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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/03/11 09:37:12 UTC
svn commit: r943303 [7/10] - 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/roadmap.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/roadmap.html (original)
+++ websites/staging/taverna/trunk/content/introduction/roadmap.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>Taverna Roadmap</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"><h2 id="taverna-3">Taverna 3</h2>
-<p>Taverna 3 is a re-engineering of the Taverna codebase to use OSGi.</p>
-<h3 id="taverna-3-command-line-tool-alpha3beta1">Taverna 3 Command Line Tool alpha3/beta1</h3>
-<ul>
-<li>Based on the /developers/work-in-progress/taverna-3/ using <a href="http://www.osgi.org/About/Technology">OSGi</a></li>
-<li>New plugin-system</li>
-<li>Usability improvements</li>
-<li>Easily customisable service sets</li>
-<li>More complete service type support</li>
-</ul>
-<h3 id="taverna-3-platform-updated-beta">Taverna 3 Platform updated beta</h3>
-<ul>
-<li>Available as an <a href="http://www.osgi.org/About/Technology">OGSi</a> bundle or Jar (for non-OGSi environments for easy embedding)</li>
-<li>Using <a href="http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2">SCUFL2</a> workflow bundle format</li>
-<li>API for running workflows</li>
-</ul>
-<h2 id="tavena-2">Tavena 2</h2>
-<p>This site only covers the Apache Taverna product.
-As Taverna 2 is not an Apache product so its roadmap can be found on the previous <a href="http://www.taverna.org.uk/introduction/roadmap/">taverna website</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/services-in-taverna.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/services-in-taverna.html (original)
+++ websites/staging/taverna/trunk/content/introduction/services-in-taverna.html Wed Mar 11 08:37:10 2015
@@ -104,172 +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>Services in Taverna</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna can access a large number of services in the fields of bioinformatics, astronomy, chemoinformatics,
- health informatics and others. Although many examples of using Taverna lie in the bioinformatics domain,
- Taverna is actually domain independent.
-This means that Taverna can be applied to a wide range of fields â even music and food sciences.</p>
-<p>Taverna can invoke generic <a href="/documentation/glossary#wsdl">WSDL-style Web services</a>.
-You do not need to alter a service in any way;
-you simply need to give Taverna the URL address of the serviceâs WSDL document.
-Please refer to our <a href="/documentation/web-service-developers">Web service developersâ documentation</a> if you are planning on developing Web services
- accessible from Taverna.</p>
-<p>Taverna can also access other types of Web services, such as <a href="/documentation/glossary#biomoby">BioMoby</a>, <a href="/documentation/glossary#biomart">BioMart</a> and <a href="/documentation/glossary#soaplab">SoapLab</a>
- services.</p>
-<p>In addition, Taverna can invoke local Java services (<a href="/documentation/glossary#beanshell">Beanshell</a> scripts), local Java API (<a href="/documentation/glossary#api_consumer">API Consumer</a>),
- R scripts on an R server (<a href="/documentation/glossary#rshell">Rshell</a> scripts), import data from a <a href="/documentation/glossary#spreadsheet_import">cvs or Excel spreadsheet</a> and interact
- with users in a browser.</p>
-<p>Taverna can also <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Interaction+service">interact</a> with a running workflow from your Web browser,
- and has the ability to incorporate workflow fragments (reusable <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Component+services">components</a>) as services in a workflow.</p>
-<p>A full list of service types is in the <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Service+types">User Manual</a>.</p>
-<p>Please see the <a href="http://biocatalogue.org/">BioCatalogue</a> for details of the services we are currently aware of that work with Taverna.
-If you would like to add your services to this list, please contact <a href="http://www.biocatalogue.org/contact">the BioCatalogue team</a>.</p>
-<h2 id="domain-and-shim-services">Domain and shim services</h2>
-<p>Services accessible from Taverna can be broadly categorised into domain services and shim services.</p>
-<ul>
-<li>Domain (scientific) services perform scientific function(s) and are often provided by third-party suppliers.
- They cannot usually be changed by individual users.</li>
-<li>Shim services are created during workflow design,
- to specifically connect the inputs and outputs of closely related services in order to achieve
- interoperation between domain services.
- This typically involves changing one serviceâs output into a different format for another service to accept. An example might include changing the output from tab to comma separated values. Taverna comes with a library of frequently used shim services. A new workflow, however, often brings about the need to develop a new shim or modify an existing one.</li>
-</ul>
-<p>A rule of thumb for distinguishing a domain service from a shim service is that a workflow,
- when the shims services are invisible, is equivalent to the methods section of a scientific paper.
-If a service needs to be explicitly mentioned in the method, then it is not a shim.</p>
-<h2 id="service-providers">Service providers</h2>
-<p>Nearly all services accessible by Taverna are neither owned nor provided by us.
-The majority of services are provided by third-party institutes and research facilities,
- all of which can be accessed from within Taverna.
-Taverna only provides most commonly used shim services, e.g. to concatenate strings, read content from a file,
- etc.</p>
-<p>Service suppliers can often be large government-funded bodies such as the <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> (United States),
- <a href="http://www.ebi.ac.uk/">EMBL-EBI</a> (Europe) or <a href="http://www.ddbj.nig.ac.jp/">DNA Databank of Japan</a>.
-Each is responsible in providing data to the global scientific community.
-These major providers generally have dedicated human resources for service development, API documentation,
- hosting and maintenance.
-In addition to programmatic access to their services these also maintain Web-form based access.</p>
-<p>A large proportion of suppliers of services and workflows are much smaller in scale â
- this includes individuals or small laboratories that have developed a tool, algorithm, database,
- or workflow that they wish to share with others.
-Developers of services from these small establishments may have limited knowledge on Web services and
- related standards when compared to their knowledge of programming/scripting.
-Such circumstances have required myGrid to develop tools like <a href="http://www.ebi.ac.uk/soaplab/">Soaplab</a> that help alleviate this limitation
- of small-scale providers by allowing simple deployment of the tool at hand.</p>
-<p>All these service providers are independent of, and usually ignorant of, their consumers.
-Thus, the suppliers and consumers in the open market are loosely coupled and asynchronous.
-Other services are private and local to the scientist (workflow designer),
- or developed specifically for a workflow to make it work.
-Creating a service accessible from Taverna</p>
-<p>If you are planning on creating a service that should be accessible from Taverna,
- please have a look at the documentation for Web service developers<a href="/documentation/web-service-developers">link text</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-features.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-features.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-features.html Wed Mar 11 08:37:10 2015
@@ -104,227 +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></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 href="/introduction">The Taverna suite of tools</a> are bringing together a range of features to make it easier for users to find, design and execute complex workflows and share them with other people.</p>
-<p>Freely available</p>
-<ul>
-<li>Java, open source, LPGL licensed (GPL for Astronomy versions)</li>
-</ul>
-<p>Suite of tools to design, edit and execute workflows</p>
-<ul>
-<li>Workflow design and execution in Taverna Workbench</li>
-<li>Command line execution of workflows</li>
-<li>Remote execution of workflows on a Taverna server</li>
-<li>Invoke workflows from the Internet</li>
-</ul>
-<p>Wide range of services and extensible architecture</p>
-<ul>
-<li>Service discovery</li>
-<li>Various service types available: WSDL-style and RESTful Web services, BioMart, BioMoby, SoapLab, R,
- Beanshell, Excel and csv spreadsheets</li>
-<li>Service creation for external tools or Java libraries</li>
-<li>Calling tools/scripts on a local machine or remote machines (via ssh)</li>
-<li>Extensible service plug-in architecture for adding new service types</li>
-<li><a href="#biocataloue-integration">Fully integrated support for browsing curated service catalogues</a>,
- such as the <a href="http://www.biocatalogue.org/">BioCatalogue</a>, for Web services (WSDL/SOAP and REST)</li>
-<li>Interaction with a running workflow within a web browser</li>
-<li>Ability to define and share semantically annotated components, and have them used as services in workflows</li>
-</ul>
-<p>Secure</p>
-<ul>
-<li>Support for secure services (HTTP authentication, WS-Security, X.509 client authentication)</li>
-<li>Secure management of usersâ credentials</li>
-</ul>
-<p>Versatile Workbench</p>
-<ul>
-<li>Tabs for finding, designing and executing workflows</li>
-<li>Fully graphical workflow design</li>
-<li>Drag and drop workflow components</li>
-<li>Comprehensive undo/redo</li>
-<li>Built-in help facility</li>
-<li>Annotations for describing workflows, services, inputs, outputs</li>
-<li>Workflow validation and debugging</li>
-</ul>
-<p>Create your own or start from existing workflows</p>
-<ul>
-<li>Easy design of new workflows</li>
-<li>Load existing workflows (from a disk, <a href="http://www.myexperiment.org/">myExperiment</a> or a URL)</li>
-<li>View workflow layout and logic</li>
-<li>Modify existing workflows</li>
-<li>Load workflows in off-line mode (when disconnected from the Internet)</li>
-<li>Nested workflows (sub workflows)</li>
-<li>Workflow validation during design time for debugging while composing a workflow</li>
-<li>Built-in detection when a serviceâs interface changes or a service go off-line during design time</li>
-</ul>
-<p>Find workflows created by others and share yours</p>
-<ul>
-<li><a href="#myexperiment-integration">Full myExperiment search options for browsing workflows</a></li>
-<li>Publish workflows on myExperiment for use by others</li>
-</ul>
-<p>Execute and debug your workflows</p>
-<ul>
-<li>Execute workflows</li>
-<li>Remember previously used workflow inputs</li>
-<li>Save workflow input values used to a file</li>
-<li>Load workflow input values from a file</li>
-<li>Pipelining and streaming of data</li>
-<li>Implicit iteration of service calls</li>
-<li>Conditional and repeated calling of services</li>
-<li>Customizable looping over a service</li>
-<li>Failover and retry of service calling</li>
-<li>Parallel execution and configurable number of concurrent threads</li>
-<li>Improved error handling and reporting for debugging during run time</li>
-<li>Monitor workflow execution</li>
-<li>Pause/resume or cancel workflow execution</li>
-<li>Manage previous runs and workflow results</li>
-<li>View intermediate results and debug workflows at run time</li>
-<li>Filter and save intermediate and final workflow results</li>
-</ul>
-<p>Track workflow runs and results</p>
-<ul>
-<li>Record workflow execution provenance</li>
-<li>Review provenance of previous workflow runs</li>
-<li>Experimental export of provenance in the <a href="http://openprovenance.org/">OPM</a> and Janus formats</li>
-</ul>
-<p>Support</p>
-<ul>
-<li>End user technical support and e-mail help desk</li>
-<li>Tutorials and workshops</li>
-</ul>
-<p><a name="myexperiment-integration"/></p>
-<h2 id="myexperiment-integration">myExperiment integration</h2>
-<p><a href="http://www.myexperiment.org/"><img src="/img/MyExperiment_logo_1672x320.png" alt="myExperiment" width="394" height="75" /></a></p>
-<p><a href="http://www.myexperiment.org/">myExperiment</a> is a social networking site and Virtual Research Environment (VRE) designed for people to share, discover and reuse workflows.</p>
-<p>myExperiment enables scientists to contribute to a pool of workflows that can be reused and repurposed by other scientists, promoting building of communities, forming of relationships and collaboration. In this way, myExperiment helps reduce time-to-experiment, share expertise and avoid reinvention.</p>
-<p>It is widely used, as demonstrated by their being 8820 members in 304 groups. Its actual take up shows that there are 2415 workflows, consisting of 604 files. The number of packs (research objects) currently in use stands at 229.</p>
-<h3 id="find-myexperiment-workflows-by-others-and-share-yours-from-taverna">Find myExperiment workflows by others and share yours from Taverna</h3>
-<p>As of version 2.1, Taverna has a built-in support for myExperiment,
-enabling users to browse myExperiment Web site from inside the Taverna Workbench.</p>
-<p>Users can access the full myExperiment search options for browsing workflows,
-load existing workflows from myExperiment or publish their workflows on myExperiment for use by others.</p>
-<p>A snapshot of the myExperiment Perspective in Taverna can be seen in the image below.</p>
-<p><img src="/img/myExperimentPerspective.png" alt="myExperiment plugin for Taverna screenshot" width="100%"/></p>
-<p><a name ="biocataloue-integration"/></p>
-<h2 id="biocatalogue-integration">BioCatalogue integration</h2>
-<p><a href="http://www.biocatalogue.org/"><img src="/img/biocatalogue_without_text.png" alt="BioCatalogue" width="488" height="97" /></a></p>
-<p>BioCatalogue is a public, centralised, curated and monitored registry of Life Science Web services which can be used for building workflows. It is a community-oriented Web site where service providers or community experts can register and curate services and users can discover them.</p>
-<p><a href="http://www.biocatalogue.org/">BioCatalogue</a> provides a single point where services can be annotated and curated by service providers or community experts â it helps service providers publicize and make their services more visible to the community and makes it easier for users to find them.</p>
-<p>Web services can be volatile â they change over time and get outdated.
-BioCatalogue monitors services periodically and provides statistics on their availability and reliability.
-Discover and reuse services in BioCatalogue from Taverna</p>
-<p>Taverna has a built-in support for searching service catalogues, such as the BioCatalogue.
-It enables users to browse a service catalogue and access its full search options for browsing services and checking their status and availability from inside the Workbench. Discovered services can then be added either directly to workflows or the Taverna Workbenchâs Service Panel.</p>
-<p>The <a href="/documentation/glossary#service_panel">service catalogue</a> accessed by Taverna is configurable,
-so you can set it to a different instance of âBioCatalogueâ, such as <a href="https://www.biodiversitycatalogue.org/">BiodiversityCatalogue</a>.</p>
-<p>A snapshot of the Service Catalogue Perspective in Taverna can be seen in the image below.</p>
-<p><img title="BioCatalogue plugin for Taverna" src="/img/BioCataloguePerspective.png" alt="BioCatalogue plugin for Taverna screenshot" width="100%" /></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/annotation.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html Wed Mar 11 08:37:10 2015
@@ -104,177 +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>Annotations</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna is used by various tools and projects for the association of metadata with data (annotation).
-These include:
- - <a href="#afawe">Automatic Functional Annotation in a distributed Web service Environment</a>(AFAWE) -
- annotation of plant genes with their functionality
- - <a href="#annotation-of-genomes">Interactive genome annotation pipeline</a></a> - automatic and manual annotation of genes
- - <a href="#taweka">TaWeka</a> - associating biological data with calculated functionality</p>
-<p>In addition, Taverna makes use of the semantic annotation that has been specified for the services provided by
- the <a href="#adoption-by-moby">MOBY consortium</a>.</p>
-<p>Taverna has also been used for the identification of mismatches and possible annotations in workflows by the
- <a href="/introduction/related-projects#ispider">iSPIDER</a> project.</p>
-<p><a name="afawe"></a></p>
-<h2 id="afawe">AFAWE</h2>
-<p>The <a href="http://www.mpiz-koeln.mpg.de/2169/en">Max Planck Institute for Plant Breeding Research</a> in Cologne, Germany have developed the
- Automatic Functional Annotation in a distributed Web Service Environment (<a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/">AFAWE</a>).
-AFAWE is a tool for the automatic functional annotation of new genes in plants and other organisms.
-The annotation involves the running of several Web services, and also the execution of a Taverna <a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/help/Tools.html#SIFTER">workflow</a>.</p>
-<p>The annotation workflow is <a href="http://www.myexperiment.org/workflows/95">available</a> on <a href="http://www.myexperiment.org/">myExperiment</a>.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a href="http://dx.doi.org/10.1093/bioinformatics/btn394">paper</a> <em>Protein function prediction and annotation in an integrated environment powered by web services
- (AFAWE)</em> by Joecker et al describes the concepts and implementation of AFAWE.</p>
-<p><a name="annotation-of-genomes"></a></p>
-<h2 id="annotation-of-genomes">Annotation of genomes</h2>
-<p>A collaboration between Tom Oinn from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
- Pal Puntervoll from the <a href="http://www.uib.no/en">University of Bergen</a>, Norway, has produced an interactive genome annotation
- pipeline.</p>
-<p>Sequencing, characterising and annotating a genome are the first steps to understanding its function.
-Important stages in this include gene prediction, comparative genomics and function prediction of genes and
- gene products.
-With workflows all of these stages can be automate, requiring little human interaction.
-However, manual inspection can be required at certain points in the process.</p>
-<h3 id="publications_1">Publications</h3>
-<p><a href="http://scholar.google.co.uk/scholar?q=Taverna+for+genome+annotation">Articles and papers</a>
- about the success of Taverna for genome annotation are available on-line.</p>
-<p><a name="taweka"></a></p>
-<h2 id="taweka">TaWeka</h2>
-<p><a href="http://homepages.inf.ed.ac.uk/ldeferra/">Luna De Ferrari</a> from the Computational Systems Biology &
- <a href="http://www.bioinformatics.ed.ac.uk/">Bioinformatics group at the University of Edinburgh</a> has developed <a href="http://mook.inf.ed.ac.uk/twiki/bin/view.cgi/PublicCSB/TaWeka">TaWeka</a>,</p>
-<blockquote>
-<p>a rapid prototyping tool for biological classifiers.</p>
-</blockquote>
-<p>TaWeka uses Taverna workflows to store data retrieved from webservices, e.g. queries of biological data,
- into a database.
-<a href="http://www.cs.waikato.ac.nz/ml/weka/">Weka</a> is then used to run machine learning experiments on the data in order to evaluate and improve
- biological classification functions.</p>
-<h3 id="publications_2">Publications</h3>
-<p>A poster <a href="http://mook.inf.ed.ac.uk/twiki/pub/PublicCSB/TaWekaPosters/colourA4_16.pdf"><em>TaWeka: from biological web services to data mining</em></a> by De Ferrara and Goryanin describes the
- purpose and implementation of TaWeka.</p>
-<p><a name="adoption-by-moby"></a></p>
-<h2 id="adoption-by-the-moby-consortium">Adoption by the Moby consortium</h2>
-<p>The <a href="http://biomoby.open-bio.org/">Moby</a> project develops a system for interoperability between biological data hosts and
- analytical services.
-Their relationship with Taverna is multiple:</p>
-<ul>
-<li>The Moby team actively collaborate with myGrid in the development of the ontologies used to describe their
- services.
- Service descriptions are then used by Taverna to find services to use in workflows.</li>
-<li>The services published on Moby are a large proportion of the services often used in Taverna workflows</li>
-<li>People wishing to combine Moby services commonly use Taverna Workbench as a platform</li>
-<li>Specific support for Moby services is available within Taverna.</li>
-</ul>
-<h3 id="publications_3">Publications</h3>
-<p>The <a href="http://dx.doi.org/10.1093/bib/bbn003">paper</a> <em>Interoperability with Moby 1.0âItâs better than sharing your toothbrush!</em> by the
- Moby consortium gives an overview of Moby and their activities.</p></div>
-
- </div>
-
- <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/arts.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html Wed Mar 11 08:37:10 2015
@@ -104,145 +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></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>Title Arts
-Notice: Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
- .
- http://www.apache.org/licenses/LICENSE-2.0
- .
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.</p>
-<p>Taverna has been used for the <a href="#composition-of-music">composition of music</a> using Web services for synthesis.</p>
-<p><a name="composition-of-music"></a></p>
-<h2 id="composition-of-music">Composition of music</h2>
-<p><a href="http://en.wikipedia.org/wiki/John_ffitch">John Ffitch</a> and others at the University of Bath have developed a service-oriented composition environment
- for music.
-The environment consists of three main components:
- - A suite of synthesis Web services that incorporate a selection of the basic atomic components required for
- sound creation and processing</li>
- - A tool that gives a description of music in terms of the construction of the instruments
- (parameters, connections) and the score they will play on>
- - An âenvironment of useâ that allows the connection and enactment of the synthesis services</p>
-<p>Both <a href="http://www.trianacode.org/">Triana</a> and Taverna have been tested as the environment of use.</p>
-<h3 id="publications">Publications</h3>
-<p>This work is described in the <a href="http://opus.bath.ac.uk/5290/">paper</a> <em>Composition with Sound Web Services and Workflows</em> by Ffitch et al</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/astronomy.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html Wed Mar 11 08:37:10 2015
@@ -104,145 +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>Astronomy</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 and <a href="http://www.myexperiment.org">myExperiment</a> are being used for astronomy research by several projects:</p>
-<ul>
-<li><a href="#astrogrid">AstroGrid</a> - plugin to allow AstroGrid utilities within Taverna 1.x</li>
-<li><a href="/introduction/related-projects#helio">HELIO</a> - workflows including heliophysical services</li>
-<li><a href="#sampo">SAMPO</a> - development of a workflow system based upon Taverna</li>
-</ul>
-<p><a name="astrogrid"></a></p>
-<h2 id="astrogrid">AstroGrid</h2>
-<p>The UKâs <a href="http://www.astrogrid.org/">AstroGrid</a> is a ~£14M (over the period 2001-2009) project aimed at building a data-grid for UK
- astronomy, which will form the UK contribution to a global VirtualObservatory.</p></p>
-<p>A <a href="http://wiki.astrogrid.org/bin/view/Astrogrid/VoWorkflowsWithTaverna">Taverna 1.x processor</a> has been written to enable client-site AstroGrid utilities to be included within
- Taverna workflows.</p>
-<h3 id="publications">Publications</h3>
-<p>A book chapter "AstroGrid and the Virtual Observatory", Walton, N. A., Gonzalez-Solareson, E., Springer,
- Lecture Notes in Physic, vol. 791, pp. 81-113, 2009. <br />
-<a href="http://www.springerlink.com/content/yk36404544k778g8">http://www.springerlink.com/content/yk36404544k778g8</a></p>
-<p>AstroGrid: Taverna in the Virtual Observatory, Benson, K. M., Walton, N. A., Memorie della Società Astronomica
- Italiana, vol. 80, p.574, 2009 <br />
-<a href="http://adsabs.harvard.edu/abs/2009MmSAI..80..574B">http://adsabs.harvard.edu/abs/2009MmSAI..80..574B</a></p>
-<p>Taverna and Workflows in the Virtual Observatory, Walton, N. A.; Witherwick, D. K.; Oinn, T.; Benson, K. M.,
- Proceedings of the Astronomical Data Analysis Software and Systems ASP Conference Series, London, UK.
-Edited by Robert W. Argyle, Peter S. Bunclark, and James R. Lewis., p.309, 2008. <br />
-<a href="http://adsabs.harvard.edu/abs/2008ASPC..394..309W">http://adsabs.harvard.edu/abs/2008ASPC..394..309W</a></p>
-<p><a name="sampo"></a></p>
-<h2 id="sampo">SAMPO</h2>
-<p>The SAMPO <a href="http://www.eso.org/sci/data-processing/software/sampo/">project</a> was part of the ongoing Finnish contribution to the <a href="http://www.eso.org/">European Southern Observatory</a>.</p>
-<p>Based upon Taverna, the SAMPO project developed the Recipe Flexible Execution workflow system <a href="http://www.eso.org/sci/data-processing/software/sampo/reflex/">ESO Reflex</a>.
-ESO Refex allows users to connect together C programs that reduce the raw data produced by ESO instruments.</p>
-<h3 id="publications_1">Publications</h3>
-<p>The <a href="http://www.springerlink.com/content/p67480k2w7311315/">paper</a> <em>ESO Reflex: A Graphical Workflow Engine for Running Recipes</em> by Hook et al, describes the
- ESO Reflex 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/biodiversity.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html Wed Mar 11 08:37:10 2015
@@ -104,116 +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>Biodiversity</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 href="/introduction/related-projects#biovel">BioVel</a> - establishing an international e-Laboratory to allow biodiversity scientists to jointly tackle
- diverse research challenges using Taverna, myExperiment and BioCatalogue</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/bioinformatics.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html (original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html Wed Mar 11 08:37:10 2015
@@ -104,220 +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>Bioinformatics</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link" href="http://www.taverna.org.uk/">taverna2</a> material that is expected to become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna can connect to a wide variety of bioinformatics resources and has been successfully applied to a number
- of bioinformatics problems, listed below according to their sub-domains.
-<img class="aligncenter"
- title="Bioinformatics services and resources"
- src="/img/BioinformaticsResources.png"
- alt="Bioinformatics services and resources" width="676" height="441" /></p>
-<p>Bioinformatics systems/tools using Taverna:</p>
-<ul>
-<li><a href="#biowep">BioWEP</a> - bioinformatics workflow enactment portal</li>
-<li><a href="#biolinux">BioLinux</a> - Ubuntu Linux distribution that includes Taverna and many other bioinformatics programs</li>
-</ul>
-<h3 id="biodiversity">Biodiversity</h3>
-<ul>
-<li><a href="/introduction/related-projects#biovel">BioVeL</a></li>
-</ul>
-<h3 id="gene-and-genome-expression">Gene and genome expression</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#next-generation-sequencing">Next Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#tavernapbs">TavernaPBS</a> - next generation sequencing analysis using a computational cluster that uses a PBS
- queuing system and Taverna 2 Workbench</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#casimir">Coordination and Sustainability of International Mouse Informatics Resources</a> (CASIMIR) -
- workflows to associate mouse genome and phenome</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#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">Examination of gene expression from MicroArray data using R</a> - statistical analysis of gene expression</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression#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/biology#planet">PLANET</a> - integration of plant genome resources</li>
-<li><a href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Annotation of genomes</a></a></li>
-<li><a href="/introduction/related-projects#shared-genomics">Shared Genomics</a></a></li>
-<li><a href="http://img.cs.man.ac.uk/efungi/">e-Fungi</a> functional genomics in fungal species</li>
-</ul>
-<h3 id="protein-and-proteomics">Protein and proteomics</h3>
-<ul>
-<li><a href="#lumc">Analysis of mass spectrometry data in proteomics</a></li>
-<li><a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Anthrax analysis</a> - identification of proteins secreted by bacteria</li>
-<li><a href="/introduction/taverna-in-use/databases#efamily">eFamily</a> - integrating data from different databases</li>
-<li><a href="http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace">European Model for Bioinformatics Research And Community Education</a> (EMBRACE) -
- calling services on a grid; recovering a database</li>
-<li><a href="/introduction/related-projects#ispider">iSpider</a> - querying multiple data sources</li>
-<li><a href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a> - running of Taverna workflows behind a portal to search a protein database</li>
-</ul>
-<h3 id="biology-and-systems-biology">Biology and systems biology</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/biology#enfin">ENFIN</a> â Enabling Systems Biology â calling of wrapped tools within workflows</li>
-<li><a href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a> (MCISB) â modelling metabolomic pathways</li>
-<li><a href="/introduction/taverna-in-use/biology#sb-os">Systems Biology Operational Software</a> (SB.OS) - a live DVD based on Ubuntu Linux that comes with a
- comprehensive list of Systems Biology Software (including Taverna)</li>
-<li><a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a> - Taverna workflows for systems biology,
- in particular for analysis of the kinetic models of biological systems</li>
-<li><a href="#measuring-enzyme-characteristics-of-yeast">Measuring of enzyme characteristics of yeast</a></li>
-<li><a href="/introduction/taverna-in-use/annotation.html#afawe">Automatic Functional Annotation in a distributed Web Service Environment</a> (AFAWE) â
- protein prediction and annotation by a tool that calls workflows</li>
-<li><a href="/introduction/taverna-in-use/biology#planet">PLANET (A Network of European Plant Databases)</a> â calling of workflows from a portal</li>
-</ul>
-<h3 id="biomedicine-and-disease-related-research">Biomedicine and disease-related research</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/disease-research#vph-dareit">Fighting dementia</a> (VP-DARE@IT and VPH-SHARE)</li>
-<li><a href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Analysis of the anthrax bacterium</a></li>
-<li><a href="/introduction/taverna-in-use#trypanosomiasis">Study of resistance into trypanosomiasis</a> (sleeping sickness)</li>
-<li><a href="/introduction/taverna-in-use/disease-research#graves-disease">Identification of genes linked to Graves disease</a></li>
-<li><a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Characterisation of genes associated with Williams-Beuren syndrome</a></li>
-<li><a href="/introduction/related-projects#cagrid">caGrid</a> - research into predicting limphoma cancer</li>
-<li><a href="/introduction/taverna-in-use/medicine#eu-adr">EU-ADR</a> - detecting adverse drug reactions through the exploitation of clinical data from electronic
- healthcare records</li>
-</ul>
-<p><a name="biowep"></a></p>
-<h3 id="biowep">BioWEP</h3>
-<p>Researchers at the Italian National Institute for Cancer Research Genoa (<a href="http://www.istge.it/">IST</a>) have developed a
- Bioinformatics Workflow Enactment Portal called <a href="http://bioinformatics.istge.it/biowep/index.html">BioWEP</a>.</p>
-<p>The <a href="http://bioinformatics.istge.it:8080/biowep/">portal</a> allows registered users to search for or select from a set of specified Taverna workflows.
-The workflow can be enacted by entering input values into a form.
-During enaction, the user can either wait for the result, or for longer running workflows,
- visit the portal later. The results of the enactment can be downloaded for external visualization.</p>
-<h4 id="publications">Publications</h4>
-<p>The http://dx.doi.org/10.1186/1471-2105-8-S1-S19 <em>Biowep: a workflow enactment portal for bioinformatics
- applications</em> by Romano et al gives an overview of the intent and design of Biowep.</p>
-<p><a naem="biolinux"></a></p>
-<h3 id="biolinux">BioLinux</h3>
-<p>The UKâs Natural Environment Research Council (NERC) Environmental Bioinformatics <a href="http://nebc.nox.ac.uk/">Centre</a> release
- <a href="http://nebc.nox.ac.uk/biolinux.html">BioLinux</a>, an installation of Ubuntu Linux that includes many bioinformatics programs.</p>
-<p>Among the programs included in the BioLinux distribution is Taverna.<br />
-The suite of programs are also available for installation on pre-existing Linux systems.</p>
-<p><a name="lumc"></a></p>
-<h3 id="lumc">LUMC</h3>
-<p>People from the Leiden University Medical Center (<a href="https://www.lumc.nl/">LUMC</a> in the Netherlands are using Taverna for analysis
- of mass spectrometry data in proteomics.</p>
-<p>They presented a <a href="http://www.taverna.org.uk/pages/wp-content/uploads/2011/06/Palmblad_ASMS_2011_LUMC.pdf">poster</a> at the 2011 ASMS (the American Society for Mass Spectrometry) Conference on
- Mass Spectrometry and Allied Topics.</p>
-<p>Please contact <a href="https://www.lumc.nl/org/proteomics-metabolomics/medewerkers/nmpalmblad">Dr. Magnus Palmblad</a> for more details.</p>
-<p><a name="measuring-enzyme-characteristics-of-yeast"></a></p>
-<h3 id="measuring-enzyme-characteristics-of-yeast">Measuring enzyme characteristics of yeast</h3>
-<p>The <a href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">Manchester Centre for Integrative Systems Biology</a> (MCISB) is in the process of measuring the
- kinetic and binding constants associated with enzyme reactions in metabolic pathways in the yeast,
- Saccharomyces cerevisiae.
-Quantitative models of these metabolic pathways are being integrated with transcriptomic, proteomic and
- metabolomic data by workflows that have been constructed and enacted using Taverna.</p>
-<h4 id="publications_1">Publications</h4>
-<p>A <a href="http://www.mygrid.org.uk/files/2008/09/peter-li-poster.pdf">poster</a> by Peter Li describing the systems biology workflows was presented at the International
- Conference of Systems Biology 2006 and he has written several publications about the work.</p>
-<p>Many of the workflows make use of Systems Biology Markup Language (<a href="http://sbml.org/">SBML</a>) as described in the
- <a href="http://bioinformatics.oxfordjournals.org/content/24/2/287.full.pdf">paper</a>
- <em>Automated manipulation of systems biology models using libSBML within Taverna workflows</em>
- by Li et al.</p>
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