using an example for Adaptive Mesh Refinement (AMR) data visualization.

  10. How to Configurate Oracle Enterprise Manager on Windows 2000 Server

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Oracle Enterprise Manager is a system management tool, which provides an integrated solution for centrally managing your heterogeneous environment Servers. Enterprise Manager combines a graphical Console, Oracle Management Servers, Oracle Intelligent Agents, common services, and tools to provide an integrated, comprehensive systems management platform for managing Oracle products, and is comprised of such as Data

  11. Graph-Based Semantic Web Service Composition for Healthcare Data Integration.

    Science.gov (United States)

    Arch-Int, Ngamnij; Arch-Int, Somjit; Sonsilphong, Suphachoke; Wanchai, Paweena

    2017-01-01

    Within the numerous and heterogeneous web services offered through different sources, automatic web services composition is the most convenient method for building complex business processes that permit invocation of multiple existing atomic services. The current solutions in functional web services composition lack autonomous queries of semantic matches within the parameters of web services, which are necessary in the composition of large-scale related services. In this paper, we propose a graph-based Semantic Web Services composition system consisting of two subsystems: management time and run time. The management-time subsystem is responsible for dependency graph preparation in which a dependency graph of related services is generated automatically according to the proposed semantic matchmaking rules. The run-time subsystem is responsible for discovering the potential web services and nonredundant web services composition of a user's query using a graph-based searching algorithm. The proposed approach was applied to healthcare data integration in different health organizations and was evaluated according to two aspects: execution time measurement and correctness measurement.

  12. A Web-based e-learning course: integration of pathophysiology into pharmacology.

    Science.gov (United States)

    Tse, Mimi M Y; Lo, Lisa W L

    2008-11-01

    The Internet is becoming the preferred place to find information. Millions of people go online in search of health and medical information. Likewise, the demand for Web-based courses is growing. This paper presents the development, utilization, and evaluation of a Web-based e-learning course for nursing students, entitled Integration of Pathophysiology into Pharmacology. The pathophysiology component included cardiovascular, respiratory, central nervous and immune system diseases, while the pharmacology component was developed based on 150 commonly used drugs. One hundred and nineteen Year 1 nursing students took part in the course. The Web-based e-learning course materials were uploaded to a WebCT for students' self-directed learning and attempts to pass two scheduled online quizzes. At the end of the semester, students were given a questionnaire to measure the e-learning experience. Their experience in the e-learning course was a positive one. Students stated that they were able to understand rather than memorize the subject content, and develop their problem solving and critical thinking abilities. Online quizzes yielded satisfactory results. In the focus group interview, students indicated that they appreciated the time flexibility and convenience associated with Web-based learning, and also made good suggestions for enhancing Web-based learning. The Web-based approach is promising for teaching and learning pathophysiology and pharmacology for nurses and other healthcare professionals.

  13. An Integrated Framework Of Web 2.0 Technology And A Collaborative Learning

    Directory of Open Access Journals (Sweden)

    Mohamed Madar

    2015-05-01

    Full Text Available Abstract This paper contributes to the suitability of web 2.0 technology in implementing collaborative learning and proposes an integrated framework of Web 2.0 tools and collaborative learning activities. This paper is also identifying the mismatch between adopting web 2.0 technologies and the delivery of the curriculum on the cloud or via the Internet. It is found that Web 2.0 and a collaborative learning are two platforms to be easily synchronized due to their common attributes that enable their complementariness. This paper argues that integrated framework of Web 2.0 and CL allow users exploit teachinglearning materials maximally and at the same upsurges learners understanding in the subject knowledge. Suitable of Web 2.0 in implementing curriculum was also encouraged since the proposed framework consists of both components of Web 2.0 functions and activities of collaborative learning environment. Pedagogically there has been a mismatch between E-learning technologies and mode of delivery for instance E-learning platforms are widely used to increase content accessibility only while now this framework introduces that Web 2.0 technology of E-learning can also be used to create share knowledge among users. The proposed framework if efficiently exploited will also allow users at all levels create personalized learning environment which suits perspective teachinglearning styles of the users. Apart from academic achievement or enhancements of the teaching and learning processes the proposed framework also would help learners develop generic skills which are very important in the workplaces. As a result of this fast and independent learning technically depend on technology based pedagogy and in this case this proposed model has two dimensions which are very crucial to the enrichment of students learning activities.

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

    Science.gov (United States)

    Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

    2004-03-22

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

  15. 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

  16. An information integration system for structured documents, Web, and databases

    OpenAIRE

    Morishima, Atsuyuki

    1998-01-01

    Rapid advance in computer network technology has changed the style of computer utilization. Distributed computing resources over world-wide computer networks are available from our local computers. They include powerful computers and a variety of information sources. This change is raising more advanced requirements. Integration of distributed information sources is one of such requirements. In addition to conventional databases, structured documents have been widely used, and have increasing...

  17. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  18. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  19. Hardening cookies in web-based systems for better system integrity

    International Nuclear Information System (INIS)

    Mohamad Safuan Sulaiman; Mohd Dzul Aiman Aslan; Saaidi Ismail; Abdul Aziz Mohd Ramli; Abdul Muin Abdul Rahman; Siti Nurbahyah Hamdan; Norlelawati Hashimuddin; Sufian Norazam Mohamed Aris

    2012-01-01

    IT Center (ITC) as technical support and provider for most of web-based systems in Nuclear Malaysia has conducted a study to investigate cookie vulnerability in a system for better integrity. A part of the result has found that cookies in a web-based system in Nuclear Malaysia can be easily manipulated. The main objective of the study is to harden the vulnerability of the cookies. Two levels of security procedures have been used and enforced which consist of 1) Penetration test (Pen Test) 2) Hardening procedure. In one of the system, study has found that 121 attempts threats have been detected after the hardening enforcement from 23 March till 20 September 2012. At this stage, it can be concluded that cookie vulnerability in the system has been hardened and integrity has been assured after the enforcement. This paper describes in detail the penetration and hardening process of cookie vulnerability for better supporting web-based system in Nuclear Malaysia. (author)

  20. 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.