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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/03 12:27:07 UTC
svn commit: r938786 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/taverna-in-use/annotation.html
Author: buildbot
Date: Tue Feb 3 11:27:07 2015
New Revision: 938786
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
Modified:
websites/staging/taverna/trunk/cgi-bin/ (props changed)
websites/staging/taverna/trunk/content/ (props changed)
Propchange: websites/staging/taverna/trunk/cgi-bin/
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==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html (added)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html Tue Feb 3 11:27:07 2015
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+<!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 - Annotations</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" : "Annotations",
+ "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">
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+ <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>
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+ </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">
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+ <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>Annotations</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 is used by various tools and projects for the association of metadata with data (annotation).
+These include:
+ - [Automatic Functional Annotation in a distributed Web service Environment]<a href="AFAWE">49</a> -
+ annotation of plant genes with their functionality
+ - [Interactive genome annotation pipeline][50]</a> - automatic and manual annotation of genes
+ - [TaWeka][51] - associating biological data with calculated functionality</p>
+<p>In addition, Taverna makes use of the semantic annotation that has been specified for the services provided by
+ the [MOBY consortium][52].</p>
+<p>Taverna has also been used for the identification of mismatches and possible annotations in workflows by the
+ [iSPIDER][53] project.</p>
+<p><a name="afawe"></a></p>
+<h2 id="afawe">AFAWE</h2>
+<p>The [Max Planck Institute for Plant Breeding Research][54] in Cologne, Germany have developed the
+ Automatic Functional Annotation in a distributed Web Service Environment ([AFAWE][55]).
+AFAWE is a tool for the automatic functional annotation of new genes in plants and other organisms.
+The annotation involves the running of several Web services, and also the execution of a Taverna [workflow][56].</p>
+<p>The annotation workflow is [available][57] on [myExperiment][58].</p>
+<h3 id="publications">Publications</h3>
+<p>The [paper][59] <em>Protein function prediction and annotation in an integrated environment powered by web services
+ (AFAWE)</em> by Joecker et al describes the concepts and implementation of AFAWE.</p>
+<p><a name="annotation-of-genomes"></a></p>
+<h2 id="annotation-of-genomes">Annotation of genomes</h2>
+<p>A collaboration between [Tom Oinn][60] from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
+ Pal Puntervoll from the [University of Bergen][61], Norway, has produced an interactive genome annotation
+ pipeline.</p>
+<p>Sequencing, characterising and annotating a genome are the first steps to understanding its function.
+Important stages in this include gene prediction, comparative genomics and function prediction of genes and
+ gene products.
+With workflows all of these stages can be automate, requiring little human interaction.
+However, manual inspection can be required at certain points in the process.</p>
+<h3 id="publications_1">Publications</h3>
+<p>[Articles and papers][62] about the success of Taverna for genome annotation are available on-line.</p>
+<p><a name="taweka"></a></p>
+<h2 id="taweka">TaWeka</h2>
+<p>[Luna De Ferrari][63] from the Computational Systems Biology &
+ [Bioinformatics group at the University of Edinburgh][64] has developed [TaWeka][65],</p>
+<blockquote>
+<p>a rapid prototyping tool for biological classifiers.</p>
+</blockquote>
+<p>TaWeka uses Taverna workflows to store data retrieved from webservices, e.g. queries of biological data,
+ into a database.
+[Weka][66] is then used to run machine learning experiments on the data in order to evaluate and improve
+ biological classification functions.</p>
+<h3 id="publications_2">Publications</h3>
+<p>A poster [<em>TaWeka: from biological web services to data mining</em>][67] by De Ferrara and Goryanin describes the
+ purpose and implementation of TaWeka.</p>
+<p><a name="adoption-by-moby"></a></p>
+<h2 id="adoption-by-the-moby-consortium">Adoption by the Moby consortium</h2>
+<p>The [Moby][68] project develops a system for interoperability between biological data hosts and
+ analytical services.
+Their relationship with Taverna is multiple:</p>
+<ul>
+<li>The Moby team actively collaborate with myGrid in the development of the ontologies used to describe their
+ services.
+ Service descriptions are then used by Taverna to find services to use in workflows.</li>
+<li>The services published on Moby are a large proportion of the services often used in Taverna workflows</li>
+<li>People wishing to combine Moby services commonly use Taverna Workbench as a platform</li>
+<li>Specific support for Moby services is available within Taverna.</li>
+</ul>
+<h3 id="publications_3">Publications</h3>
+<p>The [paper][69] <em>Interoperability with Moby 1.0âItâs better than sharing your toothbrush!</em> by the
+ Moby consortium gives an overview of Moby and their activities.</p></div>
+
+ </div>
+
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