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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/03/11 09:49:35 UTC
svn commit: r943310 [8/10] - in /websites/staging/taverna/trunk: cgi-bin/
content/ content/documentation/ content/documentation/api-consumer-tool/
content/documentation/command-line-tool/
content/documentation/command-line/ content/documentation/compon...
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,257 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Biology</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 projects and researchers for investigations into systems biology:</p>
+<ul>
+<li><a href="#enfin">ENFIN â Enabling Systems Biology</a> â calling of wrapped tools within workflows</li>
+<li><a href="#manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a>
+ (MCISB) â modelling metabolomic pathways</li>
+<li><a href="#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="#metware">MetWare</a> - applications, databases and workflows for metabolomics</li>
+<li><a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a> - Taverna workflows for systems biology,
+ in particular for analysis of the kinetic models of biological systems</li>
+<li><a href="/introduction/taverna-in-use/biology#ccpn">CCPN</a> - Taverna is used to encapsulate and combine protocols between
+ WeNMR (Worldwide e-Infrastructure for NMR and structural biology) portals and CCPN's
+ (Collaborative Computing Project for NMR) software. </li>
+</ul>
+<p>Taverna is also used for analysis of plant biology:</p>
+<ul>
+<li><a href="/introduction/taverna-in-use/annotation#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="#planet">PLANET (A Network of European Plant Databases)</a> â calling of workflows from a portal</li>
+</ul>
+<p><a name="enfin"></a></p>
+<h2 id="enfin">ENFIN</h2>
+<p>The partners within the ENFIN - Enabling Systems Biology <a href="http://www.enfin.org/">project</a>
+ developed a suite of Systems Biology tools (ENSUITE).
+These tools are also available as normal WSDL services and their possible use within workflows has been
+ demonstrated by use of Taverna.</p>
+<h3 id="publications">Publications</h3>
+<p>The <a href="http://www.springerlink.com/content/hw667700pm2170j4/">paper</a>
+ <em>ENFIN - An Integrative Structure for Systems Biology</em>
+ by Reisinger et al. describes the overall design and structure of ENFIN.</p>
+<p><a name="manchester-centre-for-integrative-systems-biology"></a></p>
+<h2 id="manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</h2>
+<p>The <a href="http://www.bbsrc.ac.uk/">BBSRC</a> and <a href="http://www.epsrc.ac.uk/">EPSRC</a> have awarded £6.3m to the
+ <a href="http://www.mcisb.org/">Manchester Centre for Integrative Systems Biology</a>
+ (MCISB) based at the <a href="http://www.mib.ac.uk/">Manchester Interdisciplinary Biocentre</a> (MIB).
+The award is to pioneer the development of new experimental and computational technologies in Systems Biology,
+ and their exploitation.</p>
+<p>The MCISB is intended to provide a hub for cutting-edge systems biology research in the Manchester area,
+ acting as a focal point for the creation of the necessary ideas and infrastructure,
+ and for establishing new methods and routines.</p>
+<p>The co-investigators in the project Professor <a href="http://www.manchester.ac.uk/research/norman.paton">Norman Paton</a>,
+ Professor <a href="http://www.manchester.ac.uk/research/Douglas.kell">Douglas Kell</a> et al.<br />
+It ran from May 2005 to April 2010.</p>
+<h3 id="metabolomic-pathways">Metabolomic Pathways</h3>
+<p>The Manchester Centre for Integrative Systems Biology 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>
+<h3 id="publications_1">Publications</h3>
+<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://bioinformatics.oxfordjournals.org/content/24/2/287.full.pdf">paper</a>
+ <em>Automated manipulation of systems biology models using libSBML within Taverna workflows</em> by Li et al.</p>
+<p>An example <a href="http://www.myexperiment.org/workflows/79">workflow</a> using SBML is available on
+ <a href="http://www.myexperiment.org">myExperiment</a>.</p>
+<p><a name="sb-os"></a></p>
+<h2 id="systems-biology-operational-software-sbos">Systems Biology Operational Software (SB.OS)</h2>
+<p><a href="http://www.sbos.eu/doku.php">SB.OS</a> is a live DVD based on Ubuntu Linux that comes with
+ a comprehensive list of Systems Biology Software.
+Text and video documentation material,
+ as well as an offline copy of the BioModels.net database and Taverna 2.1, are included.</p>
+<p><a name="metware"></a></p>
+<h2 id="metware">MetWare</h2>
+<p>The MetWare project provides applications, databases and workflows for metabolomics.
+The MetWare project is a collaboration between several metabolomics groups in the Netherlands and Germany.</p>
+<p>The work involving Taverna workflows is done by
+ <a href="http://www.ipb-halle.de/en/research/stress-and-developmental-biology/all-staff/">Steffen Neumanns group (Bioinformatics & Mass Spectrometry)</a>.</p>
+<p>They developed a Web-based player of Taverna workflows and also have uploaded their workflows on myExperiment at
+ <a href="http://www.myexperiment.org/users/937/workflows">http://www.myexperiment.org/users/937/workflows</a>.</p>
+<p><a href="http://sourceforge.net/apps/mediawiki/metware/index.php?title=Main_Page">Software project page</a> can be found at Sorceforge.</p>
+<p><a name="tav4sb"></a></p>
+<h2 id="tav4sb">Tav4SB</h2>
+<p><a href="http://bioputer.mimuw.edu.pl/tav4sb/">Tav4SB project</a> provides a grid environment with a set of Web services,
+ bundled together in Taverna workflows.
+Target application area is the system biology field,
+ in particular analysis of the kinetic models of biological systems.</p>
+<p><a name="ccpn"></a></p>
+<h2 id="ccpn">CCPN</h2>
+<p><strong>CCPN use of Taverna</strong>
+by Rasmus Fogh r.h.fogh@bioc.cam.ac.uk, Feb 2013</p>
+<p><a href="http://www.wenmr.eu/">WeNMR</a> (Worldwide e-Infrastructure for NMR and structural biology)
+ is a virtual research community project that is funded as part of the 7th EU framework.
+The infrastructure lies within the fields of structural biology, NMR and SAXS.
+Its purpose is twofold: It provides an infrastructure for sharing documentation, outreach and communications.<br />
+It also offers web portals where structural biology programs can be run, supports a grid infrastructure
+ for running associated relevant jobs and provides software that presents programs on the web portals and
+ pipes data between them for uploading and downloading.</p>
+<p>Our contribution to the WeNMR project is the development of a dual use Workflow Management System (WMS) as shown in Fig.1.
+Its two methods of use are as a:</p>
+<ul>
+<li>
+<p>means to launch, manage, and gather results generated by structural biology calculations,
+ making use of programs present on the WeNMR portals,
+ in effect to serve as an entry port for WeNMR and associated calculations in general.</p>
+</li>
+<li>
+<p>data tracking, management and access control system for structural biology laboratories.</p>
+</li>
+</ul>
+<p><img alt="CCPN Use of Taverna" src="/img/CCPNuse.png" /></p>
+<p align="center">Fig. 1</p>
+
+<p>Taverna is being used to encapsulate and combine protocols on our system,
+ so that the systems are available to, and can be combined with,
+ workflow components from other sources,
+ and to combine different protocols on our system into pipelines.
+The current test project is to develop a system to run four different structure calculation programs
+ from a single job start specification and collating the results into a single combined data source.</p>
+<p>Whether Taverna is being used in a scientific role is down to the definition of its role within the project.
+We are developing scientific software,
+ which will be used to perform actual scientific research and analysis by end users â
+ we tend to categorise our role as that of methods developers for structural biology.
+Whether that categorises the role as computer science, structural biology,
+ or software engineering depends on the point of view.</p>
+<p>The <em>methods</em> are established programs for calculating (mainly) macromolecular structures
+ from Nuclear Magnetic Resonance data, and are therefore used as the primary process for obtaining results.
+These types of calculation require the use of several different programs, sequentially, to process them.
+Passing the data and results from one program to another has been a problem for many years.
+CCPN has long been working on data exchange standards, data conversion software and integration with different programs,
+ and is now working explicitly on setting up pipelines.
+There is an ever-increasing demand for high-throughput calculations that allow the use of alternative programs and
+ that inexperienced users are able to utilise with ease.
+It is to meet these demands that Taverna is being used as a tool that enables the setup of flexible,
+ easy-to-use pipelines.</p>
+<p>About me:</p>
+<p>I am currently working at the University of Cambridge, Department of Biochemistry,
+ under Professor Ernest Laue.
+As part of my role I am attached to the <a href="http://www.ccpn.ac.uk/">CCPN project</a>,
+ led by Professor Vuister (University of Leicester), formerly led by Professor Laue.</p>
+<p><a name="planet"></a></p>
+<h2 id="planet">PLANET</h2>
+<p>As part of the <a href="http://www.eu-plant-genome.net/">PLANET</a> (A Network of European Plant Databases) project,
+ <a href="http://www.breedwheat.fr/institutions.php?id=6">URGI</a>
+ (Unité de Recherche Génomique-Info) developed BioFloWeb.</p>
+<p>BioFloWeb is a stand-alone Web application processing Web services.
+A given user can choose among predefined workflows or define their own with Taverna.
+BioFloWeb has been <a href="http://biofloweb.sourceforge.net/">demonstrated</a>
+ for retrieval of information about Arabidopsis genes from several European databases.</p>
+<p>BioFloWeb makes extensive use of <a href="/introduction/taverna-in-use/annotation#adoption-by-moby">BioMoby</a> services.</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,152 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Chemistry</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 projects for the creation of chemistry workflows. These include:</p>
+<ul>
+<li><a href="#chemistry-development-kit">Chemistry Development Kit</a> (CDK) - integration of a chemistry-specific toolkit with Taverna</li>
+<li><a href="#chemical-informatics-and-cyberinfrastructure-collaboratory">Chemical Informatics and Cyberinfrastructure Collaboratory</a> (CICC) -use of Taverna for workflow creation</li>
+</ul>
+<p><a name ="chemistry-development-kit"></a></p>
+<h2 id="chemistry-development-kit">Chemistry Development Kit</h2>
+<p>The Chemistry Development Kit (CDK) <a href="http://sourceforge.net/projects/cdk">project</a> have developed a
+ <a href="/documentation/plugins#cdk">plugin</a>
+ to allow their tools to be used within Taverna workflows.</p></p>
+<p>There is a myExperiment <a href="http://www.myexperiment.org/groups/105">group</a></a> for workflows using the CDK-Taverna plugin.</p></p>
+<p>This work has been described in the <a href="http://dx.doi.org/10.1186/1752-153X-2-S1-P27">poster</a>
+ <em>Creating chemo- & bioinformatics workflows, further developments within the CDK-Taverna Project</em>
+ by Kuhn et al.</p>
+<p>The latest posts from the CDK Taverna <a href="http://cdktaverna.wordpress.com/">Web site</a> are:</p>
+<ul>
+<li><a href="https://cdktaverna.wordpress.com/2011/07/29/cdk-taverna-2-0-final-version-released/">CDK-Taverna 2.0 Final version released</a></li>
+<li><a href="https://cdktaverna.wordpress.com/2011/02/15/cdk-taverna-2-0-released/">CDK-Taverna 2.0 released</a> </li>
+<li><a href="http://cdktaverna.wordpress.com/2010/01/18/cdk-taverna-installation-instruction/">CDK-Taverna installation instructions</a></li>
+<li><a href="http://cdktaverna.wordpress.com/2010/01/17/cdk-taverna-version-0-5-1-1-released/">CDK-Taverna Version 0.5.1.1 released</a></li>
+<li><a href="http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/">Time evaluation for calculating molecular descriptors using the cdk</a></li>
+<li><a href="http://cdktaverna.wordpress.com/2008/09/06/atom-typing-on-natural-products-with-the-cdk/">Atom typing on natural products with the cdk</a></li>
+<li><a href="http://cdktaverna.wordpress.com/2008/08/29/myexperimentorg-plug-in-for-taverna/">myExperiment.org plug-in for Taverna</a></li>
+</ul>
+<p><a name ="chemical-informatics-and-cyberinfrastructure-collaboratory"></a></p>
+<h2 id="chemical-informatics-and-cyberinfrastructure-collaboratory">Chemical Informatics and Cyberinfrastructure Collaboratory</h2>
+<p>Within the Chemical Informatics and Cyberinfrastructure Collaboratory (CICC) project</p>
+<blockquote>
+<p>uses modern Grid technology to allow convenient integration of
+distributed chemistry tools, simulations, documents and databases
+among themselves and with similar biological resources.</p>
+</blockquote>
+<p>The members of the CICC are developing Taverna workflows</p>
+<blockquote>
+<p>which encapsulate important processes in chemoinformatics and drug
+design, use diverse kinds of information together in novel ways,<br />
+and which are of demonstrated scientific merit.</p>
+</blockquote></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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,143 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Data and text mining</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 for the automation of data and text mining by various projects and researchers.<br />
+These include:</p>
+<ul>
+<li><a href="/introduction/related-projects#e-lico">e-Lico</a> - building a virtual e-science laboratory for interdisciplinary collaborative research in data mining
+ and data-intensive sciences</li>
+<li><a href="#aid">Adaptive Information Disclosure (AID) workflows</a> - workflows to extract knowledge and data to
+ associate proteins and diseases</li>
+<li><a href="/introduction/taverna-in-use/multimedia#course-generator">Course generator</a></a> - workflow to create a course based upon user requirements</li>
+<li><a href="/introduction/related-projects#refine">REFINE</a> - representing evidence for interacting network elements</li>
+<li><a href="#open-software-development-workflows">Open software development workflows</a> - modelling the development of open software projects</li>
+<li><a href="/introduction/taverna-in-use/annotation#taweka">TaWeka</a> - mining databases for subsequent machine learning</li>
+</ul>
+<p><a name="aid"></a></p>
+<h2 id="aid">AID</h2>
+<p>Taverna is used by researchers at <a href="http://www.mygrid.org.uk/outreach/collaboration/collaboration-with-nbic/">NBIC</a> as an enactment platform for <a href="http://www.adaptivedisclosure.org/aida/workflows">BioAID</a> workflows from
+ the AIDA (Adaptive Information Disclosure Application) toolkit developed by <a href="http://www.vl-e.nl/">VL-e</a>
+ that offers services for knowledge extraction, text mining and knowledge management.</p>
+<p>There is a myExperiment <a href="http://www.myexperiment.org/groups/42">group</a> for AID workflows.</p>
+<h3 id="publications">Publications</h3>
+<p>The <a href="https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CDMQFjAA&url=https%3A%2F%2Fbioinformatics.cs.vt.edu%2F~murali%2Fconference-fayfaars%2F2007-ismb-eccb%2FISMBECCB07%2FDemos%2Froos_20070511110510.pdf&ei=aBrSVPmcJYqS7AarnIG4BA&usg=AFQjCNFxsZFPdqYu7OqkwPd_-KIX4xQXPw&sig2=jqEU3XVUPOOgp0HTNVekxw&bvm=bv.85076809,d.ZGU">presentation</a> <em>My BioAID: personalised text mining with Web services from the AIDA toolbox</em>
+ by Marco Roos describes the use of the AIDA toolkit and Taverna.</p>
+<p><a name="open-software-development-workflows"></a></p>
+<h2 id="open-software-development-workflows">Open software development workflows</h2>
+<p>Taverna has been used to model the research community developing open source software together with
+ the software itself.
+This work, done by the Free/Libre Open Source Software Research community is described on the <a href="http://floss.syr.edu/">Web site</a>,
+ in particular their <a href="http://floss.syr.edu/papers">publications</a>.</p>
+<p>There is a myExperiment <a href="http://www.myexperiment.org/groups/64">group</a> for researchers studying open source software development.<br />
+The myExperiment group share some of their Taverna <a href="http://www.myexperiment.org/users/384/workflows">workflows</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,169 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Databases</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>Various projects and researchers use Taverna to access, collate and manipulate data from databases:</p>
+<ul>
+<li><a href="/introduction/taverna-in-use/multimedia#echase">Electronic Cultural Heritage made Accessible for Sustainable Exploitation</a> (eCHASE)</li>
+<li><a href="#efamily">eFamily</a></li>
+<li><a href="#embrace">European Model for Bioinformatics Research And Community Education</a> (EMBRACE)</li>
+<li><a href="/introduction/related-projects#ispider">iSpider</a></li>
+<li><a href="#omixed">omixed</a></li>
+<li><a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a> - running of Taverna workflows behind a portal to search a protein database</li>
+</ul>
+<p><a name="efamily"></a></p>
+<h2 id="efamily">eFamily</h2>
+<p>The <a href="http://www.ebi.ac.uk/pdbe/docs/sifts/efamily.html">eFamily project</a> was designed to integrate the information contained in five major protein databases.
+ The project developed webservices to allow the calculation of results based upon the content of
+ several databases, and upon annotation of the data.</p>
+<p>The project made use of Taverna workflows to integrate the webservices,
+ both those provided by the eFamily project and those developed externally.</p>
+<h3 id="publications">Publications</h3>
+<p>Some details of this work are given in the http://www.allhands.org.uk/2004/proceedings/papers/211.pdf
+ <em>eFamily: Bridging Sequence and Structure</em> by Finn et al.</p>
+<p><a name="embrace"></a></p>
+<h2 id="embrace">EMBRACE</h2>
+<p><a href="http://www.embracegrid.info/">EMBRACE</a> is the European Model for Bioinformatics Research And Community Education (EMBRACE).
+It consists of a large number of partners throughout Europe</p>
+<blockquote>
+<p>The objective of EMBRACE is to draw together a wide group of experts
+throughout Europe who are involved in the use of information
+technology in the biomolecular sciences.<br />
+The EMBRACE Network of Excellence will optimise informatics and information exploitation by
+pure and applied biological scientists in both the academic and commercial sectors.</p>
+</blockquote>
+<p>The <a href="http://www.manchester.ac.uk/">University of Manchester</a> is a member of the EMBRACE project,
+ and the Taverna Workbench has been adopted by EMBRACE as its workflow system of choice.</p>
+<p>The suitability of Taverna Workbench has been confirmed by its use in several test cases:</p>
+<ul>
+<li>The use of Taverna to access Grid Protein Sequence Analysis (GPSA) Web services as described by
+ Blanchet et al. in the <a href="http://dx.doi.org/10.1007/11946465_22">paper</a>
+ <em>Web Services Interface to Run Protein Sequence Tools on Grid, Testcase of Protein Sequence Alignment</em>.
+ This includes the running of the Web services on <a href="https://eu-egee-org.web.cern.ch/eu-egee-org/index.html">EGEE</a> grid.</li>
+<li>Taverna has been used to automate the cleaning up and extraction of data by the EMBRACE project from the
+ tGRAP database of mutated G-protein coupled receptors.</li>
+<li>The ProDom-based protein family analyses test case includes the use of Taverna within <a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a>.</li>
+</ul>
+<p>The tGRAP work is described in the <a href="http://www.myexperiment.org/files/29">document</a> <em>The reincarnation of the tGRAP database</em> by Vroling.</p>
+<p>Use of Taverna allows the members of EMBRACE to have ready access to the existing bioinformatics services and
+ also to the myGrid teamâs expertise in this area. Correspondingly, the members of EMBRACE represent
+ a diverse group of users with different backgrounds and infrastructure.</p>
+<p><a name="omixed"></a></p>
+<h2 id="omixed">omixed</h2>
+<p><a href="http://nebc.nerc.ac.uk/tools/omixed/overview">omixed</a></a> is a âcustomisable storage system for scientific data, completely managed via web servicesâ.
+Its developers have written a Taverna 1.7.x <a href="http://www.omixed.org/documentation/omixed%20taverna%20plugin">plugin</a> to allow users to access data.</p>
+<p>The plugin âprovides two endpoints giving full control of omixed resources.
+The first endpoint, known as the server endpoint, is designed for most users who want to browse, download,
+ or add to or modify existing resources.
+The second point, known as the admin endpoint, is designed for administrators to create and delete resources,
+ assign schema to them, and modify user privileges.â</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,248 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Disease-related research</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 projects and researchers for investigations into various diseases:</p>
+<ul>
+<li><a href="#vph-dareit">Dementia</a> (VPH-DARE@IT and VPH-SHARE)</li>
+<li><a href="#analysis-of-anthrax-bacterium">Analysis of the anthrax bacterium</a></li>
+<li><a href="#trypanosomiasis">Study of resistance into trypanosomiasis</a> (sleeping sickness)</li>
+<li><a href="#graves-disease">Identification of genes linked to Graves disease</a></li>
+<li><a href="#williams-beuren-syndrome">Characterisation of genes associated with Williams-Beuren syndrome</a></li>
+<li><a href="/introduction/related-projects#cagrid">Cancer research</a> (caGrid)</li>
+</ul>
+<p><a name="vph-dareit"></a></p>
+<h2 id="vph-dareit">VPH-DARE@IT</h2>
+<p>The Center for Computational Imaging and Simulation Technologies in Biomedicine at the
+ <a href="http://sheffield.ac.uk/">University of Sheffield</a>, is leading the âVirtual Physiological Human:
+ DementiA Research Enabled by ITâ (<a href="http://www.vph-dare.eu/">VPH-DARE@IT</a>) project,
+ which aims to provide a systematic,
+ multifactorial and multiscale modelling approach to understanding dementia onset and
+ progression and enable more objective, earlier,
+ predictive and individualised diagnoses and prognoses of dementias to cope with the challenge of an ageing European society.
+ See <a href="http://www.vph-dare.eu/">http://www.vph-dare.eu/</a> for more details.</p>
+<p>The project will use <a href="http://vph-share.eu/">VPH-SHARE</a> infrastructure and
+ the GIMIAS software along with Taverna Workbench and Taverna Server technology for the execution and
+ composition of medical simulation workflows.
+These workflows will be focused on the analysis of medical data from thousands of individuals and populations;
+ as well as genetic, biochemical and metabolic pathway models.
+The results of the analysis aim to support highly innovative clinical decision systems for
+ fighting the colossal health and societal burden resulting from dementias.</p>
+<p><a name="analysis-of-anthrax-bacterium"></a></p>
+<h2 id="analysis-of-anthrax-bacterium">Analysis of anthrax bacterium</h2>
+<p>Taverna has been used by Anil Wipat and others to automate a series of analyses on all the proteins
+ produced by a bacterium to create, by a process of selection and elimination,
+ a list of secreted proteins and their properties.</p>
+<p>The secreted proteins explain why anthrax can grow in animal hosts but not in soil.</p>
+<h3 id="publications">Publications</h3>
+<p>The <a href="http://www.allhands.org.uk/2006/proceedings/papers/709.pdf">paper</a>
+ <em>e-Science Tools For The Genomic Scale Characterisation Of Bacterial Secreted Proteins</em>
+ by Craddock et al. gives an overview of this work.</p>
+<p><a name="trypanosomiasis"></a></p>
+<h2 id="trypanosomiasis-sleeping-sickness">Trypanosomiasis (sleeping sickness)</h2>
+<p>One of the major goals of biology, and consequently bioinformatics,
+ is to successfully bridge the gap between genotype and phenotype.
+Microarray and Quantitative Trait Loci data are increasingly used to aid in the discovery of candidate genes
+ that might be responsible for phenotypic differences.
+In previous years, studies into genotype-phenotype correlations have been conducted manually.
+This has led to problems with regards to the identification of functional candidate genes,
+ primarily due to the scale of data being investigated and the reliance on specific expertise,
+ which may bias the investigations outcome.</p>
+<p>With the development and connection of Web services into workflows, however,
+ these large scale datasets can be processed systematically enabling detailed information to be gathered,
+ published and subsequently re-investigated,
+ enhancing the possibility of bridging the gap between genotype and phenotype using pathways.</p>
+<p>So far this investigation has highlighted the issues facing the manual analysis of microarray and QTL data,
+ and how automated approaches provide a systematic means to investigate genotype-phenotype correlations.
+We were able to illustrate how the large scale analysis of microarray gene expression and quantitative trait data,
+ investigated at the level of biological pathways,
+ enables links between genotype and phenotype to be successfully established.</p>
+<p>An example of a workflow used to gather pathway information for candidate genes from a QTL region is shown below.
+These workflows have so far been applied to two different genotype-phenotype problems:</p>
+<ul>
+<li>The study of resistance to African Trypanosomiasis in mice, infected with Trypanosoma congolen</li>
+<li>The study of immunological effects and parasite expulsion in mice infected with Trichuris muris</li>
+</ul>
+<p>Using this systematic,
+ pathway driven approach, we were able to successfully identify a candidate gene and
+ biological pathway believed to be strongly associated with resistance to African Trypanosomiasis.</p>
+<p>The workflow for performing this analysis is available on
+ <a href="http://www.myexperiment.org/workflows/16">myExperiment</a>.</p>
+<p><a href="http://www.myexperiment.org/workflows/16"><img alt="pathways_and_gene_annotations_for_qtl_phenotype_28303_3" src="/img/trypanosomiasis.jpg" /></a></p>
+<h3>Publications</h3>
+
+<p><a href="http://scholar.google.co.uk/scholar?hl=en&q=Taverna+trypanosomiasis">Articles and papers</a>
+ about the success of Taverna for trypanosomiasis (sleeping sickness) research.</p>
+<p><a name="graves-disease"></a></p>
+<h2 id="graves-disease">Graves disease</h2>
+<h3 id="graves-disease-scenario">Graves disease scenario</h3>
+<p>The aim of this scenario is to identify and characterise genes which are located in regions on human chromosomes
+ which show linkage to Graves disease (GD) (shown in figure below).
+GD is an autoimmune disease of the thyroid in which the immune system of an individual attacks cells
+ in the thyroid gland resulting in hyperthyroidism.
+This is caused by the stimulation of the thyrotrophin receptor by thyroid-stimulating autoantibodies secreted by
+ lymphocytes of the immune system.</p>
+<p><a href="/img/gravesdiseasescenario_1.png">
+ <img title="gravesdiseasescenario_1" src="/img/gravesdiseasescenario_1.png"
+ alt="Graves Disease Scenario" width="249" height="300" /></a></p>
+<h3 id="affymetrix-microarray-studies">Affymetrix microarray studies</h3>
+<p>The GD candidate genes were identified by microarray analysis.
+Affymetrix U95A arrays were probed with RNA extracted from CD4 positive lymphocytes from four GD patients
+ and four healthy controls.
+The four GD microarray datasets were then compared to the four control datasets using
+ the Affymetrix data mining tool to identify differentially expressed genes.</p>
+<h3 id="annotation-pipeline">Annotation pipeline</h3>
+<p>Over 50 genes were found to be differentially-expressed in CD4 positive lymphocytes from GD patients.
+In order to understand why these genes were expressed in lymphocytes from GD patients but not in healthy individuals,
+ the GD biologist would like to use myGrid to query public databases such as
+ EMBL, GO, HGVBASE and MEDLINE to view information about gene structure and function,
+ chromosome location, the presence of single nucleotide polymorphisms (SNPs),
+ expression control features and association with other genetic diseases.
+The experimental conditions and diseases in which the expression of the candidate genes
+ are significantly altered also need to be identified from OMIM.</p>
+<h3 id="genotype-assay-design-system">Genotype assay design system</h3>
+<p>SNPs are small (single base pair) changes genetic variations which are found in the genome amongst individuals.
+The differential expression of the candidate genes in GD individuals may be due or related to the presence of
+ SNPs associated with GD.
+The GD biologist is interested in identifying and determining the frequency of those SNPs which are found in her GD patients.</p>
+<p>Restriction fragment length polymorphism (RFLP) assays are developed to genotype SNPs in her candidate genes.
+A region flanking either side of the SNP is amplified using polymerase chain reaction (PCR).
+The amplified PCR product is digested with a suitable restriction enzyme
+ (i.e. one that will cut at one SNP allele and not the other)
+ and the products are run on agarose gels to view product size and determine the genotype.</p>
+<p>The GD biologist would like to use myGrid to:</p>
+<ul>
+<li>Query databases to retrieve SNP information associated with candidate genes.</li>
+<li>Aid in the design of primers
+ (bits of DNA which signify the start and end points of the section of the DNA sequence which she wants to amplify)
+ for the PCR experiment.</li>
+<li>Select the restriction enzyme that is specific to a particular SNP for the RFLP experiment.</li>
+</ul>
+<h3 id="3d-protein-structure-wzxhzdk12-effect-of-coding-snp-on-protein-active-site">3D protein structure & effect of coding SNP on protein active site</h3>
+<p>Any SNPs occurring in the coding regions of a candidate gene may potentially give rise to
+ a change in the amino acid sequence of the protein encoded by the gene.
+The GD biologist would like to use myGrid to:</p>
+<ul>
+<li>Query a protein structure database, e.g. PDB or MSD,
+ to determine whether a structure of the protein encoded by her candidate gene is available.
+ If so, view the protein structure to study how it relates to the function of the protein.</li>
+<li>Obtain information about the protein, e.g. its function and functional domains, by querying SWISS-PROT and InterPro.
+ Use Sheffieldâs AMBIT Web service to retrieve information about an active site whose characteristics
+ may be altered due to the presence of a coding SNP which has affected a change in the amino acid sequence
+ of the protein where the active site is encoded.</li>
+</ul>
+<p>The <a href="http://www.myexperiment.org/workflows/28">workflow</a>
+ for the Graves Disease analysis is published on <a href="http://www.myexperiment.org/">myExperiment</a>.</p>
+<h3 id="publications_1">Publications</h3>
+<p><a href="http://scholar.google.co.uk/scholar?q=Taverna+Graves+Disease">Articles and papers</a>
+ about the success of Taverna for Graves Disease research.</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,156 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Document and image analysis</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"><ul>
+<li><a href="#islandora">Islandora</a> - an open-source software framework designed to help institutions and organizations and
+ their audiences collaboratively manage, and discover digital assets using a best-practices framework.</li>
+<li><a href="/introduction/related-projects#scape">SCAPE</a> â large scale and computation intense automated digital preservation and quality assurance workflows
+ on a cloud infrastructure</li>
+<li><a href="#dae">DAE</a> - Document analysis algorithm contributions in end-to-end applications</li>
+<li><a href="/introduction/taverna-in-use/social-sciences#impact">IMPACT</a> project works on improving access to historical texts and digitisation of European cultural
+ heritage using Taverna and <a href="http://www.myexperiment.org/">myExperiment</a></li>
+</ul>
+<p><a name="islandora"></a></p>
+<h2 id="islandora">Islandora</h2>
+<p><a href="http://islandora.ca/">Islandora</a> is an open-source software framework designed to help institutions and organizations and their
+ audiences collaboratively manage, and discover digital assets using a best-practices framework.</p>
+<p>Islandora connects the <a href="http://drupal.org/">Drupal</a> and <a href="http://www.fedora-commons.org/">Fedora</a> open software applications, acting as a kind of glue between
+ the content management and presentation capabilities of Drupal with the long term preservation features of
+ Fedora.</p>
+<p>In an <a href="http://blogs.loc.gov/digitalpreservation/2013/03/islandoras-open-source-ecosystem-and-digital-preservation-an-interview-with-mark-leggott/">interview</a> with http://loomware.typepad.com/about.html, the University Librarian at the University of
+ Prince Edward Island, Mark explains how Taverna workflows are utilized by the Islandora framework to
+ call local Python scripts remotely via Web services&' wrappers.
+This allowed for extreme agility within the Islandora ecosystem and has allowed the integration of a wide range
+ of open source (and proprietary where desirable) software systems in relatively quick order.
+Read the <a href="http://blogs.loc.gov/digitalpreservation/2013/03/islandoras-open-source-ecosystem-and-digital-preservation-an-interview-with-mark-leggott/">full interview</a> with Mark Leggott.</p>
+<p><a name="dae"></a></p>
+<h2 id="dae">DAE</h2>
+<p>The <a href="http://dae.cse.lehigh.edu/DAE/">DAE project</a> (Document Analysis Algorithm Contributions in End-to-End Applications) provides the
+ <a href="http://sourceforge.net/apps/mediawiki/daeplatform/index.php?title=Platform_Architecture">DAE Platform</a> to give access to a collection of resources and applications related to machine perception
+ and document analysis.
+ Applications include binarization, text segmentation, OCR (Optical Character Recognition),
+ named entity detection, etc.</p>
+<p>The DAE Platform is accessible though a Web portal which provides a series of services related to document
+ analysis research of which the most prominent are the access to a wide range of reference datasets,
+ as well as their annotations, ground-truths or interpretations; a catalogue of state of the art algorithms
+ that can be executed on hosted or otherwise provided data, as well as the uploading and execution of
+ complex workflows combining those algorithms.</p>
+<p>One of the more advanced contributions of the DAE Platform is to provide an open and very flexible framework to
+ add, run, evaluate and contribute algorithms. These algorithms are provided as Web services and can be
+ invoked from anywhere.
+Because of its open architecture users can very easily contribute and convert their own algorithms to this
+ framework, without necessarily disclosing their source code, and without the need to port their code to
+ a particular technical environment.</p>
+<p>The Platform is integrated with the <a href="http://sourceforge.net/apps/mediawiki/daeplatform/index.php?title=Platform_Architecture#Web_Service_Orchestration">Taverna Web Service Orchestration</a> to provide the opportunity to
+ design, host and execute complete and complex workflows of combined and distributed algorithms.</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,116 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Education</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 has been used in education (as well as for teaching purposes) for the
+ <a href="/introduction/taverna-in-use/multimedia.html#course-generator">creation of courses from individual learning activities and resources</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>
+
+<script>
+ jQuery(function($) {
+ if($(window).width()>769){
+ $('.navbar .dropdown').hover(function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(250).slideDown();
+
+ }, function() {
+ $(this).find('.dropdown-menu').first().stop(true, true).delay(100).slideUp();
+
+ });
+
+ $('.navbar .dropdown > a').click(function(){
+ location.href = this.href;
+ });
+
+ }
+ });
+</script>
+
+
+ </body>
+</html>
\ No newline at end of file
Modified: websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,132 @@
<li><a href="/documentation/#tools">Tools and Services</a></li>
</ul>
</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">Which Taverna to use</a></li>
+ <li><a href="/download/workbench">TavernaWorkbench</a></li>
+ <li><a href="/download/language">Taverna's SCUFL2 Language</a></li>
+ <li><a href="/download/command-line-tool">Taverna Command Line</a></li>
+ <li><a href="/download/server">Taverna Server</a></li>
+ <li><a href="/documentation/plugins">Plugins</a></li>
+ <li><a href="/download/code">Source Code</a></li>
+ <li><a href="/download/maven">Maven Repository</a></li>
+ <li><a href="/download/system-requirements">System Requirements</a></li>
+ <li><a href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
+ </ul>
+ </li>
+ <li class="dropdown">
+ <a href="/community" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Community<span class="caret"></span></a>
+ <ul class="dropdown-menu" role="menu">
+ <li><a href="/community#mailinglists">Mailing Lists</a></li>
+ <li><a href="/community#contribute">Contribute</a></li>
+ <li><a href="/community#reportbugs">Report a Bug</a></li>
+ </ul>
+ </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="http://www.apache.org/" 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>Engineering</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 has been used in engineering projects:</p>
+<p><a href="#jpl">Jet Propusion Laboratory</a> (JPL) -using Taverna as the Web services-based infrastructure for their
+ Observing Systems Simulation Experiments (OSSE) project (modelling how mission design objectives impact science)</li></p>
+<p><a name="jpl"></a></p>
+<h2 id="jpl">JPL</h2>
+<p>NASAâs <a href="http://www.jpl.nasa.gov/">Jet Propulsion Laboratory</a> (JPL), based at the California Institute of Technology,
+ created the first American satellite,
+ sent the first robotic craft to the moon and currently has twenty spacecraft on active missions.
+The JPL have been involved in yet another giant leap for mankind: they have adopted Taverna as the Web services -
+ based infrastructure for their Observing Systems Simulation Experiments (OSSE) project.
+The JPL are applying OSSE in the study of science algorithms as part of a proposed hyper-spectral imaging mission.</p>
+<p>JPL considered a number of different research and commercial workflow systems and finally settled on Taverna.
+"The thing that really sold us on Taverna was the dynamic WSDL introspection and presentation of the
+ WSDL interface as ports of a process component" - said Hook Hua,
+ a member of the High Capability Computing and Modeling Group at JPL.
+Taverna's recent overhaul appears to have helped their decision too, as Hook Hua describes
+ "one of the initial reasons we chose to use Taverna was its polished look and feel when compared to
+ other workflow engines".</p></div>
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