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 2015/03/11 09:37:12 UTC
svn commit: r943303 [9/10] - 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/genome-and-gene-expression/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.html Wed Mar 11 08:37:10 2015
@@ -104,204 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>Genome and gene expression</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 being used by various projects and researchers for the analysis of genomes and gene expression.<br />
-These include:</p>
-<ul>
-<li><a href="#next-generation-sequencing">Next Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
-<li><a href="#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="#casimir">Coordination and Sustainability of International Mouse Informatics Resources</a>
- (CASIMIR) -workflows to associate mouse genome and phenome</li>
-<li><a href="#dgemap">Developmental Gene Expression Map</a> (DGEMap)- analysis of human gene expression during development</li>
-<li><a href="/introduction/taverna-in-use/disease-research#graves-disease">Graves disease</a> - identification of genes responsible</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">MicroArray analysis using R</a> -
- statistical analysis of gene expression</li>
-<li><a href="#sigenae">SIGENAE</a> - development of workflows to analyse breeding animal data</li>
-<li><a href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a> -
- identification of genes responsible for sleeping sickness</li>
-<li><a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren syndrome</a> -
- automation and confirmation of gene characterization</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics#planet">Integration of plant genome resources</a> (PLANET)</li>
-<li><a href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Annotation of genomes</a></li>
-<li><a href="/introduction/related-projects#shared-genomics">Shared Genomics</a></li>
-<li><a href="http://www.cs.man.ac.uk/~cornell/eFungi/">e-Fungi</a> - functional genomics in fungal species</li>
-</ul>
-<p><a name="next-generation-sequencing"</a></p>
-<h2 id="next-generation-sequencing">Next generation sequencing</h2>
-<p>Next generation sequencing presents new challenges in large scale data processing.
-In collaboration with the University of Liverpoolâs
- <a href="http://www.liv.ac.uk/infection-and-global-health/research/animal-health-and-welfare/">Animal Sciences & Physiology Research group</a>,
- in particular <a href="http://www.liv.ac.uk/integrative-biology/staff/harry-noyes/">Dr Harry Noyes</a>,<br />
- we combined Taverna scientific workflows with computing power from the Amazon cloud to create
- a powerful next generation sequencing application for whole genome Single Nucleotide Polymorphism (SNP) analysis.</p>
-<p>Through a Web portal, the application allows scientists to upload their input data,
- fire off a number of parallel cloud instances for the analysis,
- monitor progress and collect results (see figure below).</p>
-<p><img alt="" src="/img/NextGenSequencing-Figure.png" /></p>
-<p>Preliminary work on the genetic variation of African cattle showed we can run a whole genome of ~22 million SNPs
- in a matter of hours.
-This work focuses on the response to trypanomiasis infection (sleeping sickness) in different cattle species.</p>
-<p>The application was demonstrated at the European Conference of Computational Biology (ECCB) 2010, Ghent, Belgium,
- under the title âSoftware for the Data-Driven Researcher of the Futureâ â see the
- <a href="http://www.mygrid.org.uk/files/presentations/ECCB_Tech_Talk.ppt">slides</a> and
- <a href="http://www.youtube.com/watch?v=eR_iPWNYb48">video</a> (no audio or subtitles yet!) from the talk.</p>
-<p>This cloud application was based on the next generation sequencing work done presented at
- Bioinformatics Open Source Conference (BOSC) 2010, Boston, USA, under the title
- âAnalysing African and European cattle with Taverna 2.2â³.
- See the <a href="http://www.mygrid.org.uk/files/presentations/BOSC2010.ppt">slides</a> from the talk.</p>
-<p><a name="tavernapbs></a></p>
-<h2 id="tavernapbs">TavernaPBS</h2>
-<p><a href="http://obx.cphg.virginia.edu/mackey/?page_id=1348">TavernaPBS</a>
- is a plugin for Taverna developed by the
- <a href="http://obx.cphg.virginia.edu/mackey/">Mackey Lab</a>,
- Center for Public Health Genomics, University of Virginia, US.
-It allows a user to define workflows that can then be run using a computational cluster that uses a PBS queuing system.
-The workflows represent next generation sequencing analysis pipelines.</p>
-<p>To most efficiently make use of their myriad of UNIX command line tools, the project has developed a custom
- <a href="/documentation/glossary#beanshell">Beanshell</a> -
- based library to enable workflows composed of UNIX command line invocations. Furthermore, they have abstracted the command execution such that each step could be executed as an independent “job” on a remote high performance computing or grid environment. By doing so, they have essentially turned Taverna into a distributed workflow “compiler”.</p></p>
-<p>You can download the code from the project's
- <a href="http://sourceforge.net/projects/tavernapbs/">pages at SourceForge</a>.</p>
-<p><a name="casimir"></a></p>
-<h2 id="casimir">CASIMIR</h2>
-<p>The Coordination and Sustainability of International Mouse Informatics Resources (CASIMIR)
- <a href="http://www.casimir.org.uk/">project</a> carried out a
- <a href="http://www.casimir.org.uk/fullstory.php?storyid=50">pilot study</a>
- that demonstrated how (parts of) existing databases can be made accessible in a standardized way and
- data processed using the
- <a href="http://molgenis.sourceforge.net/">MOLGENIS toolkit</a>,
- <a href="http://www.biomart.org/">BioMART</a> and Taverna.</p>
-<p>The MOLGENIS toolkit was used to generate WSDL services to access the databases.
-These were then included in a Taverna workflow along with BioMart processors.</p>
-<p>An example <a href="http://www.myexperiment.org/workflows/126">workflow</a> can be found on
- <a href="http://www.myexperiment.org">myExperiment</a>.</p>
-<p><a name="dgemap"></a></p>
-<h2 id="dgemap">DGEMap</h2>
-<p>The Developmental Gene Expression Map (DGEMap)
- <a href="http://www.dgemap.org/">project</a>
- is an EU-funded study to design a pan-European infrastructure to support gene expression studies in early human development.</p>
-<p>The DGEMap team <a href="http://www.inf.ed.ac.uk/research/ICTreviewEPSRC20061207/posters/HumanDev.pdf">plan</a>
- to use Taverna workflows to link human spatio-temporal gene expression data with other bioinformatics resources.</p>
-<p><a name="sigenae"></a></p>
-<h2 id="sigenae">SIGENAE</h2>
-<p>The <a href="http://www.sigenae.org/">Systeme dâInformation des GENomes des animaux âElevage</a>
- (SIGENAE) is the Information System of Analysis of Breeding Animalsâ Genome
- (<a href="http://www.inra.fr/agenae/">AGENAE</a>) program.
-They are a group of French bioinformaticians providing services to biologists working on four mammal and one fish species.
-They are funded by the French National Institute for Agricultural Research
- (<a href="http://www.international.inra.fr/">INRA</a>).<br />
-They not only use Taverna Workbench to support e-Science
- but have been very active in promoting its adoption throughout the French bioinformatics community.</p>
-<p>Some of the workflows developed by the Sigenae community have been made available for
- <a href="http://www.sigenae.org/index.php?id=84#408">sharing</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/geoinformatics.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/geoinformatics.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/geoinformatics.html Wed Mar 11 08:37:10 2015
@@ -104,131 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>geoinformatics</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="#pml">Plymouth Marine Laboratory</a> using Taverna to orchestrate geoinfomatics and OGC (Open Geospatial Consortium)
- Web services such as WPS (Web Processing Service)</li></li>
-</ul>
-<p><a name = "pml"></a></p>
-<h2 id="pml">PML</h2>
-<p>The <a href="http://www.pml.ac.uk/default.aspx">Plymouth Marine Laboratory</a> (PML) provides capability for observing, modelling, understanding and
- forecasting marine ecosystems, to underpin evidence-based environmental solutions to societal challenges.</p>
-<p>They are now using Taverna to orchestrate geoinfomatics and OGC (Open Geospatial Consortium) Web services such as
- WPS (Web Processing Service).
-The work has been described in the following paper, to be published in a special issue of computers &
- geosciences concerning Web service orchestration: <br />
-<a href="http://dx.doi.org/10.1016/j.cageo.2011.11.011">"WPS orchestration using the Taverna workbench: The eScience approach"</a></p>
-<p>They have also developed a Web based graphical editor based on the <a href="http://neyric.github.io/wireit/docs/">WireIt API</a>.
-It will be used in conjunction with the Taverna Server allowing as a Web-based orchestration engine.
-This Web editor will be included in the future European Marine Information System (EUMIS) pilot,
-part of the <a href="http://netmar.nersc.no/">NETMAR</a> project.</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/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/index.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/index.html Wed Mar 11 08:37:10 2015
@@ -104,675 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>Taverna in use</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>More than 350 organizations around the world, both academic and commercial, are known to use Taverna.
-It is employed in a significant number of differing domains to facilitate novel research or to accelerate,
- formalise or share existing research.
-See the <a href="#by-domain">domains</a> where Taverna is in use or has been used. <br />
-Taverna applications have been implemented or deployed in several domains using a variety of platforms and technologies:<span id="more-91"></span></p></p>
-<ul>
-<li>Standalone Workbench (used by the majority of projects)</li>
-<li><a href="#server">As a server</a></li>
-<li><a href="#grid">On a grid or using services on a grid</a></li>
-<li><a href="#cloud">On a cloud</a></li>
-<li><a href="#portal">Behind a portal</a></li>
-<li><a href="#bundled-with-products">Bundled with other products</a></li>
-</ul>
-<p>Table below shows the distribution of Taverna application domains per deployment infrastructure.</p>
-<p>View by <a href="#chronology">chronological</a> order of deployment.</p>
-<table class="table table-striped table-hover table-bordered"
- id="taverna-usage-table"
- summary="Distribution of Taverna usage: domain vs. deployment">
-<caption class="taverna-usage-table">Table1. Distribution of Taverna usage: domain vs. deployment</caption>
-<tbody>
-<tr>
-<th></th>
-<th>Standalone</th>
-<th>Server</th>
-<th>Grid</th>
-<th>Cloud</th>
-<th>Portal</th>
-<th>Bundled</th>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/annotation">Annotation</a></th>
-<td><a href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Genome annotation</a><br />
-<a href="/introduction/taverna-in-use/annotation#taweka">TaWeka</a><br />
-<a href="/introduction/taverna-in-use/annotation#adoption-by-moby">Moby consortium</a><br />
-<a href="/introduction/related-projects#ispider">iSpider</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td><a href="#annotation/afawe">AFAWE</a></td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/arts">Arts</a></th>
-<td><a href="/introduction/taverna-in-use/arts#composition-of-music">Composing music</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/astronomy">Astronomy</a></th>
-<td><a href="/introduction/taverna-in-use/astronomy#sampo">SAMPO</a></td>
-<td><a href="/introduction/related-projects#helio">HELIO</a></td>
-<td><a href="/introduction/taverna-in-use/astronomy#astrogrid">AstroGrid</a><br />
-<a href="/introduction/related-projects#helio">HELIO</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/biodiversity">Biodiversity</a></th>
-<td><a href="/introduction/related-projects#biovel">BioVeL</a></td>
-<td><a href="/introduction/related-projects#biovel">BioVeL</a></td>
-<td>-</td>
-<td><a href="/introduction/related-projects#biovel">BioVel</a></td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/bioinformatics">Bioinformatics</a></th>
-<td><a href="/introduction/taverna-in-use/bioinformatics#lumc">Mass spectrometry data analysis in proteomics</a><br />
-<a href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">MicroArray analysis</a><br />
-<a href="/introduction/taverna-in-use/bioinformatics#measuring-enzyme-characteristics-of-yeast">
- Measuring yeast characteristics</a><br />
-<a href="/introduction/taverna-in-use/biology#enfin">ENFIN</a><br />
-<a href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">MCISB</a><br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#casimir">CASIMIR</a><br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#dgemap">DGEMap</a><br />
-<a href="/introduction/taverna-in-use/disease-research#graves-disease">Graves disease</a><br />
-<a href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">MicroArray analysis</a><br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#sigenae">SIGENAE</a><br />
-<a href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a><br />
-<a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren syndrome</a><br />
-<a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Anthrax analysis</a><br />
-<a href="/introduction/taverna-in-use/bioinformatics#planet">PLANET</a><br />
-<a href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Annotation of genomes</a><br />
-<a href="/introduction/related-projects#shared-genomics">Shared Genomics</a><br />
-<a href="/introduction/related-projects#e-fungi">e-Fungi</a><br />
-<a href="/introduction/taverna-in-use/medicine#eu-adr">EU-ADR</a><br />
-<a href="/introduction/taverna-in-use/databases#efamily">eFamily</a><br />
-<a href="/introduction/related-projects#ispider">iSpider</a></td>
-<td><a href="/introduction/taverna-in-use/disease-research#vph-dareit">VPH-DATE@IT</a><br />
-<a href="/introduction/taverna-in-use/disease-research#vph-dareit">VPH-SHARE</a><br />
-<a href="/introduction/related-projects#shared-genomics/>Shared Genomics</a><br />
-<a href="/introduction/related-projects#cagrid">caGrid</a></td>
-<td><a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a><br />
-<a href="/introduction/taverna-in-use/medicine#knowarc">KnowARC</a><br />
-<a href="/introduction/taverna-in-use/medicine#miasgrid">MIASGrid</a><br />
-<a href="/introduction/related-projects#cagrid">caGrid</a><br />
-<a href="/introduction/taverna-in-use/databases#embrace">EMBRACE</a></td>
-<td><a href="/introduction/taverna-in-use/genome-and-gene-expression#next-generation-sequencing">Next generation sequencing</a><br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#tavernapbs">TavernaPBS</a><br />
-<a href="/documentation/plugins#opal">Opal</a><br />
-<a href="/introduction/related-projects#tsb">TSB</a></td>
-<td><a href="/introduction/taverna-in-use/bioinformatics#biowep">BioWEP</a><br />
-<a href="/introduction/taverna-in-use/biology#planet">PLANET</a><br />
-<a href="/introduction/taverna-in-use/annotation#afawe">AFAWE</a><br />
-<a href="/introduction/taverna-in-use/biology#metware">MetWare</a><br />
-<a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a><br />
-<a href="/introduction/taverna-in-use/biology#ccpn">CCPN</a></td>
-<td><a href="/introduction/taverna-in-use/bioinformatics#biolinux">BioLinux</a><br />
-<a href="/introduction/taverna-in-use/biology#sb-os">SB.OS</a></td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/biology">Biology</a></th>
-<td><a href="/introduction/taverna-in-use/biology#enfin">Enabling Systems Biology</a><br />
-<a href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a><br />
-<a href="/introduction/taverna-in-use/biology##sb-os">Systems Biology Operational Software</a><br />
-<a href="/introduction/taverna-in-use/biology#metware">MetWare</a><br />
-<a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a><br />
-<a href="/introduction/taverna-in-use/biology#ccpn">CCPN</a><br />
-<a href="/introduction/taverna-in-use/biology#ccpn">AFAWE</a><br />
-<a href="/introduction/taverna-in-use/annotation#afawe">A Network of European Plant Databases</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td><a href="#annotation/afawe">AFAWE</a></td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/chemistry">Chemistry</a></th>
-<td><a href="/introduction/taverna-in-use/chemistry#chemistry-development-kit">CDK</a><br />
-<a href="/introduction/taverna-in-use/chemistry#chemical-informatics-and-cyberinfrastructure-collaboratory">CICC</a><br />
-<a href="/introduction/related-projects#chemtaverna">ChemTaverna</a><br />
-<a href="http://usefulchem.wikispaces.com/" target="_blank">UsefulChem</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/data-and-text-mining">Data and text mining</a></th>
-<td><a href="/introduction/taverna-in-use/data-and-text-mining#aid">AID</a><br />
-<a href="/introduction/taverna-in-use/multimedia#course-generator">Course generator</a><br />
-<a href="/introduction/taverna-in-use/data-and-text-mining#refine">REFINE</a><br />
-<a href="/introduction/taverna-in-use/data-and-text-mining#open-software-development-workflows">Open software development wfs</a><br />
-<a href="/introduction/taverna-in-use/annotation#taweka">TaWeka</a><br />
-<a href="/introduction/related-projects#e-lico">e-LICO</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/databases">Databases</a></th>
-<td><a href="/introduction/taverna-in-use/multimedia#echase">eCHASE</a><br />
-<a href="/introduction/taverna-in-use/databases#efamily">eFamily</a><br />
-<a href="/introduction/related-projects#ispider">iSpider</a><br />
-<a href="/introduction/taverna-in-use/databases#omixed">omixed</a></td>
-<td>-</td>
-<td><a href="/introduction/taverna-in-use/databases#embrace">EMBRACE</a></td>
-<td>-</td>
-<td><a href="/introduction/taverna-in-use/databases#prodom">ProDom</a></td>
-<td><a href="http://code.google.com/p/calctav/" target="_blank">CalcTav</a></td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/disease-research">Disease</a></th>
-<td><a href="/introduction/taverna-in-use/disease-research#vph-dareit">VPH-DARE@IT</a><br />
- <a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Analysis of the anthrax bacterium</a><br />
- <a href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a><br />
- <a href="/introduction/taverna-in-use/disease-research#graves-disease">Graves disease</a><br />
- <a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren syndrome</a><br />
- <a href="/introduction/related-projects#cagrid">caGrid</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/document-analysis">Document and image analysis<br />
-Digital preservation</a></th>
-<td><a href="/introduction/taverna-in-use/document-analysis#islandora">Islandora</a><a href="/introduction/related-projects#scape/"><br />
-SCAPE</a><br />
-<a href="/introduction/taverna-in-use/document-analysis#impact">IMPACT</a><br />
-<a href="/introduction/taverna-in-use/document-analysis#dae">DAE</a></td>
-<td><a href="http://blogs.loc.gov/digitalpreservation/2013/03/islandoras-open-source-ecosystem-and-digital-preservation-an-interview-with-mark-leggott/">Islandora</a><br />
-<a href="/introduction/related-projects#scape">SCAPE</a><br />
-<a href="/introduction/taverna-in-use/document-analysis#impact">IMPACT</a><br />
-<a href="/introduction/taverna-in-use/document-analysis#dae">DAE</a></td>
-<td>-</td>
-<td><a href="/introduction/related-projects#scape">SCAPE</a></td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/education">Education</a></th>
-<td><a href="/introduction/taverna-in-use/multimedia#course-generator">Course generator</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/engineering">Engineering</a></th>
-<td><a href="/introduction/taverna-in-use/engineering#jpl">JPL</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/geoinformatics">Geoinformatics</a></th>
-<td><a href="/introduction/taverna-in-use/geoinformatics#pml">PML</a></td>
-<td><a href="/introduction/taverna-in-use/geoinformatics#pml">PML</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/information-quality">Information quality</a></th>
-<td><a href="/introduction/taverna-in-use/information-quality#qurator">Qurator<br />
-</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/medicine">Medicine</a></th>
-<td><a href="/introduction/taverna-in-use/medicine#knowarc">KnowARC</a><br />
- <a href="/introduction/taverna-in-use/medicine#miasgrid">Medical Imaging and Signals Grid (MIASGrid)</a><br/>
- <a href="/introduction/related-projects#cagrid">caGrid</a><br/>
- <a href="/introduction/taverna-in-use/medicine#eu-adr">EU-ADR</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/multimedia">Multimedia</a></th>
-<td><a href="/introduction/taverna-in-use/multimedia#course-generator">Course generator</a><br />
- <a href="/introduction/taverna-in-use/multimedia#echase">eCHASE</a>
-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/natural-language-processing">Natural language processing</a></th>
-<td><a href="/introduction/taverna-in-use/natural-language-processing#panacea">PANACEA</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a /introduction/taverna-in-use/protein-and-proteomics">Protein and proteomics</a></th>
-<td><a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Analysis of anthrax bacterium</a></td>
-<td><a href="/introduction/taverna-in-use/databases#efamily">eFamily</a></td>
-<td><a href="http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace/">EMBRACE</a></td>
-<td><a href="/introduction/related-projects#ispider">iSpider</a></td>
-<td><a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">Protein and proteomics</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-
-<tr>
-<th><a href="/introduction/taverna-in-use/service-provision">Service provision</a></th>
-<td><a href="/introduction/related-projects#engage">ENGAGE</a></td>
-<td><a href="/introduction/related-projects#shared-genomics">Shared Genomics</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/service-testing">Service testing</a></th>
-<td><a href="/introduction/related-projects#e-fungi">e-Fungi</a><br />
-<a href="/introduction/taverna-in-use/annotation#adoption-by-moby">Moby consortium</a><br />
-<a href="/introduction/taverna-in-use/arts#composition-of-music">Music composition</a><br />
-<a href="/introduction/related-projects#ondex">ONDEX</a></td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-<td>-</td>
-</tr>
-
-<tr>
-<th><a href="/introduction/taverna-in-use/social-sciences">Social sciences</a></th>
-<td><a href="/introduction/taverna-in-use/social-sciences#impact">IMPACT</a></td>
-<td><a href="/introduction/related-projects#neiss">NeISS</a></td>
-<td>-</td>
-<td>-</td>
-<td><a href="/introduction/related-projects#neiss">NeISS</a></td>
-<td>-</td>
-</tr>
-
-<tr>
-<th>Other</th>
-<td>-</td>
-<td>-</td>
-<td><a href="/introduction/taverna-in-use/other#moteur">MOTEUR</a><br />
-<a href="http://www.mygrid.org.uk/outreach/collaboration#collaboration-with-nbic/" target="_blank">NBIC</a><br />
-<a href="/introduction/taverna-in-use/other#simdat">SIMDAT</a><br />
-NGS</td>
-<td>-</td>
-<td>-</td>
-<td><a href="http://en.wikipedia.org/wiki/OMII-UK" target="_blank">OMII</a><br />
-<a href="http://code.google.com/p/calctav/" target="_blank">CalcTav</a></td>
-</tr>
-</tbody>
-</table>
-
-<p><a name="server" </a></p>
-<h2 id="as-a-server">As a server</h2>
-<p>Taverna has been used as a service and deployed using <a href="/download/server/">Taverna Server</a> by several projects:</p>
-<ul>
-<li><a href="/introduction/related-projects#biovel">BioVel</a> - establishing an international e-Laboratory to enable scientists to work in
- biodiversity sciences</li>
-<li>VPH-DARE@IT - using Taverna in research to fight dementia</li>
-<li><a href="http://www.vph-share.eu/">VPH-SHARE</a> - online environment for the development, construction and storage of biomedical workflows</li>
-<li><a href="/introduction/related-projects#shared-genomics/">Shared Genomics</a></a> - using Taverna Server to run genetic data workflows</li>
-<li><a href="/introduction/related-projects#helio">HELIO</a> - using Taverna Server to run heliophysics workflows</li>
-<li><a href="/introduction/related-projects#cagrid">caGrid</a> - submit Taverna workflows using caGrid's analytic and data services for execution to a
- Remote Workflow Execution Service on caGrid</li>
-<li><a href="/introduction/related-projects#neiss">NeISS</a> - runnig social science workflows deployed on a Taverna server from a portal</li>
-</ul>
-<p><a name="grid" </a></p>
-<h2 id="on-a-grid">On a grid</h2>
-<p>Various projects and institutions use mechanisms to run Taverna workflows on a <a href="http://en.wikipedia.org/wiki/Grid_computing">grid</a>
- or allow them to access services on a grid:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use#genome-and-gene-expression/tavernapbs">TavernaPBS</a> â next generation sequencing analysis using a computational cluster that uses a PBS queuing
- system and Taverna 2 Workbench</li>
-<li><a href="/introduction/related-projects#cagrid">caGrid</a> â the use of Taverna 2 workflows to link together resources provided by the open source grid
- software infrastructure developed by the US NCI caBIG aimed at enabling multi-institutional cancer data
- sharing and analysis in the US</li></li>
-<li>Europeâs leading grid computing project <a href="http://eu-egee-org.web.cern.ch">EGEE</a>, piloted Taverna over EGEE gLite services</li>
-<li><a href="/introduction/taverna-in-use/databases#embrace">European Model for Bioinformatics Research And Community Education</a> (EMBRACE)</li>
-<li><a href="/introduction/taverna-in-use/medicine#knowarc">Know-how Sharing Technology Based on ARC Services and Open Standards</a> (KnowARC) developed prototype to
- use Taverna as direct interface to Grid resources running ARC</li>
-<li><a href="/introduction/taverna-in-use/other#moteur">MOTEUR</a> - running Taverna 1 workflows on EGEE grid</li>
-<li><a href="http://www.mygrid.org.uk/outreach/collaboration/collaboration-with-nbic/">Netherlands BioInformatics Centre</a> (NBIC)</li>
-<li><a href="/introduction/taverna-in-use/other#simdat">Grids for Industrial Product Development</a> (SIMDAT)</li>
-<li><a href="http://www.mygrid.org.uk/dev/wiki/display/plugins/Submitting+HPC+jobs+from+Taverna+using+GridSAM">JSDL plugin for Taverna 1.7.x</a> that allows you to submit services within a workflow to a grid using
- GridSAM</li>
-<li>Taverna and myExperiment on NGS</li>
-</ul>
-<p>Learn more about how
- <a href="http://dev.mygrid.org.uk/wiki/display/tav250/Taverna+and+grids+and+clouds">Taverna workï¬ows can â©operate â©over a grid infrastructure</a></p>
-<p><a name="cloud" </a></p>
-<h2 id="on-a-cloud">On a cloud</h2>
-<p>Taverna has been used as a service deployed on a cloud by several projects:</p>
-<ul>
-<li><a href="/introduction/related-projects#tsb">TSB grant</a> - to address NHS requirements for accessing and comparing large amounts of information and
- find common genetic links when testing new treatments (in partnership with Eagle Genomics)</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#next-generation-sequencing">Next generation sequencing</a> - using Taverna for the genome Single Nucleotide Polymorphism (SNP)
- analysis on the Amazon cloud</li>
-<li><a href="/introduction/related-projects#scape">SCAPE</a></a> - large scale and computation intense automated digital preservation and quality assurance
- workflows on a cloud infrastructure</li>
-<li>National Biomedical Computation Resource (<a href="http://www.nbcr.net/">NBCR</a>)'s <a href="/documentation/plugins#opal">Opal toolkit</a> - a mechanism to wrap up
- existing scientific applications rapidly as Web services on a cloud</li>
-<li><a href="/documentation/plugins#esc">e-Science Central</a> - allows e-Science Central workflows to be included as services within a Taverna
- workflow</li>
-<li>Cloud-based Taverna workflows for <a href="http://knoesis.wright.edu/library/resource.php?id=835">NMR-based metabolomics data analysis</a></li>
-<li>The <a href="/introduction/related-projects#biovel">BioVeL</a> project uses the <a href="https://wiki.biovel.eu/display/doc/Taverna+Server">Taverna Server</a> within the Amazon Cloud by employing
- a <a href="https://wiki.biovel.eu/display/doc/Taverna+Server+AMI">Taverna Server Amazon Machine Image (AMI)</a></li>
-<li>The <a href="http://www.vph-share.eu">VPH-Share</a> project does rapid deployment of Taverna Server in their Cloud platform to execute
- workflows for clinical physiology.
- These workflows then use <a href="https://vph.cyfronet.pl/tutorial/doku.php?id=as_instantiation">further Cloud instances to run applications</a> that are displayed back to users
- within <a href="https://portal.vph-share.eu">the VPH-Share portal</a> the resource and data management are all handled by the workflow inside
- the Taverna Server instance.</li>
-</ul>
-<p><a name="portal" </a></p>
-<h2 id="behind-a-portal">Behind a portal</h2>
-<p>Various projects and tools use portals to allow users to perform actions that run Taverna workflows
- âbehind the scenesâ.<br />
-These projects include:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/annotation#afawe">Automatic Functional Annotation in a distributed Web Service Environment</a> (AFAWE) -
- a tool for the automatic functional annotation of new genes in plants and other organisms making use
- of Taverna workflows</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics#biowep">Bioinformatics Workflow Enactment Portal</a> (BioWEP) – running pre-selected Taverna workflows
- from the BioWEP portal</li>
-<li><a href="/introduction/taverna-in-use/biology#planet">PLANET (A Network of European Plant Databases)</a>âs BioFloWeb - using Tavenra workfows for the retrieval
- of information about Arabidopsis genes from several European databases</li>
-<li><a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a> - using Taverna workflowa to perform searches and comparisons on the content of the ProDom
- database</li>
-<li><a href="/introduction/taverna-in-use/biology#metware">MetWare</a> - provides applications, databases and workflows for metabolomics</li>
-<li><a href="/introduction/related-projects#neiss">NeISS</a> â runnig social simulations workflows deployed on a Taverna 2 Server in a social simulations
- platform with a portal front-end</li>
-</ul></li>
-</ul>
-<p><a name="bundled-with-products" </a></p>
-<h2 id="bundled-with-products">Bundled with products</h2>
-<p>Several packages include Taverna as part of their distribution:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use#bioinformatics/biolinux">BioLinux</a> - a version of Ubuntu Linux that includes distributions of many bioinformatics programs and
- Taverna</li>
-<li><a href="http://en.wikipedia.org/wiki/OMII-UK">OMII-UK</a> - included with the OMII-UK's open-source software developed to enable a sustained future for
- the UK e-Research community</li>
-<li><a href="/introduction/taverna-in-use/biology#sb-os">Systems Biology Operational Software (SB.OS)</a> - Systems Biology Software based on Ubuntu Linux
- containing the distribution of Taverna</li>
-<li><a href="http://code.google.com/p/calctav/">CalcTav</a> (bundled with OpenCalc) - a plugin to OpenOffice Calc with the aim of allowing calling
- bioinformatics services as spreadsheet functions</li>
-</ul>
-<p><a name="by-domain" </a></p>
-<h2 id="by-domain">By domain</h2>
-<p>Various domains where scientists have used Taverna so far include:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/annotation">Annotation</a></li>
-<li><a href="/introduction/taverna-in-use/arts">Arts</a></li>
-<li><a href="/introduction/taverna-in-use/astronomy">Astronomy</a></li>
-<li><a href="/introduction/taverna-in-use/biodiversity">Biodiversity</a></li>
-<li><a href="/introduction/taverna-in-use/bioinformatics">Bioinformatics</a></li>
-<li><a href="/introduction/taverna-in-use/biology">Biology</a></li>
-<li><a href="/introduction/taverna-in-use/chemistry">Chemistry</a></li>
-<li><a href="/introduction/taverna-in-use/data-and-text-mining">Data and text mining</a></li>
-<li><a href="/introduction/taverna-in-use/databases">Databases</a></li>
-<li><a href="/introduction/taverna-in-use/document-analysis">Document and image analysis</a>
- (digital preservation)</li>
-<li><a href="/introduction/taverna-in-use/education">Education</a></li>
-<li><a href="/introduction/taverna-in-use/engineering">Engineering</a></li>
-<li><a href="/introduction/taverna-in-use/geoinformatics">Geoinformatics</a></li>
-<li><a href="/introduction/taverna-in-use/information-quality">Information quality</a></li>
-<li><a href="/introduction/taverna-in-use/medicine">Medicine</a></li>
-<li><a href="/introduction/taverna-in-use/multimedia">Multimedia</a></li>
-<li><a href="/introduction/taverna-in-use/natural-language-processing">Natural language processing</a></li>
-<li>Protein and proteomics(/introduction/taverna-in-use/protein-and-proteomics)</li>
-<li><a href="/introduction/taverna-in-use/service-provision">Service provision</a></li>
-<li><a href="/introduction/taverna-in-use/service-testing">Service testing</a></li>
-<li><a href="/introduction/taverna-in-use/social-sciences">Social sciences</a></li>
-</ul>
-<p><a name="chronology"<a/></p>
-<h2 id="taverna-in-use-chronology">Taverna in use chronology</h2>
-<p>More than 350 organizations around the world, both academic and commercial, are known to use Taverna.
-It is employed in a significant number of differing domains to facilitate novel research or to accelerate,
-formalise or share existing research. </p>
-<p><a name="2013"></a></p>
-<h3 id="2013">2013</h3>
-<p><a href="/introduction/taverna-in-use/disease-research#vph-dareit">VP-DATE@IT</a> and <a href="http://www.vph-share.eu/">VPH-SHARE</a> - active</p>
-<p><a name="2012"></a></p>
-<h3 id="2012">2012</h3>
-<p><a href="/introduction/taverna-in-use/geoinformatics#pml">PML</a> Plymouth Marine Laboratory (Institute)</p>
-<p><a name="2011"></a></p>
-<h3 id="2011">2011</h3>
-<p><a href="/introduction/related-projects#tsb">TSB</a> Completed Dec-2012 <br />
-<a href="/introduction/related-projects#biovel">BioVeL</a> - Active <br />
-<a href="/introduction/taverna-in-use/bioinformatics#lumc">Mass spectrometry data analysis in proteomics</a> - Active <br />
-<a href="/introduction/related-projects#scape">SCAPE</a> - Active <br />
-<a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a> - Software <br />
-<a href="/introduction/taverna-in-use/bioinformatics#biowep">BioWEP</a>- Software <br />
-<a href="/introduction/taverna-in-use/data-and-text-mining#open-software-development-workflows">Open software development wfs</a> - Active <br />
-<a href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a> - Active <br />
-<a href="http://code.google.com/p/calctav/">CalcTav</a> - Active</p>
-<p><a name="2012"></a></p>
-<h3 id="2010">2010</h3>
-<p><a href="/introduction/taverna-in-use/natural-language-processing#panacea">PANACEA</a> - Completed Dec-2012 <br />
-<a href="/introduction/taverna-in-use/document-analysis#dae">DAE</a> - Active <br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#tavernapbs">TavernaPBS</a> - Active <br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#next-generation-sequencing">Next generation sequencing</a> - Active <br />
-<a href="/introduction/taverna-in-use/biology#sb-os">SB.OS</a> - Software <br />
-<a href="/introduction/taverna-in-use/engineering#jpl">JPL</a> - Active <br />
-<a href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">MCISB</a> - Completed May-2012 <br />
-<a href="/introduction/related-projects#chemtaverna">ChemTaverna</a> - Active</p>
-<p><a name="2009"></a></p>
-<h3 id="2009">2009</h3>
-<p><a href="/introduction/related-projects#neiss">NeISS</a> - Completed Mar-2012 <br />
-<a href="/introduction/related-projects#e-lico">e-LICO</a> - Completed 2012 <br />
-<a href="/introduction/related-projects#helio">HELIO</a> - Completed Dec-2012</p>
-<p><a name="2008"></a></p>
-<h3 id="2008">2008</h3>
-<p><a href="/introduction/taverna-in-use/social-sciences#impact">IMPACT</a> - Completed Jan-2012 <br />
-<a href="/introduction/taverna-in-use/biology#metware">MetWare</a> - Software <br />
-<a href="/introduction/taverna-in-use/medicine#eu-adr">EU-ADR</a> - Completed Jan-2012<br />
-<a href="/introduction/taverna-in-use/bioinformatics#biolinux">BioLinux</a> - Software <br />
-<a href="/introduction/taverna-in-use/annotation#afawe">AFAWE</a> - Institute <br />
-<a href="/introduction/related-projects#cagrid">caGrid</a> - Completed Nov-2009 <br />
-<a href="/introduction/related-projects#engage">ENGAGE</a> - Active <br />
-<a href="/introduction/related-projects#ondex">ONDEX</a> Completed Mar-2011</p>
-<p><a name="2007"></a></p>
-<h3 id="2007">2007</h3>
-<p><a href="/introduction/related-projects#shared-genomics">Shared Genomics</a> - Completed Feb-2010 <br />
-<a href="/introduction/taverna-in-use/data-and-text-mining#aid">AID</a> - Active
-<a href="/introduction/taverna-in-use/disease-research#graves-disease">Graves disease</a> - Active
-<a href="/introduction/taverna-in-use/multimedia#course-generator">Course generator</a> - Active <br />
-<a href="/introduction/taverna-in-use/annotation#taweka">TaWeka</a> - Active
-<a href="/introduction/taverna-in-use/arts#composition-of-music">Composing music</a> - Active <br />
-<a href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">MicroArray analysis</a> <br />
-<a href="/introduction/taverna-in-use/data-and-text-mining#refine">REFINE</a> - Completed Jun-2010</p>
-<p><a name="2006"></a></p>
-<h3 id="2006">2006</h3>
-<p><a href="/introduction/taverna-in-use/biology#ccpn">CCPN</a> - Active <br />
-<a href="/introduction/taverna-in-use/biology#planet">PLANET</a> - Active <br />
-<a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Anthrax analysis</a> - Active <br />
-<a href="/introduction/taverna-in-use/medicine#knowarc">KnowARC</a> - Completed 2009 <br />
-<a href="/introduction/taverna-in-use/medicine#miasgrid">MIASGrid</a> - Completed 2006 <br />
-<a href="/introduction/taverna-in-use/multimedia#echase">eCHASE</a> - Completed2006 <br />
-<a href="/introduction/taverna-in-use/other#moteur">MOTEUR</a> - Active <br />
-<a href="/introduction/taverna-in-use/bioinformatics#planet">PLANET</a> - Active</p>
-<p><a name="2005"></a></p>
-<h2 id="2005">2005</h2>
-<p><a href="/introduction/taverna-in-use/biology#enfin">ENFIN</a> - Completed Nov-2010 <br />
-<a href="/introduction/taverna-in-use/chemistry#chemical-informatics-and-cyberinfrastructure-collaboratory">CICC</a> - Completed 2008<br />
-<a href="/introduction/taverna-in-use/databases#embrace">EMBRACE</a> - Completed May-2006 <br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#dgemap">DGEMap</a> - Completed 2009 <br />
-<a href="/introduction/taverna-in-use/genome-and-gene-expression#sigenae">SIGENAE</a> - Active <br />
-<a href="/introduction/taverna-in-use/bioinformatics#measuring-enzyme-characteristics-of-yeast">Measuring yeast characteristics</a> - Completed Apr-2010</p>
-<p><a name="2004"></a></p>
-<h2 id="2004">2004</h2>
-<p><a href="/introduction/taverna-in-use/databases#efamily">eFamily</a> - Active <br />
-<a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren syndrome</a> - Active <br />
-<a href="/introduction/taverna-in-use/information-quality#qurator">Qurator</a> - Completed Jul-2007
-<a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a> - Database <br />
-<a href="/introduction/related-projects#e-fungi">e-Fungi</a> - Completed Jun-2008 <br />
-<a href="/introduction/related-projects#ispider">iSpider</a> - Completed Jun-2007</p>
-<p><a name="2002"></a></p>
-<h2 id="2002">2002</h2>
-<p><a href="/introduction/taverna-in-use/genome-and-gene-expression#casimir">CASIMIR</a> - Completed May-2006</p>
-<p><a name="2001"></a></p>
-<h2 id="2001">2001</h2>
-<p><a href="/introduction/taverna-in-use/other#simdat">SIMDAT</a> - Active <br />
-<a href="/introduction/taverna-in-use/annotation#adoption-by-moby">Moby consortium</a> - Active <br />
-<a href="/introduction/taverna-in-use/astronomy#astrogrid">AstroGrid</a> - Completed 2009</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/information-quality.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/information-quality.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/information-quality.html Wed Mar 11 08:37:10 2015
@@ -104,133 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>Information quality</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 applied to document the quality of e-Science information by the Qurator project.</p>
-<p><a name="qurator></a></p>
-<h2 id="qurator">Qurator</h2>
-<p>The Qurator <a href="http://www.qurator.org/">project</a> was a UK EPSRC-funded project (grant ref. <a href="http://gow.epsrc.ac.uk/NGBOViewGrant.aspx?GrantRef=GR/S67593/01">GR/S67593/01</a>).</p>
-<p>The Qurator project aimed to develop and test tools to discover and document the quality of e-Science information.</p>
-<p>The tools were developed in close collaboration with user-scientists,
- with the long term goal of providing generic information quality support in e-Science.</p>
-<p>The Qurator project developed an information quality management workbench that supports data experts in the
- specification, rapid deployment and testing of personal quality hypotheses for specific types of data.
-This is achieved by providing a declarative model and language for the definition of usersâ hypotheses,
- called âquality viewsâ, and a compilation of views into executable components that can be embedded in a
- userâs data processing application. Quality views are described in terms of an extensible semantic model
- for Information Quality.</p>
-<p>The Qurator workbench compiles quality views into Taverna workflows,
- effectively creating reusable quality sub-workflows that can be integrated into a host workflow during
- a deployment step.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a href="http://doi.acm.org/10.1145/1247480.1247638">paper</a> <em>Managing information quality in e-science: the qurator workbench</em> by Missier et al,
- describes the Qurator workbench.</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/medicine.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/medicine.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/medicine.html Wed Mar 11 08:37:10 2015
@@ -104,179 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>Medicine</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 in medicine:</p>
-<ul>
-<li><a href="#knowarc">Know-how Sharing Technology Based on ARC Services and Open Standards</a> (KnowARC) -
- rapid iteration and large datasets on a grid for for medical imaging</li>
-<li><a href="#miasgrid">Medical Imaging and Signals Grid</a> (MIASGrid) -
- workflows for MRI and mammogram analysis</li>
-<li><a href="/introduction/related-projects#cagrid">caGrid</a> - cancer research</li>
-<li><a href="#eu-adr">EU-ADR</a> - detecting adverse drug reactions through the exploitation of clinical data from
- electronic healthcare records</li>
-</ul>
-<p><a name="knowarc"></a></p>
-<h2 id="knowarc">KnowARC</h2>
-<p>The Grid-enabled Know-how Sharing Technology Based on ARC Services and Open Standards (KnowARC)
- <a href="http://www.knowarc.eu/">project</a> is: </p>
-<blockquote>
-<p>a Sixth Framework Programme Specific Targeted Research Project, under
-Priority IST-2005-2.5.4 âAdvanced Grid Technologies, Systems and
-Servicesâ. The operative comencement date of the project is June 1,
-2006, and the planned duration is 3 years.</p>
-<p>The objectives of the project are:</p>
-<ul>
-<li>to create a novel, powerful Next Generation Grid middleware based on NorduGridâs
- <a href="http://www.nordugrid.org/">ARC</a>, widely respected for its simplicity,
- non-invasiveness and cost-efficiency;</li>
-<li>to promote Grid standardization and interoperability;</li>
-<li>to contribute to Grid technologies take-up, bridging the gaps between business and academia in Grid development</li>
-</ul>
-</blockquote>
-<p>The KnowARC team have adopted Taverna to specify their workflows.<br />
-They have also developed the <a href="/documentation/plugins#usecase_plugin">ARC plugin</a> for Taverna.</p>
-<p>The functionality of the ARC plugin has been <a href="http://www.knowarc.eu/demos/">demonstrated</a>
- in the domain of medical imaging.</p>
-<p><a name="miasgrid"></a></p>
-<h2 id="miasgrid">MIASGrid</h2>
-<p>The MIAS project examined the requirements of Medical Imaging and Signals.<br />
-The [MIASGrid]http://www.robots.ox.ac.uk/~irc/grid_mias-grid.html) sub-project,
- took examples of those requirements and investigated how e-Science and the myGrid tools in particular could satisfy them.
-The project was funded by the <a href="http://www.epsrc.ac.uk/">EPSRC</a> for £494k and ran until April 2006.</p>
-<p>The project produced several workflows that demonstrated the applicability of Taverna to the handling
- of large amounts of medical image data.
-The workflows made use of <a href="http://www.mathworks.com/products/matlab/">MATLAB</a> and also interaction with users.</p>
-<p>The workflows covered two domains:</p>
-<ul>
-<li>The analysis of MRI scans of knees to detect changes in cartilage</li>
-<li>The <a href="http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.111.3846&rep=rep1&type=pdf">description and searching</a>
- of a database of mammograms</li>
-</ul>
-<p><a name="eu-adr"></a></p>
-<h2 id="eu-adr">EU-ADR</h2>
-<p>The <a href="http://euadr-project.org/">EU-ADR</a> project aims to develop an innovative computerised system to
- detect adverse drug reactions (ADRs) through the exploitation of clinical data from electronic healthcare records (EHRs).
-This process will rely on the usage and development of various computational techniques to analyse the EHRs in order to
- detect âsignalsâ (combination of drugs and suspected adverse events that warrant further investigation).
-These techniques will be made available as a set of secure Web services, combining secure HTTPS connection with
- WS-Security user authentication.</p>
-<p>However, to obtain final readable results, the various services must work with each other, constructing one or more workflows.
-An interdisciplinary team of researchers, requiring a software application that enhances workflow development in
- an elegant manner, will develop these workflows.
-The chosen platform is Taverna, which provides a very easy to use interface and strong core features for
- Web services interconnection and management, improving researchersâ collaboration and general system functionality.
-Taverna will support the remaining system components and end-user applications.
-In the end, the project should demonstrate that scientific and clinical evidence could quickly and
- directly be translated into patient safety and, thus, health benefit.</p>
-<p><a href="http://www.taverna.org.uk/pages/wp-content/uploads/2010/10/EUADR_project.pdf">Presentation slides</a>
- by Pedro Lopes describe the use of Taverna by the EU-ADR project.</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/multimedia.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/multimedia.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/multimedia.html Wed Mar 11 08:37:10 2015
@@ -104,143 +104,3 @@
<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/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC chat</a></li>
- <li><a href="/community#contribute">Contribute</a></li>
- <li><a href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit website</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>Multimedia</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 handling and collating multimedia resources.<br />
-These include:</p>
-<ul>
-<li><a href="#course-generator">Course generator</a>- generation of a multimedia user-oriented teaching course
-<a href="#echase">Electronic Cultural Heritage made Accessible for Sustainable Exploitation</a> (eCHASE) -
- aggregation of heterogeneous multimedia data</li>
-</ul>
-<p><a name="course-generator"></a></p>
-<h2 id="course-generator">Course generator</h2>
-<p><a href="http://www.carstenullrich.net/">Carsten Ullrich</a> from the Shanghai Jiaotong University and others have used Taverna to integrate VIACIPA
- (a Web-based digital library of multimedia objects) and Paigos (a course generator) in order to formalize and
- automate the creation of learning courses based upon specific user requirements and individual learning
- activities and resources.</p>
-<h3 id="publications">Publications</h3>
-<p>The work is detailed in the <a href="http://dx.doi.org/10.1007/978-3-540-77255-2_61">paper</a> <em>Multimedia-Learning in a Life Science Workflow Environment</em>
- by Ullrich et al.</p>
-<p><a name="course-generator"></a></p>
-<h2 id="echase">eCHASE</h2>
-<p>The electronic Cultural Heritage made Accessible for Sustainable Exploitation <a href="http://www.it-innovation.soton.ac.uk/projects/echase/">project</a> depends upon being </p>
-<blockquote>
-<p>able to access, aggregate and exploit multimedia content from multiple
-sources across Europe.</p>
-</blockquote>
-<p>The project has used Taverna workflows to manipulate the data held by several legacy database systems.
-The mapping services within the workflows deal with inconsistent formatting of particular types of data,
- such as place and date.</p>
-<h3 id="publications_1">Publications</h3>
-<p>The <a href="http://eprints.ecs.soton.ac.uk/14265/1/eCHASE_axmedis2006.pdf">paper</a> <em>The eCHASE System for Cross-border Use of European Multimedia Cultural Heritage Content in
- Education and Publishing</em> by Addis et al, describes the technical structure of the eCHASE system.</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