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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 [2/10] - 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/dataviewer-tool/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/dataviewer-tool/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/dataviewer-tool/index.html Wed Mar 11 08:37:10 2015
@@ -104,140 +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>DataViewer Tool</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>DataViewer Tool is a utility for viewing Baclava data files.
-Baclava is an XML format used to save workflow inputs and/or outputs from the
- <a href="/documentation">Workbench</a> or <a href="/documentation/command-line-tool">Command Line Tool</a> for later
- re-use or inspection.
-It is useful for saving all workflow inputs or outputs in a single file but is not really meant
- for reading by humans as the data inside is Base64-encoded.</p>
-<p>DataViewer Tool comes in the form of a command prompt script called <em>dataviewer</em>.
-In Taverna 1.x, the script used to be bundled together with the Workbench.
-It has now been updated to use the Taverna 2 codebase and is available as a
- <a href="http://www.taverna.org.uk/download/associated-tools/dataviewer-tool/">separate download</a>.
-The functionality of the tool remained (almost) the same as in the previous 1.x version.
-Check out the a
- <a href="http://www.taverna.org.uk/download/associated-tools/dataviewer-tool/release-notes/">release notes</a>
-for the minor changes in the latest version.</p>
-<h2 id="creating-baclava-files">Creating Baclava files</h2>
-<p>From the Workbench, you can save the inputs you have specified for a workflow to a Baclava file
- from the <em>Run Dialog</em> (which is used to launch a workflow).
-From the same dialog you can also load inputs from a previously saved Baclava file so you do
- not have to specify them manually.</p>
-<p>From the <em>Results Perspective</em> of the Workbench you can save workflow inputs and outputs,
- once workflow has finished executing and results become available.
-You have the option to select input and output ports which you want to include in the saved
- Baclava file.</p>
-<p><a href="/documentation/command-line-tool">Command Line Tool</a> can load workflow inputs from a Baclava
- data file using the <code>-inputdoc</code> option and save the workflow results in a Baclava
- data file using the <code>-outputdoc</code>option.</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/example-workflows/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/example-workflows/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/example-workflows/index.html Wed Mar 11 08:37:10 2015
@@ -104,124 +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>Example workflows</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>Example workflows to get you started with Taverna are available from the
- <em>myExperiment Perspective</em> in the Taverna Workbench, by selecting the âStarter Packâ tab.</p>
-<p>They can also be downloaded from <a href="http://myexperiment.org/">myExperiment</a>.
-Additional workflows from other users can be found by browsing myExperiment.</p>
-<ul>
-<li><a href="http://www.myexperiment.org/packs/612.html">Taverna 2.5 Starter Pack</a></li>
-<li><a href="http://www.myexperiment.org/packs/254.html">Taverna 2.4 Starter Pack</a></li>
-<li><a href="http://www.myexperiment.org/packs/192.html">Taverna 2.3 Starter Pack</a></li>
-<li><a href="http://www.myexperiment.org/packs/122.html">Taverna 2.2 Starter Pack</a></li>
-</ul></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/glossary/index.html
==============================================================================
Binary files - no diff available.
Modified: websites/staging/taverna/trunk/content/documentation/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/index.html Wed Mar 11 08:37:10 2015
@@ -104,156 +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 Documentation</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 Workbench is a redesign of the Taverna Workbench 1.7.x series from the ground up.
-It has a greater emphasis on scalability to enable the manipulation of larger and more diverse data.</p>
-<p>In addition to the improvements to the engine, Taverna Workbench provides more support for workflow design
- with a graphical workflow editor for direct manipulation of the workflow diagram,
- context-specific views over Web services and other resources,
- and standard editing facilities such as copy/paste and undo/redo.</p>
-<p>For a list of our plans on adding new features to Taverna, please see the
- <a href="/introduction/roadmap">Taverna Roadmap</a>.</p>
-<p>A list of available documentation for Taverna includes:</p>
-<ul>
-<li><a href="/documentation/glossary">Glossary</a> of terms</li>
-<li><a href="/documentation/quick-start-guide">Quick start guide</a></li>
-<li><a href="http://dev.mygrid.org.uk/wiki/display/tav250/Frequently+Asked+Questions">FAQ</a> (None Apache Wiki)</li>
-<li><a href="http://www.mygrid.org.uk/dev/wiki/display/taverna/User+Manual">User Manual</a> (None Apache Wiki)</li>
-<li><a href="/documentation/components">Components</a> (Since Taverna 2.5)</li>
-<li><a href="/documentation/interaction">Interaction Service</a> (Since Taverna 2.5)</li>
-<li><a href="/documentation/tutorials">Tutorials</a></li>
-<li><a href="/documentation/videos">Videos</a></li>
-<li><a href="/documentation/example-workflows">Example workflows</a> to help you get started with Taverna </li>
-<li><a href="/documentation/service-sets">Service sets</a> for various domains</li>
-<li><a href="http://www.slideshare.net/khettne/10-best-practices-for-workflow-design">10 Best practices for workflow design</a> (slides)</li>
-<li>paper: <a href="http://ceur-ws.org/Vol-952/paper_23.pdf">Best practices for workflow design: how to prevent workflow decay</a></li>
-<li><a href="/documentation/provenance">Provenance management</a> in Taverna</li>
-<li>Taverna <a href="/documentation/command-line-tool">Command Line Tool</a> and how to use it</li>
-<li>Taverna <a href="/documentation/server">Server</a> (REST API, SOAP API explained) and how to use it</li>
-<li><a href="/documentation/taverna-player">Taverna Player</a></li>
-<li>Various <a href="/documentation/plugins">plugins</a> for Taverna</li>
-<li><a href="http://www.mygrid.org.uk/dev/wiki/display/developer/Home">None Apache Developersâ wiki</a>
- containing the
- <a href="http://www.mygrid.org.uk/dev/wiki/display/developer/Developers+Guide">Developersâ guide</a> and more</li>
-</ul>
-<p><a name="tools"></a></p>
-<h2 id="tool-and-services">Tool and Services</h2>
-<p>There are a number of None Apache tools and services available to use with Taverna.</p>
-<ul>
-<li><a href="/documentation/components/component-profile-editor">Component profile editor</a></li>
-<li><a href="/documentation/components/component-validator">Component validator</a></li>
-<li><a href="/documentation/dataviewer-tool">DataViewer Tool</a> for viewing result data</li>
-<li><a href="/documentation/api-consumer-tool/">API Consumer Tool</a></li>
-<li><a href="/documentation/taverna-galaxy/">Taverna Galaxy</a></li>
-<li><a href="/documentation/online">Taverna Online</a></li>
-</ul></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/interaction/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/interaction/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/interaction/index.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>Interactions</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="interacting-with-a-workflow-in-your-browser">Interacting with a workflow in your browser</h2>
-<p>Many workflows, when run, require interaction with a user.
-This can be to enter data values, confirm that intermediate results are OK to proceed with the
- run, or to control the functionality of a service.
-When running a workflow in <a href="/download/workbench">Taverna Workbench</a> you can use beanshells
- to show Java swing components; Taverna Workbench includes a set of pre-defined beanshells to,
- for example, <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Ask">Ask</a> the user for data.</p>
-<p>If you run your workflow in a portal or on a <a href="/download/server">server</a>, then using beanshells
- for interaction will not work â attempts to use Swing will either fail or, worse,
- open dialogs on the machine where the workflow is running.</p>
-<p>To support interaction with workflows running on a server, the <a href="http://www.biovel.eu">BioVeL</a>
- project developed a new
- <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Interaction+service">interaction service</a>.
-The interaction service allows users to interact with a running workflow within a standard web
- browser.
-The interaction can be as simple as acknowledging a message,
- or as complex as controlling a tool running on a remote machine.
-The interaction can be parameterized by data from the workflow and can return data from the
- browser to the workflow.</p>
-<iframe src="http://www.youtube.com/embed/S9X6E4PdFcM?start=60" frameborder="0"
- width="420" height="315"></iframe>
-
-<p>Interactions have already been used for many purposes. These include:</p>
-<ul>
-<li>to manipulate data inside <a href="http://openrefine.org/">Open Refine</a> (previously Google Refine),</li>
-<li>to show information on maps and</li>
-<li>to show the results of species population modelling</li>
-</ul>
-<h2 id="notification-of-interaction-requests">Notification of interaction requests</h2>
-<p>One of the advantages of running workflows on a server is that you do not need to monitor them
- constantly.
-However, you then need a way to be alerted that a workflow requires an interaction.
-The interaction service uses <a href="http://en.wikipedia.org/wiki/Atom_(standard)">ATOM</a> feeds to send
- out notifications.
-ATOM feeds can be read by many different clients, including mobile phone Apps and mail readers.
-The ATOM message will include a link to the HTML page for the interaction required.</p>
-<h2 id="usage-scenarios">Usage scenarios</h2>
-<p>The interaction service combines standard protocols such as ATOM and HTML.
-As a result there are many ways in which users can interact with their workflow run.</p>
-<h3 id="on-your-phone">On your phone</h3>
-<p>Most modern mobile/cell phones support web browsers and also ATOM feed Apps.
-If you subscribe to the ATOM feed for a workflow run,
- then you can open the HTML page in the phone's browser, interact with the workflow run,
- and then go back to whatever you were doing.</p>
-<p>This has been demonstrated for simple interactions; complex interactions can be limited a
- phone's screen resolution.</p></p>
-<h3 id="inside-another-web-page">Inside another web page</h3>
-<p>It is common to use a web page to run workflows on a server.
-This could be, for example, within a
- <a href="/documentation/taverna-player">Taverna Player</a>,
- or a more complex portal such as the Taverna 2.4 Server Demonstrator.
-When a workflow is run, the page creates a subscription to the run&'s ATOM feed.
-When a notification is sent on the feed, the page can then show the interaction.
-An example of this is demonstrated in this video.</p>
-<h3 id="in-the-workbench">In the workbench</h3>
-<p>The Taverna Workbench is also able to run interaction services.
-When a notification is sent, it opens up the HTML page in your preferred browser.
-You can choose to use <a title="Jetty" href="http://www.eclipse.org/jetty/">Jetty</a> to handle the feed and hosting of pages, or an external site.</p></p>
-<h2>Installing the interaction service</h2>
-
-<p>The interaction service is an official plugin for the workbench. Installation instructions can be found in the <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Finding+plugins">user manual</a>.</p>
-
-<p>A version of the Taverna Server including the interaction service is available. For details about access, please contact <a href="mailto:support@mygrid.org.uk">support@mygrid.org.uk</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/online.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/online.html (original)
+++ websites/staging/taverna/trunk/content/documentation/online.html Wed Mar 11 08:37:10 2015
@@ -104,123 +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 Online</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 Institute for Information Transmission Problems of Russian Academy of Sciences
- (<a href="http://www.iitp.ru/en/about">IITP</a>) in Moscow, Russia are developing a Web application called
- <a href="http://onlinehpc.com/">Taverna Online</a> to allow the creation and running of Taverna workflows from a Web browser.</p>
-<p>Try <a href="http://onlinehpc.com/">Taverna Online</a> out!</p>
-<p>The workflows are created using the <a href="http://www.jgraph.com/mxgraph.html">mxgraph</a>
- Javascript library and are run on a <a href="/documentation/server">Taverna Server</a>.</p>
-<p>You can view a QuickTime
- <a href="http://www.taverna.org.uk/pages/wp-content/uploads/2013/04/demo-metagenomics-merged.mp4">movie</a>
- showing the current state of Taverna Online.</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/plugins/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/plugins/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/plugins/index.html Wed Mar 11 08:37:10 2015
@@ -104,411 +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>Plugins</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 design of Taverna is modular in nature so that various plugins can be added in order to
- increase its functionality.
-In Taverna 2, plugins are specific to versions of Taverna.
-We are hoping to change this in future, when we move to the <a href="http://www.osgi.org/">OSGi</a>
- platform (see our <a href="/introduction/roadmap">Roadmap</a> for details).</p>
-<p>There are several different things that can be plugged into Taverna.
-Of most interest are plugins that enable search and invocation of a specific service type from
- worflows (e.g. a Web service plugin that enables adding a Web service based on its
- WSDL description document and invoking it from a workflow).</p>
-<h2 id="installing-plugins">Installing plugins</h2>
-<p>To install a plugin for Taverna, use the <em>Plugin Manager</em> - it can be found under
- <em>Updates and plugins</em> from the <em>Advanced</em> menu.
-If your plugin is not visible, select âFind New Pluginsâ.
-You may need to add the plugin site using âAdd Plugin Siteâ for specific plugins.
-Check the box for the plugin and click install.
-You may need to restart Taverna for the plugin to become visible and fully functional.</p>
-<h2 id="available-plugins">Available plugins</h2>
-<p>Various plugins for Taverna 2 have been developed by us or by third parties in collaboration
- with the Taverna team:</p>
-<ul>
-<li><a href="#astrotaverna">AstroTaverna</a> plugin</li>
-<li><a href="#oauth">OAuth</a> plugin</li>
-<li><a href="#taverna-prov">Taverna PROV</a> plugin</li>
-<li><a href="#vamdc">VAMDC</a> plugin</li>
-<li><a href="#bifi">BIFI</a> plugin</li>
-<li><a href="#vphshare">VPH-Share</a> plugin</li>
-<li><a href="#interaction">Interaction</a> plugin</li>
-<li><a href="#xpath">XPath</a> plugin</li>
-<li><a href="#rest">REST</a> plugin</li>
-<li><a href="#biocatalogue_plugin">BioCatalogue</a> plugin</li>
-<li><a href="#pbs">PBS</a> plugin</li>
-<li><a href="#sadi_plugin">SADI</a> plugin</li>
-<li><a href="#usecase_plugin">External Tools</a> (UseCase) plugin</li>
-<li><a href="#unicore">UNICORE plugin</a></li>
-<li><a href="#cdk">CDK</a> plugin</li>
-<li><a href="#cagrid_plugin">caGrid</a> plugin</li>
-<li><a href="#xws">XWS plugin</a></li>
-<li><a href="#glite">gLite plugin</a></li>
-</ul>
-<p><a name="astrotaverna"></a></p>
-<h3 id="astrotaverna-plugin">AstroTaverna plugin</h3>
-<p><em>Available for Taverna 2.4, 2.5, included in
- <a href="http://www.taverna.org.uk/download/workbench/2-5/astronomy/">Taverna Workbench Astronomy 2.5</a></em>.</p>
-<p><a href="http://amiga.iaa.es/p/290-astrotaverna.htm">AstroTaverna</a> is a plugin that enables the
- building of astronomy workflows using <a href="http://www.ivoa.net/">Virtual Observatory</a> services
- discovery and efficient manipulation of
- <a href="http://www.ivoa.net/documents/VOTable/">VOTable</a>s .
-It integrates <a href="http://www.ivoa.net/documents/SAMP/">SAMP</a> - enabled software,
- allowing data exchange and communication among local VO tools,
- as well as the ability to execute <a href="http://aladin.u-strasbg.fr/">Aladin</a> scripts and macros.
-AstroTaverna was developed by the <a href="http://www.wf4ever-project.org/">Wf4Ever</a> and
- <a href="http://amiga.iaa.es/p/294-open-science-canube.htm">CANUBE</a> projects by
- <a href="http://amiga.iaa.es/">IAA Amiga</a> group and the <a href="http://www.mygrid.org.uk/">myGrid group</a>
- at University of Manchester.</p>
-<p><a name="oauth"></a></p>
-<h3 id="oauth-plugin">OAuth plugin</h3>
-<p><em>Available for Taverna 2.4 and 2.5.</em></p>
-<p>The OAuth <a href="http://dev.mygrid.org.uk/wiki/display/taverna/OAuth+services">plugin</a> allows users
- to call REST services that are protected by <a href="http://oauth.net/">OAuth</a>.
-It was developed by Mark Borkum of the University of Southampton.</p>
-<p><a name="taverna-prov"></a></p>
-<h3 id="taverna-prov-plugin">Taverna PROV plugin</h3>
-<p><em>Available for Taverna 2.4. Integrated in Taverna 2.5.</em></p>
-<p>The <a href="http://www.wf4ever-project.org/">Wf4Ever project</a> further developed the
- <a href="/documentation/provenance">provenance support</a> in Taverna to export
- <a href="http://www.w3.org/TR/prov-o/">W3C PROV-O</a> compliant provenance traces. </p>
-<p>The plugin is part of Taverna since 2.5. <a href="https://github.com/taverna/taverna-prov">Description and source code</a> are at GitHub.</p></p>
-<p><a name="vamdc"></a></p>
-<h3 id="vamdc-plugin">VAMDC plugin</h3>
-<p><em>Available for Taverna 2.2, 2.3, 2.4. Included in
- <a href="http://www.taverna.org.uk/download/workbench/2-5/astronomy/">Taverna Workbench Astronomy 2.5</a></em>.</p>
-<p>The <a href="http://www.vamdc.eu/">VAMDC</a> has created
- <a href="http://voparis-twiki.obspm.fr/twiki/bin/view/VAMDC/TavernaUserGuide">integrated plugins</a>
- for Taverna Workflow to run XSAMS Queries, and specific VAMDC Codes.
-Since Taverna 2.5 the VAMDC plugin is part of the
- [Astronomy edition]((http://www.taverna.org.uk/download/workbench/2-5/astronomy/).</p>
-<p><a name="bifi"></a></p>
-<h3 id="bifi-beautiful-interfaces-for-inputs-plugin">BIFI (Beautiful Interfaces for Inputs) plugin</h3>
-<p><em>Available for Taverna 2.4.</em></p>
-<p>The <a href="http://www.xworx.org/#!bifi-plugin/c1tou">BIFI (Beautiful Interfaces for Inputs)</a> plug-in
- for Taverna Workbench provides a GUI definition language that is used to lay out user
- interfaces and define parameter options for Taverna workflows.
-BIFI is also able to submit GUI definition files (GDF) directly to or locate appropriate
- instances from the repository configured.
-Moreover, BIFI includes an algorithm used to generate a default user interface if no GDF can be
- found in the repository by making use of the meta-information from process definitions.</p>
-<p><a name="vphshare"></a></p>
-<h3 id="vph-share-plugin">VPH-Share plugin</h3>
-<p><em>Available for Taverna 2.4 and 2.5.</em></p>
-<p>The <a href="http://www.vph-share.eu/">VPH-Share</a> project has developed a
- [plugin]http://www.vph-share.eu/content/vph-share-taverna-plugin) for Taverna that allows the
- usage of any VPH-Share Web Service to be included as services within a Taverna workflow.</p>
-<p>The VPH-Share services are run on virtual machines (VM) within a cloud,
- but the VPH-Share Plugin makes this transparent to the users.
-VPH-Share manages the handling of VMs, so the user can connect to the available Web Services
- like any other Web Service, without dealing with starting or shutting down the virtual
- machines.
-VPH-Share also handles user access control in all steps of the workflow composition and
- execution.</p>
-<p>The <a href="http://www.vph-share.eu/content/vph-share-taverna-plugin">VPH-Share Plugin</a> works with
- Taverna Workbench as well as with Taverna Server.
-Planned improvements include allowing web-based composition of workflows with VPH-Share
- services through <a href="/documentation/online">Taverna Online</a>.</p>
-<p>This <a href="http://www.vph-share.eu/content/vph-share-taverna-plugin">VPH-Share Plugin</a> is currently
- under development by the Scientific Software Development Team of
- <a href="http://www.cistib.org/">CISTIB</a> (Center for Computational Imaging & Simulation Technologies
- in Biomedicine), at <a href="http://www.shef.ac.uk/">The University of Sheffield</a>,
- and can be installed in Taverna by adding the
- <a href="http://repository.cistib.org/nexus/content/repositories/releases/">CISTIB Plugin Site</a>.
-You can contact the development team at <a href="mailto:ssd.cistib@lists.shef.ac.uk">ssd.cistib@lists.shef.ac.uk</a>.</p>
-<p><a name="interaction"></a></p>
-<h3 id="interaction-plugin">Interaction plugin</h3>
-<p><em>Available for Taverna 2.4; integrated in Taverna 2.5</em> </p>
-<p>The Interaction plugin allows users to interact in a web browser within a workflow run using an Interaction service.
-The run can be on <a href="/download/workbench">Taverna Workbench</a> or on a
- <a href="/documentation/server">Taverna Server</a>.
-A detailed description of the Interaction service can be found in the online
- <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Interaction+service">manual</a>.</p>
-<p>The Interaction service was developed by the <a href="http://www.biovel.eu">BioVeL project</a>.</p>
-<p><a name="xpath"></a></p>
-<h3 id="xpath-plugin">XPath plugin</h3>
-<p><em>Available for Taverna 2.2; integrated in Taverna 2.3, 2.4 and 2.5</em></p>
-<p>XPath plugin provides enhanced support for creating and executing XPath expressions over XML
- data in order to extract specific fragments of the data.
-This plugin offers an intuitive and easy-to-use way of creating XPath expressions and does not
- require detailed knowledge of the XPath language - expressions are generated by selection of
- relevant nodes in the tree-like view of the provided example XML data.
-Ability to modify automatically-generated XPath expressions and control over namespace handling
- make this a powerful tool.
-This plugin was written by Sergejs Aleksejevs.</p>
-<p><a name="rest"></a></p>
-<h3 id="rest-plugin">REST plugin</h3>
-<p><em>Available for Taverna 2.2; integrated in Taverna 2.3, 2.4 and 2.5.</em></p>
-<p>REST plugin allows users to access remote services via four different types of HTTP requests:
- GET, POST, PUT and DELETE.
-Configuration options of the plugin include MIME types of the sent and received data and the
- URL template that can have configurable parameters
- (with an individual input port created for each).
-The plugin integrates with the Credential Manager of the Workbench for added convenience when
- accessing secure web services.
-This plugin was written by Sergejs Aleksejevs.</p>
-<p><a name="biocatalogue_plugin"></a></p>
-<h3 id="biocatalogue-plugin">BioCatalogue plugin</h3>
-<p><em>Available for Taverna 2.1.2, 2.2; integrated in Taverna 2.3, 2.4 and 2.5.</em></p>
-<p>BioCatalogue plugin alpha for Taverna 2.1.2 allows users to browse services in the
- <a href="http://www.biocatalogue.org/">BioCatalogue</a> Life Sciences Web Services registry from the
- Workbench and add them to workflows.
-Being an alpha, some pieces of functionality have not been fully implemented.
-The plugin has been developed by Sergejs Aleksejevs.</p>
-<p>The plugin for Taverna 2.2 is still an alpha but several small fixes and improvements have been
- made in this version:</p>
-<ul>
-<li>Services added to the Service Panel are now saved and re-appear in the Service Panel when
- the Workbench is restarted</li>
-<li>An option to choose which BioCatalogue instance to work with has been added
- (available from <em>File</em> -> <em>Preferences</em> -> <em>BioCatalogue</em>).
- This means that Taverna can use not only the main instance of BioCatalogue,
- but also other instances (e.g. the <a href="https://www.biodiversitycatalogue.org/">BioDiversity</a>
- catalogue that is based on the BioCatalogue codebase).</li>
-<li>The user interface of the tree with Filtering options (in the Filter Services tab of the
- BioCatalogue Perspective) has been fixed - now it looks identical on Windows, Linux and
- Mac OS.</li>
-<li>Contextual views are not shown for the types of workflow elements that the BioCatalogue does
- not work with.</li>
-</ul>
-<p><a name="pbs"></a></p>
-<h3 id="pbs-plugin">PBS plugin</h3>
-<p><em>Available for Taverna 2.2.</em></p>
-<p><a href="http://cphg.virginia.edu/mackey/projects/sequencing-pipelines/tavernapbs/">TavernaPBS</a> plugin
- is developed by the <a href="http://obx.cphg.virginia.edu/mackey/">Mackey Lab</a>,
- Center for Public Health Genomics, University of Virginia, US.
-It allows a user to define workflows that can then be run using a computational cluster that
- uses a <a href="http://en.wikipedia.org/wiki/Portable_Batch_System">PBS</a> (Portable Batch System)
- queuing system.
-The workflows represent next generation sequencing analysis pipelines.</p>
-<p>To most efficiently make use of their myriad of UNIX command line tools, the project has
- developed a custom <a href="/documentation/glossary/#beanshell">Beanshell</a> - based library to enable
- workflows composed of UNIX command line invocations.
-Furthermore, they have abstracted the command execution such that each step could be executed
- as an independent âjobâ on a remote high performance computing or grid environment.
-By doing so, they have essentially turned Taverna into a distributed workflow âcompilerâ.</p>
-<p>You can download the code from the project's
- <a href="http://sourceforge.net/projects/tavernapbs/">pages at SourceForge</a>.</p>
-<p><a name="sadi_plugin"></a></p>
-<h3 id="sadi-plugin">SADI plugin</h3>
-<p><em>Available for Taverna 2.1.2, 2.2.</em></p>
-<p><a href="http://sadiframework.org/content/">Semantic Automated Discovery and Integration</a> (SADI) is a
- set of standards-compliant best practices that simplify interoperability between semantic
- Web services.
-The SADI codebase make it easy for people to deploy services that adhere to the SADI framework
- practices.
-The SADI plugin allows semantic services to be accessed from Taverna.
-The plugin has been developed by David Withers
- (with the support of the
- <a href="http://www.gcbioinformatics.ca">Genome Canada Bioinformatics Platform</a>).
-It requires Java 6.</p>
-<p><a name="usecase_plugin"></a></p>
-<h3 id="external-tools-usecase-plugin">External Tools (UseCase) plugin</h3>
-<p><em>Available for Taverna 2.1.2, 2.2; integrated in Taverna 2.3, 2.4 and 2.5.</em></p>
-<p><a href="http://taverna.nordugrid.org/">External Tools (previously UseCase) plugin</a> that was developed
- for Taverna 1.7 as part of the <a href="http://www.knowarc.eu/">KnowARC project</a> (previously ARC
- project) has now been updated to work with Taverna 2.x and extended in functionality.
-The plugin was originally written by Hajo Krabbenhöft and Steffen Möller and updated to work
- with Taverna 2.2 by Alan Williams.
-It allows users to run tools on a grid, or a remote/local machine using grid or ssh
- authentication.<br />
-At the moment a prototype set of tool descriptions is available.
-Read more on
- <a href="http://www.mygrid.org.uk/dev/wiki/display/developer/Calling+external+commands+from+Taverna">how to use the plugin</a>.</p>
-<p><a name="unicore"></a></p>
-<h3 id="unicore-plugin">UNICORE plugin</h3>
-<p><em>Available for Taverna 2.3</em></p>
-<p>Sonja Holl of the Distributed Systems and Grid Computing division of the Jülich Supercomputing
- Centre (JSC) in Germany developed a <a href="http://www.unicore.eu/">UNICORE</a> plugin for Taverna.
- âUNICORE (Uniform Interface to Computing Resources) offers a ready-to-run Grid system and
- makes distributed computing and data resources available in a seamless and secure way.â<br />
-The UNICORE plugin for Taverna enables users to submit jobs from Taverna Workbench to any
- UNICORE resource.</p>
-<p>To get access to UNICORE resources from Taverna, the user registers a new UNICORE registry in
- Taverna's <a href="/documentation/glossary/#service_panel">Service Panel</a>.
-This UNICORE registry is then queried and the UNICORE services orchestrator returns a list of
- available applications.
-The applications are selected from various UNICORE resources, as each installation holds a file
- that describes the available applications, including metadata on the specific resource.</p>
-<p>The list of applications is then used in Taverna to display available UNICORE services
- (applications), which can be added as services to Taverna workflows.
-The metadata is used to create input and output ports of the specific application/service.
-Users can than connect inputs/outputs to other workflow services in the usual manner.</p>
-<p>During the worfklow execution, a job description is created and submitted to the UNICORE
- service orchestrator(SO).
-Files are being uploaded and stored under a logical filename.
-The SO then manages the execution and file transmission.
-The status of the submitted job is polled in the background from Taverna.
-After the job finished, some files are downloaded, and for further modification,
- only the logical file name is retrieved.</p>
-<p>Additionally, the UNICORE services are using Taverna's
- <a href="/documentation/glossary/#credential_manager">Credential Manager</a> to get access to the
- user's X.509 certificate, which user has to load prior to service invocation,
- along with the other CA's certificates.
-The UNICORE services then access the user's certificate and use it for job submission
- (since UNICORE's security concept is based upon grid security and X.509 certificates).</p>
-<p>To install the plugin, follow the
- <a href="http://www.mygrid.org.uk/dev/wiki/display/taverna/Finding+plugins">installation instructions</a>
- from the User Manual and use the following URL when installing the plugin:
- <a href="http://unicore-dev.zam.kfa-juelich.de/taverna/plugins/">http://unicore-dev.zam.kfa-juelich.de/taverna/plugins/</a>.</p>
-<p><a name="cdk"></a></p>
-<h3 id="cdk-plugin">CDK plugin</h3>
-<p><em>Available for Taverna 2.2, 2.3.</em>
-<a href="mailto:atruszkowski@gmx.de">Andreas Truszkowski</a> has updated the plugin that the
- <a href="/introduction/taverna-in-use/chemistry#chemistry-development-kit/">Chemistry Development Kit (CDK) project</a>
- have developed for Taverna 1.7.2, to allow the CDK tools to be used within Taverna 2
- workflows as services.
-More information about the plugin is available from their
- <a href="http://cdk-taverna-2.ts-concepts.de/wiki/index.php?title=Main_Page">wiki pages</a>.</p>
-<p>See our
- <a href="http://www.mygrid.org.uk/dev/wiki/display/taverna23/CDK-Taverna+plugin">User Manual pages</a>
- for more information on how to download, install and use the plugin.</p>
-<p><a name="cagrid_plugin"></a></p>
-<h3 id="cagrid-plugin">caGrid plugin</h3>
-<p><em>Available for Taverna 2.1.2.</em></p>
-<p>The Taverna team together with the caGrid team have developed the caGrid service discoverer
- plugin for Taverna 2.1.2.
-This plugin is used to query caGrid services from the caGrid Index Service.
-This allows you to easily find the available caGrid services, add them in Taverna's
- <a href="/documentation/glossary#service_panel">Service Panel</a> and then invoke them from workflows.
-The <a href="http://wiki.cagrid.org/display/workflow13/Taverna+Users+Guide">documentation</a> for the
- plugin is available on-line, as well as the
- <a href="https://github.com/NCIP/taverna-grid">source code</a>. <br />
-<em>Note: As of May 2013, this plugin does not install correctly from the caGrid plugin site.
-Users are advised to build the plugin from <a href="https://github.com/NCIP/taverna-grid">source code</a>.</em></p>
-<p><a name="cagrid_remote_execution_plugin"></a></p>
-<h3 id="cagrid-remote-execution-plugin">caGrid remote execution plugin</h3>
-<p><em>Available for Taverna 2.1.2.</em></p>
-<p>The caGrid team have also developed a remote workflow execution service plugin for
- Taverna 2.1.2.
-The plugin passes a workflow definition file, including the appropriate inputs,
- to a generic remote caGrid service, where the workflow is then executed.
-This is useful in instances where the workflow is long-running and relies on constant access to
- the caGrid to execute properly.
-The <a href="http://wiki.cagrid.org/display/workflow13/Taverna+Users+Guide">documentation</a> for the
- plugin is available on-line, as well as the
- <a href="https://github.com/NCIP/taverna-grid">source code</a>.
-*Note: As of May 2013, this plugin does not install correctly from the caGrid plugin site.
-Users are advised to build the plugin from <a href="https://github.com/NCIP/taverna-grid">source code</a>.</p>
-<p><a name="xws"></a></p>
-<h3 id="xws-plugin">XWS plugin</h3>
-<p><em>Available for Taverna 2.0.</em></p>
-<p><a href="http://chem-bla-ics.blogspot.com/">Egon Willighagen</a> then at Uppsala University, Sweden, has
- developed a <a href="http://github.com/egonw/xws-taverna/tree/master">plugin</a> that allows workflows
- to include XWS (XMPP IO-DATA) cloud services.</p>
-<p><a name="glite"></a></p>
-<h3 id="glite-plugin">gLite plugin</h3>
-<p><em>Available for Taverna 2.0.</em></p>
-<p>Richard Holland of <a href="http://www.eaglegenomics.com/">Eagle Genomics</a> while working for
- <a href="http://grid.sara.nl/">Sara Grid</a> has developed a
- <a href="https://grid.sara.nl/wiki/index.php/TavernaGrid">gLite plugin</a> that allows workflows to
- include services that run on a grid.</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/provenance/index.html
==============================================================================
--- websites/staging/taverna/trunk/content/documentation/provenance/index.html (original)
+++ websites/staging/taverna/trunk/content/documentation/provenance/index.html Wed Mar 11 08:37:10 2015
@@ -104,234 +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>Provenance management</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"><blockquote>
-<p>Provenance is information about entities, activities, and people
-involved in producing a piece of data or thing, which can be used to
-form assessments about its quality, reliability or trustworthiness.<br />
-- <small><a href="http://www.w3.org/TR/prov-overview/">W3C PROV-Overview</a>*</small></p>
-</blockquote>
-<p>For a scientific workflow system, provenance can have several aspects:</p>
-<ol>
-<li>Provenance of the workflow definition</li>
-<li>Provenance of a workflow run</li>
-<li>Provenance of data</li>
-</ol>
-<h2 id="provenance-of-workflow-definitions">Provenance of workflow definitions</h2>
-<p>Taverna does not capture provenance of editing a <em>workflow definition</em>,
- but assume the scientist manages the evolution of workflow definitions through existing
- means for versioning files, such as filenames and folders,
- version control systems like <a href="https://help.github.com/articles/set-up-git">git</a>,
- or workflow sharing websites like <a href="http://www.myexperiment.org/">myExperiment</a>.</p>
-<p>Within Taverna, a
- <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Annotations">workflow can be annotated</a>
- to give <em>attribution</em> to the <strong>Authors</strong> of a workflow (or nested workflow).
-We recommend using comma or linefeed for multiple authors.</p>
-<p>Taverna's workflow fileformat has an internal workflow identifier (UUID) which is updated for
- every workflow change.
-A log of previous workflow identifiers is included within the workflow definition formats
- <a href="http://taverna.googlecode.com/svn/taverna/dev/xsd/trunk/t2flow/t2flow.xsd">t2flow</a> and
- <a href="http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle">Taverna 3 workflow bundle</a>,
- allowing
- <a href="http://www.myexperiment.org/workflows/2899">detection of workflows with common ancestry</a>>. </p>
-<h2 id="provenance-of-workflow-runs">Provenance of workflow runs</h2>
-<p>Taverna can
- <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Data+and+provenance+preferences">capture provenance of workflow runs</a>,
- including individual processor iterations and their inputs and outputs.
-This provenance is kept in an internal database,
- which is used to populate <em>Previous runs</em> and <em>Intermediate results</em> in the
- <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Result+Perspective">Results perspective</a>
- in the Taverna Workbench.</p>
-<p>The provenance trace can be used by the
- <a href="https://github.com/wf4ever/taverna-prov">Taverna-PROV plugin</a>
- to export the workflow run, including the output and intermediate values,
- and the provenance trace as a <a href="http://www.w3.org/TR/prov-o/">PROV-O</a> RDF graph which can
- be queried using <a href="http://www.w3.org/TR/sparql11-overview/">SPARQL</a> and processed with other
- PROV tools, such as the <a href="https://github.com/lucmoreau/ProvToolbox/">PROV Toolbox</a>.</p>
-<p>We are planning to extend myExperiment to handle uploading of such provenance traces,
- which would give a mechanism to present and browse values and details of a workflow runs
- within the browser.</p>
-<p>This <a href="http://www.slideshare.net/soilandreyes/20130529-taverna-provenance">presentation about Taverna's provenance support</a>
- gives an overview of the model and software architecture.</p>
-<h2 id="provenance-of-data">Provenance of data</h2>
-<p>Scientists using Taverna to perform analysis are often less concerned about the detailed provenance of a workflow run, which semantically just describes inputs and outputs to a chain of processes, but are rather interested in <em>derivation</em> and <em>attribution</em> of the data that is involved in a workflow. For instance, a workflow might be performing text-mining on a biomedical article to extract gene names, and then retrieve the genome sequences for those genes by looking up in a database. The sequences can then be said to be derived from that database and should (according to the license of the web service) also be attributed to its maintainers. The <em>list</em> of sequences can be said to be derived from the biomedical article.</p>
-<p>The typical world of Taverna workflows is to combine web services “in the wild” (say found on <a href="">http://www.biocatalogue.org/</a> BioCatalogue) with local tools. Neither of these will typical have any facility to provide such “science-level provenance”. myGrid is planning a facility for such data provenance in different ways:</p>
-<ol>
-<li>Merging and propagation of <a href="http://www.w3.org/TR/prov-aq/">PROV-AQ</a> provided provenance
- traces for <a href="http://dev.mygrid.org.uk/wiki/display/taverna/REST">REST services</a>
- (including matching data identity) -- âwhite-box serviceâ</li>
-<li>A provenance âbackchannelâ for <a href="/documentation/components">Components</a>,
- which can be populated either by the underlying service directly or by shims within the
- component.
- This allows higher level provenance that is meaningful for a set of components instead of
- service-specific execution details.</li>
-<li>Annotation of workflow fragments by
- <a href="http://www.slideshare.net/dgarijo/common-motifs-in-scientific-workflows-an-empirical-analysis">common motifs</a>,
- which can provide higher-level provenance for data generated by the workflow</li>
-</ol>
-<p>The paper <a href="http://www.edbt.org/Proceedings/2013-Genova/papers/workshops/a45-alper.pdf">Enhancing and Abstracting Scientific Workflow Provenance for Data
- Publishing</a>
- (doi <a href="http://dx.doi.org/10.1145/2457317.2457370">10.1145/2457317.2457370</a>) details these
- approaches.</p>
-<h2 id="collaborations">Collaborations</h2>
-<p>myGrid actively participated in the
- <a href="http://www.w3.org/2011/prov/wiki/Main_Page">W3C Provenance Working Group</a>
- which developed the <a href="http://www.w3.org/TR/prov-overview/">PROV family of standards</a>.
-The <a href="https://github.com/wf4ever/taverna-prov">Taverna-PROV plugin</a> has been developed for
- Taverna that allows the export of workflow run provenance as
- <a href="http://www.w3.org/TR/prov-o/">PROV-O RDF</a>.</p>
-<p>The <a href="http://www.wf4ever-project.org">wf4ever project</a> is investigating the sharing of workflows
- and workflow runs as <a href="http://www.researchobject.org/">research objects</a>, in particular for
- Taverna is the development of the <a href="https://w3id.org/bundle">Research Object Bundle</a>,
- which will form a single archive of a workflow run, including run <em>provenance</em>, <em>inputs</em>,
- <em>outputs</em>, <em>intermediate values</em>, <em>workflow definition</em> and (for Taverna 3)
- information about the <em>run environment</em>.</p>
-<h2 id="past-collaborations">Past collaborations</h2>
-<p>Since early 2010, we are invited partners of the <a href="https://dataone.org/">NSF DataONE project</a>,
- dedicated to large-scale preservation of scientific data, and founding members of the
- Worklow and Provenance Working Group promoted by the project, along with Prof. Ludaescher
- at UC Davis, USA and Juliana Freire at University of Utah, USA.</p>
-<p>Historically, work on provenance within the myGrid consortium and Taverna team has been
- focusing on multiple aspects, beginning with the design and implementation of <em>Janus</em>,
- a data model and software component for provenance capture and analysis for Taverna.
-Our research in this area is often pursued in collaboration with external partners:</p>
-<ul>
-<li>A model and architecture for capturing provenance.
- We have designed a data model for <em>Janus</em> that is at the same time specific to Taverna,
- but can also be exported to other models,
- notably the <a href="http://openprovenance.org/">Open Provenance Model</a> (OPM),
- to enable interoperability with third party provenance-generating systems.
- Taverna has been retrofitted with provenance generation capabilities.</li>
-<li>An expressive provenance query language and efficient query processing model for large
- provenance graphs.</li>
-<li>Investigation into provenance interoperability and exchange, using the OPM.
- The Taverna provenance component now exports data as OPM graphs,
- and can also import OPM graphs (with basic features) received from third parties.<br />
- We have also been working with the Kepler group on a project to promote provenance
- interoperability, in collaboration with Prof. Ludaescher at UC Davis, CA, and
- Ilkay Antintas at UCSD, CA .</li>
-<li>Investigation into the role of semantics and of Linked Open Data (LOD) in provenance
- modelling and management, in collaboration with the Knoesis Centre at Wright University,
- Ohio (Prof. Amit Sheth, Dr. Satya Sahoo) and with Jun Zhao of Oxford University.</li>
-</ul>
-<p>Other past collaborations on the topic of provenance include:</p>
-<ul>
-<li>
-<p>Participation in the
- <a href="http://twiki.ipaw.info/bin/view/Challenge/ThirdProvenanceChallenge">Third Provenance Challenge</a></p>
-</li>
-<li>
-<p><a href="http://www.mygrid.org.uk/projects/semantic-provenance-project/">The Semantic Provenance project</a>,
- with Ely Lilly and IU</p>
-</li>
-</ul></div>
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