You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/03 14:40:38 UTC
svn commit: r938796 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/taverna-in-use/bioinformatics.html
Author: buildbot
Date: Tue Feb 3 13:40:38 2015
New Revision: 938796
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
Propchange: websites/staging/taverna/trunk/cgi-bin/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 3 13:40:38 2015
@@ -1 +1 @@
-1656688
+1656729
Propchange: websites/staging/taverna/trunk/content/
------------------------------------------------------------------------------
--- cms:source-revision (original)
+++ cms:source-revision Tue Feb 3 13:40:38 2015
@@ -1 +1 @@
-1656688
+1656729
Added: websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html (added)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html Tue Feb 3 13:40:38 2015
@@ -0,0 +1,261 @@
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
+ <meta http-equiv="X-UA-Compatible" content="IE=edge">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <title>Apache Taverna - Bioinformatics</title>
+
+ <meta http-equiv="Content-Type" content="text/html;charset=UTF-8">
+ <meta property="og:image" content="/img/taverna-logo-145x134.png" />
+
+ <link rel="shortcut icon" href="/favicon.ico">
+ <link rel="icon" type="image/png" sizes="145x134" href="/img/taverna-logo-145x134.png">
+ <link rel="apple-touch-icon" sizes="145x134" href="/img/taverna-logo-145x134.png">
+
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap.min.css">
+ <link rel="stylesheet" href="/lib/bootstrap/css/bootstrap-theme.min.css">
+ <link rel="stylesheet" href="/css/sticky-footer-navbar.css">
+ <link rel="stylesheet" href="/css/taverna.css">
+
+
+
+
+ <!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The ASF licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. -->
+
+ <!-- JSON-LD markup for Google Structured Data -->
+
+ <!-- generic JSON-LD for this page -->
+ <script type="application/ld+json">
+ {
+ "@context" : "http://schema.org",
+ "@type" : ["CreativeWork"],
+ "@id": "",
+ "name" : "Bioinformatics",
+ "publisher" : {
+ "@type" : "Organization",
+ "url" : "http://www.apache.org/",
+ "name" : "The Apache Software Foundation (ASF)"
+ },
+ "license": {
+ "@type": "CreativeWork",
+ "@id": "http://www.apache.org/licenses/LICENSE-2.0",
+ "url": "http://www.apache.org/licenses/LICENSE-2.0",
+ "name": "Apache License, Version 2.0"
+ }
+ }
+</script>
+
+ </head>
+
+ <body>
+
+ <!-- Static navbar -->
+ <nav class="navbar navbar-default" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false" aria-controls="navbar">
+ <span class="sr-only">Toggle navigation</span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="/"><img src="/img/taverna-logo-145x134.png" alt="">Apache Taverna</a>
+
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li class="dropdown">
+ <a class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Introduction<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/introduction/">Introduction</a></li>
+ <li><a href="/introduction/taverna-features.html">Taverna features</a></li>
+ <li><a href="/introduction/why-use-workflows.html">Why use workflows?</a></li>
+ <li><a href="/introduction/what-is-in-silico-experimentation.html">What is âin silicoâ experimentation?</a></li>
+ <li><a href="/introduction/what-is-a-workflow-management-system.html">What is a Workflow Management System?</a></li>
+ <li><a href="/introduction/how-can-taverna-help-me.html">How can Taverna help me?</a></li>
+ <li><a href="/introduction/services-in-taverna.html">Services in Taverna</a></li>
+ <li><a href="/introduction/related-projects.html">Related projects</a></li>
+ </ul>
+ </li>
+ <li><a href="/about/">About</a></li>
+ <li class="dropdown">
+ <a href="/download/" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Download<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/download/">Apache Taverna 3.x</a></li>
+ <li><a href="/download/pre-apache.html">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li><a href="/doc/">Documentation</a></li>
+ <li><a href="/code/">Code</a></li>
+ <li><a href="/contact/">Contact</a></li>
+ </ul>
+
+ <form >
+
+
+ <!--<input type="submit" id="submit" value="Search">-->
+ </form>
+
+ <form class="navbar-form navbar-right" role="search"
+ name="search" id="search" action="http://www.google.com/search" method="get">
+ <input value="taverna.incubator.apache.org" name="sitesearch" type="hidden"/>
+ <div class="form-group input-group">
+ <input type="text" name="q" id="query" placeholder="Search" class="form-control">
+ <span class="input-group-btn">
+ <button type="submit" class="btn btn-default">Search</button>
+ </span>
+ </div>
+ </form>
+
+ <ul class="nav navbar-nav navbar-right">
+ <li class="dropdown">
+ <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">ASF<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="http://www.apache.org/">Apache Software Foundation</a></li>
+ <li><a href="http://www.apache.org/foundation/how-it-works.html">How it works</a></li>
+ <li><a href="http://www.apache.org/foundation/thanks.html">Thanks</a></li>
+ <li><a href="http://www.apache.org/foundation/sponsorship.html">Become a Sponsor</a></li>
+ <li><a href="http://incubator.apache.org/projects/taverna.html">Taverna Incubation Status</a></li>
+ </ul>
+ </li>
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container-->
+ </nav>
+
+
+ <div id="page" class="container">
+ <h1>Bioinformatics</h1>
+ <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
+
+Taverna is transitioning to the Apache Incubator.
+This webpage reflects material not yet released under Apache Incubator.
+Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
+</div>
+
+
+ <div id="content"><p>Taverna can connect to a wide variety of bioinformatics resources and has been successfully applied to a number
+ of bioinformatics problems, listed below according to their sub-domains.
+<img class="aligncenter"
+ title="Bioinformatics services and resources"
+ src="/img/BioinformaticsResources.png"
+ alt="Bioinformatics services and resources" width="676" height="441" /></p>
+<p>Bioinformatics systems/tools using Taverna:</p>
+<ul>
+<li><a href="#biowep">BioWEP</a> - bioinformatics workflow enactment portal</li>
+<li><a href="#biolinux">BioLinux</a> - Ubuntu Linux distribution that includes Taverna and many other bioinformatics programs</li>
+</ul>
+<h3 id="biodiversity">Biodiversity</h3>
+<ul>
+<li><a href="/introduction/related-projects/biovel">BioVeL</a></li>
+</ul>
+<h3 id="gene-and-genome-expression">Gene and genome expression</h3>
+<ul>
+<li><a href="/introduction/taverna-in-use/genome-and-gene-expression.html#next-generation-sequencing">Next Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
+<li><a href="/introduction/taverna-in-use/genome-and-gene-expression.html#tavernapbs">TavernaPBS</a> - next generation sequencing analysis using a computational cluster that uses a PBS
+ queuing system and Taverna 2 Workbench</li>
+<li><a href="/introduction/taverna-in-use/genome-and-gene-expression.html#casimir">Coordination and Sustainability of International Mouse Informatics Resources</a> (CASIMIR) -
+ workflows to associate mouse genome and phenome</li>
+<li><a href="/introduction/taverna-in-use/genome-and-gene-expression.html#dgemap">Developmental Gene Expression Map</a> (DGEMap)- analysis of human gene expression during development</li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#graves-disease">Graves disease</a> - identification of genes responsible</li>
+<li><a href="/introduction/taverna-in-use/bioinformatics.html#gene-expression-from-microarray">Examination of gene expression from MicroArray data using R</a> - statistical analysis of gene expression</li>
+<li><a href="/introduction/taverna-in-use/genome-and-gene-expression.html#sigenae">SIGENAE</a> - development of workflows to analyse breeding animal data</li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#trypanosomiasis">Trypanosomiasis</a> - identification of genes responsible for sleeping sickness</li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#williams-beuren-syndrome">Williams-Beuren syndrome</a> - automation and confirmation of gene characterization</li>
+<li><a href="/introduction/taverna-in-use/biology.html#planet">PLANET</a> - integration of plant genome resources</li>
+<li><a href="/introduction/taverna-in-use/annotation.html#annotation-of-genomes">Annotation of genomes</a></a></li>
+<li><a href="/introduction/related-projects.html#shared-genomics">Shared Genomics</a></a></li>
+<li><a href="http://img.cs.man.ac.uk/efungi/">e-Fungi</a> functional genomics in fungal species</li>
+</ul>
+<h3 id="protein-and-proteomics">Protein and proteomics</h3>
+<ul>
+<li><a href="#lumc">Analysis of mass spectrometry data in proteomics</a></li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#analysis-of-anthrax-bacterium">Anthrax analysis</a> - identification of proteins secreted by bacteria</li>
+<li><a href="/introduction/taverna-in-use/databases.html#efamily">eFamily</a> - integrating data from different databases</li>
+<li><a href="http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace">European Model for Bioinformatics Research And Community Education</a> (EMBRACE) -
+ calling services on a grid; recovering a database</li>
+<li><a href="/introduction/related-projects.html#ispider">iSpider</a> - querying multiple data sources</li>
+<li><a href="/introduction/taverna-in-use/protein-and-proteomics.html#prodom">ProDom</a> - running of Taverna workflows behind a portal to search a protein database</li>
+</ul>
+<h3 id="biology-and-systems-biology">Biology and systems biology</h3>
+<ul>
+<li><a href="/introduction/taverna-in-use/biology.html#enfin">ENFIN</a> â Enabling Systems Biology â calling of wrapped tools within workflows</li>
+<li><a href="/introduction/taverna-in-use/biology.html#manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a> (MCISB) â modelling metabolomic pathways</li>
+<li><a href="/introduction/taverna-in-use/biology.html#sb-os">Systems Biology Operational Software</a> (SB.OS) - a live DVD based on Ubuntu Linux that comes with a
+ comprehensive list of Systems Biology Software (including Taverna)</li>
+<li><a href="/introduction/taverna-in-use/biology.html#tav4sb">Tav4SB</a> - Taverna workflows for systems biology,
+ in particular for analysis of the kinetic models of biological systems</li>
+<li><a href="#measuring-enzyme-characteristics-of-yeast">Measuring of enzyme characteristics of yeast</a></li>
+<li><a href="/introduction/taverna-in-use/annotation.html#afawe">Automatic Functional Annotation in a distributed Web Service Environment</a> (AFAWE) â
+ protein prediction and annotation by a tool that calls workflows</li>
+<li><a href="/introduction/taverna-in-use/biology.html#planet">PLANET (A Network of European Plant Databases)</a> â calling of workflows from a portal</li>
+</ul>
+<h3 id="biomedicine-and-disease-related-research">Biomedicine and disease-related research</h3>
+<ul>
+<li><a href="/introduction/taverna-in-use/disease-research.html#vph-dareit">Fighting dementia</a> (VP-DARE@IT and VPH-SHARE)</li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#analysis-of-anthrax-bacterium">Analysis of the anthrax bacterium</a></li>
+<li><a href="/introduction/taverna-in-use.html#trypanosomiasis">Study of resistance into trypanosomiasis</a> (sleeping sickness)</li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#graves-disease">Identification of genes linked to Graves disease</a></li>
+<li><a href="/introduction/taverna-in-use/disease-research.html#williams-beuren-syndrome">Characterisation of genes associated with Williams-Beuren syndrome</a></li>
+<li><a href="/introduction/related-projects.html#cagrid">caGrid</a> - research into predicting limphoma cancer</li>
+<li><a href="/introduction/taverna-in-use/medicine.html#eu-adr">EU-ADR</a> - detecting adverse drug reactions through the exploitation of clinical data from electronic
+ healthcare records</li>
+</ul>
+<p><a name="biowep"></a></p>
+<h3 id="biowep">BioWEP</h3>
+<p>Researchers at the Italian National Institute for Cancer Research Genoa (<a href="http://www.istge.it/">IST</a>) have developed a
+ Bioinformatics Workflow Enactment Portal called <a href="http://bioinformatics.istge.it/biowep/index.html">BioWEP</a>.</p>
+<p>The <a href="http://bioinformatics.istge.it:8080/biowep/">portal</a> allows registered users to search for or select from a set of specified Taverna workflows.
+The workflow can be enacted by entering input values into a form.
+During enaction, the user can either wait for the result, or for longer running workflows,
+ visit the portal later. The results of the enactment can be downloaded for external visualization.</p>
+<h4 id="publications">Publications</h4>
+<p>The http://dx.doi.org/10.1186/1471-2105-8-S1-S19 <em>Biowep: a workflow enactment portal for bioinformatics
+ applications</em> by Romano et al gives an overview of the intent and design of Biowep.</p>
+<p><a naem="biolinux"></a></p>
+<h3 id="biolinux">BioLinux</h3>
+<p>The UKâs Natural Environment Research Council (NERC) Environmental Bioinformatics <a href="http://nebc.nox.ac.uk/">Centre</a> release
+ <a href="http://nebc.nox.ac.uk/biolinux.html">BioLinux</a>, an installation of Ubuntu Linux that includes many bioinformatics programs.</p>
+<p>Among the programs included in the BioLinux distribution is Taverna.<br />
+The suite of programs are also available for installation on pre-existing Linux systems.</p>
+<p><a name="lumc"></a></p>
+<h3 id="lumc">LUMC</h3>
+<p>People from the Leiden University Medical Center (<a href="http://www.lumc.nl/home/?setlanguage=English&amp;setcountry=en">LUMC</a>) in the Netherlands are using Taverna for analysis
+ of mass spectrometry data in proteomics.</p>
+<p>They presented a <a href="/pages/wp-content/uploads/2011/06/Palmblad_ASMS_2011_LUMC.pdf">poster</a> at the 2011 ASMS (the American Society for Mass Spectrometry) Conference on
+ Mass Spectrometry and Allied Topics.</p>
+<p>Please contact <a href="https://www.lumc.nl/org/proteomics-metabolomics/medewerkers/nmpalmblad">Dr. Magnus Palmblad</a> for more details.</p>
+<p><a name="measuring-enzyme-characteristics-of-yeast"></a></p>
+<h3 id="measuring-enzyme-characteristics-of-yeast">Measuring enzyme characteristics of yeast</h3>
+<p>The <a href="/introduction/taverna-in-use/biology/manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a> (MCISB) is in the process of measuring the
+ kinetic and binding constants associated with enzyme reactions in metabolic pathways in the yeast,
+ Saccharomyces cerevisiae.
+Quantitative models of these metabolic pathways are being integrated with transcriptomic, proteomic and
+ metabolomic data by workflows that have been constructed and enacted using Taverna.</p>
+<h4 id="publications_1">Publications</h4>
+<p>A <a href="http://www.mygrid.org.uk/files/2008/09/peter-li-poster.pdf">poster</a> by Peter Li describing the systems biology workflows was presented at the International
+ Conference of Systems Biology 2006 and he has written several publications about the work.</p>
+<p>Many of the workflows make use of Systems Biology Markup Language (<a href="http://sbml.org/">SBML</a>) as described in the
+ <a href="http://www.mygrid.org.uk/outreach/publications/li2007/">paper</a> <em>Automated manipulation of systems biology models using libSBML within Taverna workflows</em>
+ by Li et al.</p>
+<p>An <a href="http://www.myexperiment.org/workflows/79">example workflow</a> using SBML is available on <a href="http://www.myexperiment.org/">myExperiment</a>.</p></div>
+
+ </div>
+
+ <footer class="footer">
+ <div class="container">
+ <p id="copyright" class="text-muted">
+ Copyright © 2014-2015 The Apache Software Foundation, Licensed under the
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
+ Apache and the Apache feather logo are trademarks of The Apache Software Foundation.
+ </p>
+ </div>
+ </footer>
+
+ <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
+ <script src="/lib/bootstrap/js/bootstrap.min.js"></script>
+
+
+ </body>
+</html>
\ No newline at end of file