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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 [5/10] - 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/documentation/service-sets/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/service-sets/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/service-sets/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,150 @@
<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>Service sets</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>A service set is a collection of services that have something in common,
+ for example a compatible functionality or suitability for a domain.</p>
+<p>You can save the set of services that are in the
+ <a href="/documentation/glossary#service_panel">Service Panel</a> of the Workbench by right-clicking on
+ <em>Available Services</em> in the Service Panel.</p>
+<p>You can add a set of services to the Service Panel by right-clicking on <em>Available Services</em>.
+The service set can either be specified in a file, or downloaded from a URL on the Web that
+ points to the service description file.
+You have the choice to replace your current set of services, or to add to your set of services.</p>
+<p>Note that the service templates and local services are not removed when you replace your service
+ set.</p>
+<p>Currently available service sets include:</p>
+<ul>
+<li>
+<p><a href="http://www.myexperiment.org/packs/132.html">NCBI Entrez Utilities Web service set</a> -
+ a set of
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esoap_help.html">NCBI Entrez services</a>
+ providing access to
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/egquery_help.html">EGQuery</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esummary_help.html">ESummary</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/einfo_help.html">EInfo</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html">ELink</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html">ESearch</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/espell_help.html">ESpell</a>,
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html">EPost</a> and
+ <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html">EFetch</a> utilities.</p>
+</li>
+<li>
+<p><a href="http://www.myexperiment.org/packs/135.html">Chemistry Web service set</a> -
+ a set of Web services for chemistry provided by
+ <a href="/introduction/chemistry-web-services#chemspider">ChemSpider</a>,
+ <a href="/introduction/chemistry-web-services#chebi">ChEBI</a> and <br />
+<a href="/introduction/chemistry-web-services#pubchem">PubChem</a>.</p>
+</li>
+</ul>
+<p>You can also find <a href="http://www.myexperiment.org/tags/1963.html">service sets on myExperiment</a>.</p></div>
+
+ </div>
+
+ <footer class="footer">
+ <div class="container">
+ <p id="copyright" class="text-muted">
+ Copyright © 2014-2015 The Apache Software Foundation, Licensed under the
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache License, Version 2.0</a>.
+ Apache and the Apache feather logo are trademarks of The Apache Software Foundation.
+ </p>
+ </div>
+ </footer>
+
+
+
+ <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
+<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
+
+<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/documentation/taverna-galaxy/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/taverna-galaxy/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/taverna-galaxy/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,149 @@
<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>Taverna Galaxy</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>Galaxy is an open, Web-based platform for data intensive biomedical research.
+Taverna 2-Galaxy integration is a first step towards making <a href="http://galaxy.psu.edu/">Galaxy</a>
+ and Taverna 2 more interoperable.
+It allows the automatic generation of Galaxy tools from Taverna workflows.
+The tools can then be installed as usual in a Galaxy server and allow the Taverna workflows to
+become part of a Galaxy pipeline.
+It has been developed by Kostas Karasavvas of <a href="http://www.nbic.nl/">NBIC</a>.</p>
+<p>Users do not need to install Taverna Galaxy themselves.
+It is available as part of the myExperiment <a href="http://www.myexperiment.org/">Web site</a>.
+While browsing Taverna workflows the user will see an additional link
+ âDownload as Galaxy Toolâ in the download section of the workflow.
+The tool can then be installed into Galaxy in the usual manner by the Galaxy administrator.
+They will also need a <a href="/documentation/server/">Taverna Server</a> that will run the
+ Taverna Galaxy tools.</p>
+<p>Also check out the Taverna-Galaxy <a href="https://trac.nbic.nl/elabfactory/wiki/eGalaxy">wiki</a>.</p>
+<h3 id="for-taverna-galaxy-users">For Taverna-Galaxy users</h3>
+<ul>
+<li>You can now include Taverna workflows as part of your Galaxy workflows</li>
+<li>The Taverna workflow will be made available as a Galaxy tool</li>
+<li>You can <a href="http://www.myexperiment.org/workflows">search/browse</a> Taverna workflows from the
+ <a href="http://www.myexperiment.org/">myExperiment</a> workflow repository, and</li>
+<li>Just let your Galaxy administrator know which Taverna workflows you want installed in Galaxy</li>
+</ul>
+<h3 id="try-it-out">Try it out</h3>
+<ul>
+<li>The <a href="http://galaxy.nbic.nl">NBIC Galaxy Server</a> provides a demo platform to run some
+ pre-installed Taverna workflows in Galaxy</li>
+</ul>
+<h3 id="taverna-galaxy-in-use">Taverna-Galaxy in use</h3>
+<p>Dr Casey Bergman and his group of Life Sciences researchers from the
+ <a href="http://bergmanlab.smith.man.ac.uk">Bergman Lab</a> @ University of Manchester working on
+ eukaryotic genome biology have successfully installed and used the integrated Taverna-Galaxy
+ tools.</p>
+<p>See <a href="http://bergmanlab.smith.man.ac.uk/?p=943">their blog</a> about their experiences in
+ installing and running Taverna-Galaxy.</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/documentation/taverna-player/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/taverna-player/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/taverna-player/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,180 @@
<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>Taverna Player</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>The Taverna Player is a Web-based interface (implemented as Ruby on Rails plugin) for executing
+ existing workflows through the <a href="/documentation/server">Taverna Server</a>.
+It can be considered analogous to playing videos on <a href="http://www.youtube.com">YouTube</a>.
+Workflows can be run with data supplied by the creator, or with new data uploaded by the user,
+ but the workflows themselves cannot be altered.</p>
+<p>Taverna Player enables the running of Taverna workflows within a Ruby-on-Rails application.
+Taverna Player has a REST API that allows inputs to the workflow to be specified,
+ a run to be started and monitored, and the resultant outputs to be retrieved.
+Any interactions the workflow includes are presented to the user in a Web browser for them to
+ complete.
+Taverna Player has been released in the RubyGems registry and is used within the
+ <a href="http://www.biovel.eu/">BioVeL Portal</a> to run a wide range of biodiversity workflows.</p>
+<p>Taverna Player is not limited to the biodiversity domain â it is generic and can be used to run
+ any Taverna workflow and can be integrated into various online environments - for example it
+ can be embedded into (static) HTML pages to run specific workflows with pre-defined data.</p>
+<p>For more information on Taverna Player or to download it, please see the following:</p>
+<ul>
+<li>Package (Ruby on Rails plugin): <a href="https://rubygems.org/gems/taverna-player">https://rubygems.org/gems/taverna-player</a></li>
+<li>Documentation: <a href="http://mygrid.github.io/taverna-player/">http://mygrid.github.io/taverna-player/</a></li>
+<li>Source: <a href="https://github.com/myGrid/taverna-player">https://github.com/myGrid/taverna-player</a></li>
+<li>Metrics: <a href="https://codeclimate.com/github/myGrid/taverna-player">https://codeclimate.com/github/myGrid/taverna-player</a></li>
+</ul>
+<h2 id="integration-of-taverna-player-into-web-apps">Integration of Taverna Player into Web apps</h2>
+<h3 id="biovel-portal">BioVeL Portal</h3>
+<p><a href="http://www.biovel.eu/">BioVeL</a> provides workflows for the processing of data in major areas of
+ biodiversity research: ecological niche modelling, ecosystem functioning, and taxonomy.
+Taverna Player has been successfully used within the <a href="https://portal.biovel.eu/">BioVeL Portal</a>
+ to submit and run a wide range of biodiversity workflows using the
+ <a href="/documentation/server">Taverna Server</a>.</p>
+<h3 id="scratchpads">Scratchpads</h3>
+<p><a href="http://scratchpads.eu/">Scratchpads</a>, developed as part of the <a href="http://vbrant.eu/">ViBRANT</a>
+ project, are online virtual research environments for biodiversity, allowing anyone to
+ share their data and create their own research networks.
+Sites are hosted at the Natural History Museum London, and offered freely to any scientist.</p>
+<p>Taverna Player has been integrated with Scratchpads in two ways.
+Firstly, workflows can be embedded in a page in the same way as a video from YouTube would be
+ embedded; the workflow itself is running on the BioVeL Portal, but all data entry and
+ user-interaction is done in the embedded widget within the Scratchpads site.
+Secondly, the Scratchpads can use the Taverna Player REST API directly;
+ this allows workflows to be run with a higher degree of control and results to be ingested
+ back into the Scratchpads for further analysis.
+In both cases, data can be automatically injected into the workflow run from the host
+ Scratchpads site.
+The actual execution of the workflow is done by the Taverna Server -
+ the Player just interacts with the Server to submit a workflow for execution,
+ monitor its progress and fetch results.</p>
+<p>Read more about
+ <a href="http://dev.mygrid.org.uk/wiki/display/TavernaStrategy/Scratchpads">Scratchpads integration</a>
+ and see relevant publications.</p>
+<h3 id="ipython-notebook">IPython Notebook</h3>
+<p><a href="http://ipython.org/">IPython Notebook</a> is a browser-based environment for interactive
+ computing.
+Users can write, edit and replay Python scripts.
+IPython Notebook has support for interactive data visualization and report presentation.
+A Notebook can be saved and shared.
+Notebooks can be replayed using the same or different data.
+The record of a Notebook ârunâ can be saved and displayed in a
+ <a href="http://nbviewer.ipython.org/">Notebook Viewer</a>.</p>
+<p>Taverna Player, through its API and and the use of HTML iframes, enables the running of
+ workflows within a portal like the BioVeL Portal to be included as part of another Web site.
+It uses the REST API of the Taverna Player to allow workflow inputs to be specified,
+ a run started and monitored, and the resultant outputs retrieved - all within the IPython
+ Notebook.</p>
+<p>Read more about
+ <a href="http://dev.mygrid.org.uk/wiki/display/TavernaStrategy/IPython+Notebook">IPython Notebook integration</a>
+ and see relevant publications.</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/documentation/training-and-workshops/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/training-and-workshops/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/training-and-workshops/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,123 @@
<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>Training and workshops</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>Education and training in the use of the Taverna tools is provided in a number of different ways.
+There are dedicated workshops, <a href="/documentation/tutorials">online tutorials</a>,
+ <a href="http://dev.mygrid.org.uk/wiki/display/about/Publications">presentations and publications</a>.</p>
+<p>Over fifty tutorials have been given on the use of Taverna, and not just by us.
+For example, the French <a href="http://www.sigenae.org/">Signen@e</a> consortium have trained over 200
+ people and produced tutorials in French.
+Over 800 people have been trained by the Taverna team.</p>
+<p>We are always keen to organise training and tutorials for users and workshops for developers.
+Please <a href="/community">get in touch</a> if you want to arrange a training or a workshop.</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/documentation/tutorials/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/tutorials/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/tutorials/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,124 @@
<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>Tutorials</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>An introductory Taverna 2
+ <a href="http://www.myexperiment.org/files/997/versions/1/download/SimplifiedTutorial.ppt">tutorial</a>
+ @ [MyExperiment]((http://www.myexperiment.org)
+ on building simple workflows is available to show some of the features of Taverna 2.</p>
+<p>A webinar
+ â<a href="http://bitesizebio.com/webinars/the-taverna-project/">The Taverna Project â a workbench for bioinformatics design</a>â<br />
+ @ <a href="http://bitesizebio.com/">BitesizeBio</a> given by Paul Fisher on March 8th 2011 is also
+ available on-line.</p>
+<p>Also check out our <a href="/documentation/videos">video tutorials</a> and
+ <a href="http://www.mygrid.org.uk/dev/wiki/display/taverna/Videos">videos from the old Wiki</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/documentation/videos/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/videos/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/videos/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,130 @@
<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>Videos</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>Videos below showcase Taverna's capabilities or how Taverna can be used in a specific domain:</p>
+<ul>
+<li><a href="http://www.youtube.com/watch?v=Zh0tn8amjAY">Taverna 2 in action video</a></li>
+<li><a href="http://www.youtube.com/watch?v=ZjsO6NQfIRI">Quick Taverna 2.1-myExperiment video tutorial</a>
+ (shows downloading a workflow from <a href="http://www.myexperiment.org/">myExperiment</a>
+ using the Workbench, modifying it and running)</li>
+<li><a href="http://www.youtube.com/watch?v=m3XTY8rnceQ">Building data mining workflows video tutorial</a>
+ (using the <a href="/introduction/related-projects#e-lico">e-LICO</a> project tools)</li>
+<li><a href="http://www.youtube.com/watch?v=JtmqZfzyEKs">e-LICO demo</a></li>
+<li><a href="http://www.youtube.com/watch?v=17WBk1fqX3c">Shared Genomics demo @ 2010 AMIA Summit on Translational Bioinformatics</a>
+ (demonstrates searching for genomic features inside genes and their categorisation using
+ the Taverna Server)</li>
+</ul>
+<p>A set of
+ <a href="http://www.mygrid.org.uk/dev/wiki/display/taverna/Videos">videos that accompany the User Manual</a>
+ are also available to show how particular task can be done in Taverna.</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/documentation/web-service-developers/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/web-service-developers/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/web-service-developers/index.html Wed Mar 11 08:49:34 2015
@@ -104,3 +104,183 @@
<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>Web service developers</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 aims to support Web services that are
+ <a href="http://www.ws-i.org/Profiles/BasicProfile-1.1-2004-08-24.html">WS-I</a> (Web Services Interoparability) compliant,
+ but this is a long-term goal and currently there are a few nuances.
+However, it should be possible to create Web services that are compatible with Taverna if you follow certain guidelines.</p>
+<h2 id="wsdl-web-service-description-language-style-web-services">WSDL (Web Service Description Language) style Web services</h2>
+<p><a href="/documentation/glossary#wsdl">WSDL</a> binding describes how the Web service is bound to a messaging protocol;
+ particularly the SOAP messaging protocol.
+A WSDL SOAP binding can be either a <strong>Remote Procedure Call (RPC)</strong> style binding or a <strong>document</strong> style binding.
+A SOAP binding can also have an <strong>encoded</strong> use or a <strong>literal</strong> use.
+This gives you four style/use models:</p>
+<ol>
+<li>RPC/encoded</li>
+<li>RPC/literal</li>
+<li>Document/encoded</li>
+<li>Document/literal</li>
+</ol>
+<p>There is also a fifth binding style that is commonly referred to as the document/literal wrapped.
+Thus, developers have five binding styles to choose from when creating a WSDL file.</p>
+<p>A good description of the differences between these styles can be found
+ <a href="http://www-128.ibm.com/developerworks/webservices/library/ws-whichwsdl/">here</a>.</p>
+<p>Although Taverna supports bindings that are <strong>RPC/encoded</strong> and <strong>RPC/literal</strong> to a fair extent,
+ the preferred binding style is <strong>document/literal wrapped</strong>,
+ i.e. the WSDL should have âstyleâ attributes that are set to âdocumentâ and âuseâ attributes set to âliteralâ.
+This is particularly the case when dealing with complex types; for primitive types no problems are anticipated.</p>
+<h3 id="currently-un-tested">Currently un-tested</h3>
+<p>The following are untested, and although not proven to fail the behaviour is currently undefined.
+For this reason it is advised that these features are avoided.</p>
+<ul>
+<li>Multiple WSDL imports.
+ Taverna has only been tested on services that contain either no, or only one import of an additional wsdl file.
+ For WSDLs that import more than one additional WSDL, particularly if that WSDL has a different service endpoint to the others,
+ the behaviour of Taverna is currently unclear.
+ Its expected that it will fail when invoking the Web service.
+ This does not affect imports of schemas.
+ This has been thoroughly tested and works as expected.</li>
+<li>Multiple service endpoints. For a given WSDL Taverna currently only references the first service endpoint.
+ If more than one exists then operations belonging to the second endpoint are expected to fail.</li>
+<li>Ambiguous type names.
+ In the unusual case that an operation requires inputs that contain identically named types
+ that belong to different namespaces it is expected that Taverna should not have any problems.
+ However, because of the unusual nature of this it is untested and therefore not recommended.</li>
+</ul>
+<h3 id="currently-known-to-fail">Currently known to fail</h3>
+<p>The following are situations that are known to fail in Taverna.</p>
+<ul>
+<li>Cyclic references.
+ When processing the result of invoking an operation, Taverna resolves the XML into a single document.
+ If the response contains cyclic references, this is detected and an error occurs (to prevent an infinitely long document!).
+ For this reason cyclic references should be avoided.
+ (Taverna will, however,
+ work with such an operation as long as the cyclic reference is not contained within the response data structure).</li>
+<li>Overloaded operations. Within the UI,
+ Taverna only distinguishes between operations, for a given service, by name.
+ The operation signature is not used to distinguish between operations of the same name.
+ For this simple reason, Taverna does not support overloaded operations.</li>
+<li>anyType.
+ Although Taverna can invoke a service that deals with the anyType type,
+ the XML splitting mechanism cannot work since there is no information about the data structure required or received.
+ Such services can only be used by providing and/or manipulating the XML directly.</li>
+</ul>
+<h2 id="advertise-your-services-with-biocatalogue">Advertise your services with BioCatalogue</h2>
+<p>If your services are in the Life Sciences domain,
+ one of the best ways to make people aware of your services and make them easily discoverable from Taverna and
+ the Web is to register and describe them in <a href="http://www.biocatalogue.org/">BioCatalogue</a>
+ Life Sciences Web Services registry.</p></p>
+<p>With BioCatalogue, service providers can easily register, describe, advertise and monitor their Web services.
+ Users can easily find the right Web service using BioCatalogue's powerful search and filtering.
+BioCatalogue provides combined information about services from both providers and community
+ as it has on-going expert curation as well as social curation by the community.</p></div>
+
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