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:[email protected]";>[email protected]</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:[email protected]";>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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