Modified: websites/staging/taverna/trunk/content/introduction/roadmap.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/roadmap.html (original)
+++ websites/staging/taverna/trunk/content/introduction/roadmap.html Wed Mar 11
08:37:10 2015
@@ -104,133 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Taverna Roadmap</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><h2 id="taverna-3">Taverna 3</h2>
-<p>Taverna 3 is a re-engineering of the Taverna codebase to use OSGi.</p>
-<h3 id="taverna-3-command-line-tool-alpha3beta1">Taverna 3 Command Line Tool
alpha3/beta1</h3>
-<ul>
-<li>Based on the /developers/work-in-progress/taverna-3/ using <a
href="http://www.osgi.org/About/Technology";>OSGi</a></li>
-<li>New plugin-system</li>
-<li>Usability improvements</li>
-<li>Easily customisable service sets</li>
-<li>More complete service type support</li>
-</ul>
-<h3 id="taverna-3-platform-updated-beta">Taverna 3 Platform updated beta</h3>
-<ul>
-<li>Available as an <a href="http://www.osgi.org/About/Technology";>OGSi</a>
bundle or Jar (for non-OGSi environments for easy embedding)</li>
-<li>Using <a
href="http://dev.mygrid.org.uk/wiki/display/developer/SCUFL2";>SCUFL2</a>
workflow bundle format</li>
-<li>API for running workflows</li>
-</ul>
-<h2 id="tavena-2">Tavena 2</h2>
-<p>This site only covers the Apache Taverna product.
-As Taverna 2 is not an Apache product so its roadmap can be found on the
previous <a href="http://www.taverna.org.uk/introduction/roadmap/";>taverna
website</a>. </p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/services-in-taverna.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/services-in-taverna.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/services-in-taverna.html
Wed Mar 11 08:37:10 2015
@@ -104,172 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Services in Taverna</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna can access a large number of
services in the fields of bioinformatics, astronomy, chemoinformatics,
- health informatics and others. Although many examples of using Taverna lie
in the bioinformatics domain,
- Taverna is actually domain independent.
-This means that Taverna can be applied to a wide range of fields â even
music and food sciences.</p>
-<p>Taverna can invoke generic <a
href="/documentation/glossary#wsdl">WSDL-style Web services</a>.
-You do not need to alter a service in any way;
-you simply need to give Taverna the URL address of the serviceâs WSDL
document.
-Please refer to our <a href="/documentation/web-service-developers">Web
service developersâ documentation</a> if you are planning on developing Web
services
- accessible from Taverna.</p>
-<p>Taverna can also access other types of Web services, such as <a
href="/documentation/glossary#biomoby">BioMoby</a>, <a
href="/documentation/glossary#biomart">BioMart</a> and <a
href="/documentation/glossary#soaplab">SoapLab</a>
- services.</p>
-<p>In addition, Taverna can invoke local Java services (<a
href="/documentation/glossary#beanshell">Beanshell</a> scripts), local Java API
(<a href="/documentation/glossary#api_consumer">API Consumer</a>),
- R scripts on an R server (<a
href="/documentation/glossary#rshell">Rshell</a> scripts), import data from a
<a href="/documentation/glossary#spreadsheet_import">cvs or Excel
spreadsheet</a> and interact
- with users in a browser.</p>
-<p>Taverna can also <a
href="http://dev.mygrid.org.uk/wiki/display/taverna/Interaction+service";>interact</a>
with a running workflow from your Web browser,
- and has the ability to incorporate workflow fragments (reusable <a
href="http://dev.mygrid.org.uk/wiki/display/taverna/Component+services";>components</a>)
as services in a workflow.</p>
-<p>A full list of service types is in the <a
href="http://dev.mygrid.org.uk/wiki/display/taverna/Service+types";>User
Manual</a>.</p>
-<p>Please see the <a href="http://biocatalogue.org/";>BioCatalogue</a> for
details of the services we are currently aware of that work with Taverna.
-If you would like to add your services to this list, please contact <a
href="http://www.biocatalogue.org/contact";>the BioCatalogue team</a>.</p>
-<h2 id="domain-and-shim-services">Domain and shim services</h2>
-<p>Services accessible from Taverna can be broadly categorised into domain
services and shim services.</p>
-<ul>
-<li>Domain (scientific) services perform scientific function(s) and are often
provided by third-party suppliers.
- They cannot usually be changed by individual users.</li>
-<li>Shim services are created during workflow design,
- to specifically connect the inputs and outputs of closely related
services in order to achieve
- interoperation between domain services.
- This typically involves changing one serviceâs output into a different
format for another service to accept. An example might include changing the
output from tab to comma separated values. Taverna comes with a library of
frequently used shim services. A new workflow, however, often brings about the
need to develop a new shim or modify an existing one.</li>
-</ul>
-<p>A rule of thumb for distinguishing a domain service from a shim service is
that a workflow,
- when the shims services are invisible, is equivalent to the methods
section of a scientific paper.
-If a service needs to be explicitly mentioned in the method, then it is not a
shim.</p>
-<h2 id="service-providers">Service providers</h2>
-<p>Nearly all services accessible by Taverna are neither owned nor provided by
us.
-The majority of services are provided by third-party institutes and research
facilities,
- all of which can be accessed from within Taverna.
-Taverna only provides most commonly used shim services, e.g. to concatenate
strings, read content from a file,
- etc.</p>
-<p>Service suppliers can often be large government-funded bodies such as the
<a href="http://www.ncbi.nlm.nih.gov/";>NCBI</a> (United States),
- <a href="http://www.ebi.ac.uk/";>EMBL-EBI</a> (Europe) or <a
href="http://www.ddbj.nig.ac.jp/";>DNA Databank of Japan</a>.
-Each is responsible in providing data to the global scientific community.
-These major providers generally have dedicated human resources for service
development, API documentation,
- hosting and maintenance.
-In addition to programmatic access to their services these also maintain
Web-form based access.</p>
-<p>A large proportion of suppliers of services and workflows are much smaller
in scale â
- this includes individuals or small laboratories that have developed a tool,
algorithm, database,
- or workflow that they wish to share with others.
-Developers of services from these small establishments may have limited
knowledge on Web services and
- related standards when compared to their knowledge of
programming/scripting.
-Such circumstances have required myGrid to develop tools like <a
href="http://www.ebi.ac.uk/soaplab/";>Soaplab</a> that help alleviate this
limitation
- of small-scale providers by allowing simple deployment of the tool at
hand.</p>
-<p>All these service providers are independent of, and usually ignorant of,
their consumers.
-Thus, the suppliers and consumers in the open market are loosely coupled and
asynchronous.
-Other services are private and local to the scientist (workflow designer),
- or developed specifically for a workflow to make it work.
-Creating a service accessible from Taverna</p>
-<p>If you are planning on creating a service that should be accessible from
Taverna,
- please have a look at the documentation for Web service developers<a
href="/documentation/web-service-developers">link text</a>.</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-features.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/taverna-features.html
(original)
+++ websites/staging/taverna/trunk/content/introduction/taverna-features.html
Wed Mar 11 08:37:10 2015
@@ -104,227 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1></h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p><a href="/introduction">The Taverna suite
of tools</a> are bringing together a range of features to make it easier for
users to find, design and execute complex workflows and share them with other
people.</p>
-<p>Freely available</p>
-<ul>
-<li>Java, open source, LPGL licensed (GPL for Astronomy versions)</li>
-</ul>
-<p>Suite of tools to design, edit and execute workflows</p>
-<ul>
-<li>Workflow design and execution in Taverna Workbench</li>
-<li>Command line execution of workflows</li>
-<li>Remote execution of workflows on a Taverna server</li>
-<li>Invoke workflows from the Internet</li>
-</ul>
-<p>Wide range of services and extensible architecture</p>
-<ul>
-<li>Service discovery</li>
-<li>Various service types available: WSDL-style and RESTful Web services,
BioMart, BioMoby, SoapLab, R,
- Beanshell, Excel and csv spreadsheets</li>
-<li>Service creation for external tools or Java libraries</li>
-<li>Calling tools/scripts on a local machine or remote machines (via ssh)</li>
-<li>Extensible service plug-in architecture for adding new service types</li>
-<li><a href="#biocataloue-integration">Fully integrated support for browsing
curated service catalogues</a>,
- such as the <a href="http://www.biocatalogue.org/";>BioCatalogue</a>,
for Web services (WSDL/SOAP and REST)</li>
-<li>Interaction with a running workflow within a web browser</li>
-<li>Ability to define and share semantically annotated components, and have
them used as services in workflows</li>
-</ul>
-<p>Secure</p>
-<ul>
-<li>Support for secure services (HTTP authentication, WS-Security, X.509
client authentication)</li>
-<li>Secure management of usersâ credentials</li>
-</ul>
-<p>Versatile Workbench</p>
-<ul>
-<li>Tabs for finding, designing and executing workflows</li>
-<li>Fully graphical workflow design</li>
-<li>Drag and drop workflow components</li>
-<li>Comprehensive undo/redo</li>
-<li>Built-in help facility</li>
-<li>Annotations for describing workflows, services, inputs, outputs</li>
-<li>Workflow validation and debugging</li>
-</ul>
-<p>Create your own or start from existing workflows</p>
-<ul>
-<li>Easy design of new workflows</li>
-<li>Load existing workflows (from a disk, <a
href="http://www.myexperiment.org/";>myExperiment</a> or a URL)</li>
-<li>View workflow layout and logic</li>
-<li>Modify existing workflows</li>
-<li>Load workflows in off-line mode (when disconnected from the Internet)</li>
-<li>Nested workflows (sub workflows)</li>
-<li>Workflow validation during design time for debugging while composing a
workflow</li>
-<li>Built-in detection when a serviceâs interface changes or a service go
off-line during design time</li>
-</ul>
-<p>Find workflows created by others and share yours</p>
-<ul>
-<li><a href="#myexperiment-integration">Full myExperiment search options for
browsing workflows</a></li>
-<li>Publish workflows on myExperiment for use by others</li>
-</ul>
-<p>Execute and debug your workflows</p>
-<ul>
-<li>Execute workflows</li>
-<li>Remember previously used workflow inputs</li>
-<li>Save workflow input values used to a file</li>
-<li>Load workflow input values from a file</li>
-<li>Pipelining and streaming of data</li>
-<li>Implicit iteration of service calls</li>
-<li>Conditional and repeated calling of services</li>
-<li>Customizable looping over a service</li>
-<li>Failover and retry of service calling</li>
-<li>Parallel execution and configurable number of concurrent threads</li>
-<li>Improved error handling and reporting for debugging during run time</li>
-<li>Monitor workflow execution</li>
-<li>Pause/resume or cancel workflow execution</li>
-<li>Manage previous runs and workflow results</li>
-<li>View intermediate results and debug workflows at run time</li>
-<li>Filter and save intermediate and final workflow results</li>
-</ul>
-<p>Track workflow runs and results</p>
-<ul>
-<li>Record workflow execution provenance</li>
-<li>Review provenance of previous workflow runs</li>
-<li>Experimental export of provenance in the <a
href="http://openprovenance.org/";>OPM</a> and Janus formats</li>
-</ul>
-<p>Support</p>
-<ul>
-<li>End user technical support and e-mail help desk</li>
-<li>Tutorials and workshops</li>
-</ul>
-<p><a name="myexperiment-integration"/></p>
-<h2 id="myexperiment-integration">myExperiment integration</h2>
-<p><a href="http://www.myexperiment.org/";><img
src="/img/MyExperiment_logo_1672x320.png" alt="myExperiment" width="394"
height="75" /></a></p>
-<p><a href="http://www.myexperiment.org/";>myExperiment</a> is a social
networking site and Virtual Research Environment (VRE) designed for people to
share, discover and reuse workflows.</p>
-<p>myExperiment enables scientists to contribute to a pool of workflows that
can be reused and repurposed by other scientists, promoting building of
communities, forming of relationships and collaboration. In this way,
myExperiment helps reduce time-to-experiment, share expertise and avoid
reinvention.</p>
-<p>It is widely used, as demonstrated by their being 8820 members in 304
groups. Its actual take up shows that there are 2415 workflows, consisting of
604 files. The number of packs (research objects) currently in use stands at
229.</p>
-<h3
id="find-myexperiment-workflows-by-others-and-share-yours-from-taverna">Find
myExperiment workflows by others and share yours from Taverna</h3>
-<p>As of version 2.1, Taverna has a built-in support for myExperiment,
-enabling users to browse myExperiment Web site from inside the Taverna
Workbench.</p>
-<p>Users can access the full myExperiment search options for browsing
workflows,
-load existing workflows from myExperiment or publish their workflows on
myExperiment for use by others.</p>
-<p>A snapshot of the myExperiment Perspective in Taverna can be seen in the
image below.</p>
-<p><img src="/img/myExperimentPerspective.png" alt="myExperiment plugin for
Taverna screenshot" width="100%"/></p>
-<p><a name ="biocataloue-integration"/></p>
-<h2 id="biocatalogue-integration">BioCatalogue integration</h2>
-<p><a href="http://www.biocatalogue.org/";><img
src="/img/biocatalogue_without_text.png" alt="BioCatalogue" width="488"
height="97" /></a></p>
-<p>BioCatalogue is a public, centralised, curated and monitored registry of
Life Science Web services which can be used for building workflows. It is a
community-oriented Web site where service providers or community experts can
register and curate services and users can discover them.</p>
-<p><a href="http://www.biocatalogue.org/";>BioCatalogue</a> provides a single
point where services can be annotated and curated by service providers or
community experts â it helps service providers publicize and make their
services more visible to the community and makes it easier for users to find
them.</p>
-<p>Web services can be volatile â they change over time and get outdated.
-BioCatalogue monitors services periodically and provides statistics on their
availability and reliability.
-Discover and reuse services in BioCatalogue from Taverna</p>
-<p>Taverna has a built-in support for searching service catalogues, such as
the BioCatalogue.
-It enables users to browse a service catalogue and access its full search
options for browsing services and checking their status and availability from
inside the Workbench. Discovered services can then be added either directly to
workflows or the Taverna Workbenchâs Service Panel.</p>
-<p>The <a href="/documentation/glossary#service_panel">service catalogue</a>
accessed by Taverna is configurable,
-so you can set it to a different instance of âBioCatalogueâ, such as <a
href="https://www.biodiversitycatalogue.org/";>BiodiversityCatalogue</a>.</p>
-<p>A snapshot of the Service Catalogue Perspective in Taverna can be seen in
the image below.</p>
-<p><img title="BioCatalogue plugin for Taverna"
src="/img/BioCataloguePerspective.png" alt="BioCatalogue plugin for Taverna
screenshot" width="100%" /></p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/annotation.html
Wed Mar 11 08:37:10 2015
@@ -104,177 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Annotations</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna is used by various tools and
projects for the association of metadata with data (annotation).
-These include:
- - <a href="#afawe">Automatic Functional Annotation in a distributed Web
service Environment</a>(AFAWE) -
- annotation of plant genes with their functionality
- - <a href="#annotation-of-genomes">Interactive genome annotation
pipeline</a></a> - automatic and manual annotation of genes
- - <a href="#taweka">TaWeka</a> - associating biological data with calculated
functionality</p>
-<p>In addition, Taverna makes use of the semantic annotation that has been
specified for the services provided by
- the <a href="#adoption-by-moby">MOBY consortium</a>.</p>
-<p>Taverna has also been used for the identification of mismatches and
possible annotations in workflows by the
- <a href="/introduction/related-projects#ispider">iSPIDER</a> project.</p>
-<p><a name="afawe"></a></p>
-<h2 id="afawe">AFAWE</h2>
-<p>The <a href="http://www.mpiz-koeln.mpg.de/2169/en";>Max Planck Institute for
Plant Breeding Research</a> in Cologne, Germany have developed the
- Automatic Functional Annotation in a distributed Web Service Environment (<a
href="http://bioinfo.mpiz-koeln.mpg.de/afawe/";>AFAWE</a>).
-AFAWE is a tool for the automatic functional annotation of new genes in plants
and other organisms.
-The annotation involves the running of several Web services, and also the
execution of a Taverna <a
href="http://bioinfo.mpiz-koeln.mpg.de/afawe/help/Tools.html#SIFTER";>workflow</a>.</p>
-<p>The annotation workflow is <a
href="http://www.myexperiment.org/workflows/95";>available</a> on <a
href="http://www.myexperiment.org/";>myExperiment</a>.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a href="http://dx.doi.org/10.1093/bioinformatics/btn394";>paper</a>
<em>Protein function prediction and annotation in an integrated environment
powered by web services
- (AFAWE)</em> by Joecker et al describes the concepts and implementation of
AFAWE.</p>
-<p><a name="annotation-of-genomes"></a></p>
-<h2 id="annotation-of-genomes">Annotation of genomes</h2>
-<p>A collaboration between Tom Oinn from the myGrid team and Anders Lanzen,
Svenn Helge Grindhaug and
- Pal Puntervoll from the <a href="http://www.uib.no/en";>University of
Bergen</a>, Norway, has produced an interactive genome annotation
- pipeline.</p>
-<p>Sequencing, characterising and annotating a genome are the first steps to
understanding its function.
-Important stages in this include gene prediction, comparative genomics and
function prediction of genes and
- gene products.
-With workflows all of these stages can be automate, requiring little human
interaction.
-However, manual inspection can be required at certain points in the
process.</p>
-<h3 id="publications_1">Publications</h3>
-<p><a
href="http://scholar.google.co.uk/scholar?q=Taverna+for+genome+annotation";>Articles
and papers</a>
- about the success of Taverna for genome annotation are available
on-line.</p>
-<p><a name="taweka"></a></p>
-<h2 id="taweka">TaWeka</h2>
-<p><a href="http://homepages.inf.ed.ac.uk/ldeferra/";>Luna De Ferrari</a> from
the Computational Systems Biology &
- <a href="http://www.bioinformatics.ed.ac.uk/";>Bioinformatics group at the
University of Edinburgh</a> has developed <a
href="http://mook.inf.ed.ac.uk/twiki/bin/view.cgi/PublicCSB/TaWeka";>TaWeka</a>,</p>
-<blockquote>
-<p>a rapid prototyping tool for biological classifiers.</p>
-</blockquote>
-<p>TaWeka uses Taverna workflows to store data retrieved from webservices,
e.g. queries of biological data,
- into a database.
-<a href="http://www.cs.waikato.ac.nz/ml/weka/";>Weka</a> is then used to run
machine learning experiments on the data in order to evaluate and improve
- biological classification functions.</p>
-<h3 id="publications_2">Publications</h3>
-<p>A poster <a
href="http://mook.inf.ed.ac.uk/twiki/pub/PublicCSB/TaWekaPosters/colourA4_16.pdf";><em>TaWeka:
from biological web services to data mining</em></a> by De Ferrara and
Goryanin describes the
- purpose and implementation of TaWeka.</p>
-<p><a name="adoption-by-moby"></a></p>
-<h2 id="adoption-by-the-moby-consortium">Adoption by the Moby consortium</h2>
-<p>The <a href="http://biomoby.open-bio.org/";>Moby</a> project develops a
system for interoperability between biological data hosts and
- analytical services.
-Their relationship with Taverna is multiple:</p>
-<ul>
-<li>The Moby team actively collaborate with myGrid in the development of the
ontologies used to describe their
- services.
- Service descriptions are then used by Taverna to find services to use in
workflows.</li>
-<li>The services published on Moby are a large proportion of the services
often used in Taverna workflows</li>
-<li>People wishing to combine Moby services commonly use Taverna Workbench as
a platform</li>
-<li>Specific support for Moby services is available within Taverna.</li>
-</ul>
-<h3 id="publications_3">Publications</h3>
-<p>The <a href="http://dx.doi.org/10.1093/bib/bbn003";>paper</a>
<em>Interoperability with Moby 1.0âItâs better than sharing your
toothbrush!</em> by the
- Moby consortium gives an overview of Moby and their activities.</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/arts.html
Wed Mar 11 08:37:10 2015
@@ -104,145 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1></h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Title Arts
-Notice: Licensed to the Apache Software Foundation (ASF) under one
- or more contributor license agreements. See the NOTICE file
- distributed with this work for additional information
- regarding copyright ownership. The ASF licenses this file
- to you under the Apache License, Version 2.0 (the
- "License"); you may not use this file except in compliance
- with the License. You may obtain a copy of the License at
- .
- http://www.apache.org/licenses/LICENSE-2.0
- .
- Unless required by applicable law or agreed to in writing,
- software distributed under the License is distributed on an
- "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- KIND, either express or implied. See the License for the
- specific language governing permissions and limitations
- under the License.</p>
-<p>Taverna has been used for the <a href="#composition-of-music">composition
of music</a> using Web services for synthesis.</p>
-<p><a name="composition-of-music"></a></p>
-<h2 id="composition-of-music">Composition of music</h2>
-<p><a href="http://en.wikipedia.org/wiki/John_ffitch";>John Ffitch</a> and
others at the University of Bath have developed a service-oriented composition
environment
- for music.
-The environment consists of three main components:
- - A suite of synthesis Web services that incorporate a selection of the basic
atomic components required for
- sound creation and processing</li>
- - A tool that gives a description of music in terms of the construction of
the instruments
- (parameters, connections) and the score they will play on>
- - An âenvironment of useâ that allows the connection and enactment of the
synthesis services</p>
-<p>Both <a href="http://www.trianacode.org/";>Triana</a> and Taverna have been
tested as the environment of use.</p>
-<h3 id="publications">Publications</h3>
-<p>This work is described in the <a
href="http://opus.bath.ac.uk/5290/";>paper</a> <em>Composition with Sound Web
Services and Workflows</em> by Ffitch et al</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/astronomy.html
Wed Mar 11 08:37:10 2015
@@ -104,145 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Astronomy</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna and <a
href="http://www.myexperiment.org";>myExperiment</a> are being used for
astronomy research by several projects:</p>
-<ul>
-<li><a href="#astrogrid">AstroGrid</a> - plugin to allow AstroGrid utilities
within Taverna 1.x</li>
-<li><a href="/introduction/related-projects#helio">HELIO</a> - workflows
including heliophysical services</li>
-<li><a href="#sampo">SAMPO</a> - development of a workflow system based upon
Taverna</li>
-</ul>
-<p><a name="astrogrid"></a></p>
-<h2 id="astrogrid">AstroGrid</h2>
-<p>The UKâs <a href="http://www.astrogrid.org/";>AstroGrid</a> is a ~£14M
(over the period 2001-2009) project aimed at building a data-grid for UK
- astronomy, which will form the UK contribution to a global
VirtualObservatory.</p></p>
-<p>A <a
href="http://wiki.astrogrid.org/bin/view/Astrogrid/VoWorkflowsWithTaverna";>Taverna
1.x processor</a> has been written to enable client-site AstroGrid utilities
to be included within
- Taverna workflows.</p>
-<h3 id="publications">Publications</h3>
-<p>A book chapter "AstroGrid and the Virtual Observatory", Walton, N. A.,
Gonzalez-Solareson, E., Springer,
- Lecture Notes in Physic, vol. 791, pp. 81-113, 2009. <br />
-<a
href="http://www.springerlink.com/content/yk36404544k778g8";>http://www.springerlink.com/content/yk36404544k778g8</a></p>
-<p>AstroGrid: Taverna in the Virtual Observatory, Benson, K. M., Walton, N.
A., Memorie della Società Astronomica
- Italiana, vol. 80, p.574, 2009 <br />
-<a
href="http://adsabs.harvard.edu/abs/2009MmSAI..80..574B";>http://adsabs.harvard.edu/abs/2009MmSAI..80..574B</a></p>
-<p>Taverna and Workflows in the Virtual Observatory, Walton, N. A.;
Witherwick, D. K.; Oinn, T.; Benson, K. M.,
- Proceedings of the Astronomical Data Analysis Software and Systems ASP
Conference Series, London, UK.
-Edited by Robert W. Argyle, Peter S. Bunclark, and James R. Lewis., p.309,
2008. <br />
-<a
href="http://adsabs.harvard.edu/abs/2008ASPC..394..309W";>http://adsabs.harvard.edu/abs/2008ASPC..394..309W</a></p>
-<p><a name="sampo"></a></p>
-<h2 id="sampo">SAMPO</h2>
-<p>The SAMPO <a
href="http://www.eso.org/sci/data-processing/software/sampo/";>project</a> was
part of the ongoing Finnish contribution to the <a
href="http://www.eso.org/";>European Southern Observatory</a>.</p>
-<p>Based upon Taverna, the SAMPO project developed the Recipe Flexible
Execution workflow system <a
href="http://www.eso.org/sci/data-processing/software/sampo/reflex/";>ESO
Reflex</a>.
-ESO Refex allows users to connect together C programs that reduce the raw data
produced by ESO instruments.</p>
-<h3 id="publications_1">Publications</h3>
-<p>The <a
href="http://www.springerlink.com/content/p67480k2w7311315/";>paper</a> <em>ESO
Reflex: A Graphical Workflow Engine for Running Recipes</em> by Hook et al,
describes the
- ESO Reflex workbench.</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biodiversity.html
Wed Mar 11 08:37:10 2015
@@ -104,116 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Biodiversity</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p><a
href="/introduction/related-projects#biovel">BioVel</a> - establishing an
international e-Laboratory to allow biodiversity scientists to jointly tackle
- diverse research challenges using Taverna, myExperiment and
BioCatalogue</p></div>
-
- </div>
-
- <footer class="footer">
- <div class="container">
- <p id="copyright" class="text-muted">
- Copyright © 2014-2015 The Apache Software Foundation,
Licensed under the
- <a href="http://www.apache.org/licenses/LICENSE-2.0";>Apache
License, Version 2.0</a>.
- Apache and the Apache feather logo are trademarks of The Apache
Software Foundation.
- </p>
- </div>
- </footer>
-
-
-
- <script src="/lib/jquery/jquery-1.11.1.min.js"></script>
-<script src="/lib/bootstrap/js/bootstrap.min.js"></script>
-
-<script>
- jQuery(function($) {
- if($(window).width()>769){
- $('.navbar .dropdown').hover(function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(250).slideDown();
-
- }, function() {
- $(this).find('.dropdown-menu').first().stop(true,
true).delay(100).slideUp();
-
- });
-
- $('.navbar .dropdown > a').click(function(){
- location.href = this.href;
- });
-
- }
- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/bioinformatics.html
Wed Mar 11 08:37:10 2015
@@ -104,220 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Bioinformatics</h1>
- <div class="alert alert-info" role="alert"><p><span class="glyphicon
glyphicon-info-sign" aria-hidden="true"></span>
-
-Taverna is transitioning to the Apache Incubator.
-This webpage reflects material not yet released under Apache Incubator.
-Instead it shows <a class="alert-link"
href="http://www.taverna.org.uk/";>taverna2</a> material that is expected to
become part of the Apache Incubator project in the future.
-</div>
-
-
- <div id="content"><p>Taverna can connect to a wide variety of
bioinformatics resources and has been successfully applied to a number
- of bioinformatics problems, listed below according to their sub-domains.
-<img class="aligncenter"
- title="Bioinformatics services and resources"
- src="/img/BioinformaticsResources.png"
- alt="Bioinformatics services and resources" width="676" height="441"
/></p>
-<p>Bioinformatics systems/tools using Taverna:</p>
-<ul>
-<li><a href="#biowep">BioWEP</a> - bioinformatics workflow enactment
portal</li>
-<li><a href="#biolinux">BioLinux</a> - Ubuntu Linux distribution that includes
Taverna and many other bioinformatics programs</li>
-</ul>
-<h3 id="biodiversity">Biodiversity</h3>
-<ul>
-<li><a href="/introduction/related-projects#biovel">BioVeL</a></li>
-</ul>
-<h3 id="gene-and-genome-expression">Gene and genome expression</h3>
-<ul>
-<li><a
href="/introduction/taverna-in-use/genome-and-gene-expression#next-generation-sequencing">Next
Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
-<li><a
href="/introduction/taverna-in-use/genome-and-gene-expression#tavernapbs">TavernaPBS</a>
- next generation sequencing analysis using a computational cluster that uses
a PBS
- queuing system and Taverna 2 Workbench</li>
-<li><a
href="/introduction/taverna-in-use/genome-and-gene-expression#casimir">Coordination
and Sustainability of International Mouse Informatics Resources</a> (CASIMIR)
-
- workflows to associate mouse genome and phenome</li>
-<li><a
href="/introduction/taverna-in-use/genome-and-gene-expression#dgemap">Developmental
Gene Expression Map</a> (DGEMap)- analysis of human gene expression during
development</li>
-<li><a
href="/introduction/taverna-in-use/disease-research#graves-disease">Graves
disease</a> - identification of genes responsible</li>
-<li><a
href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">Examination
of gene expression from MicroArray data using R</a> - statistical analysis of
gene expression</li>
-<li><a
href="/introduction/taverna-in-use/genome-and-gene-expression#sigenae">SIGENAE</a>
- development of workflows to analyse breeding animal data</li>
-<li><a
href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a>
- identification of genes responsible for sleeping sickness</li>
-<li><a
href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren
syndrome</a> - automation and confirmation of gene characterization</li>
-<li><a href="/introduction/taverna-in-use/biology#planet">PLANET</a> -
integration of plant genome resources</li>
-<li><a
href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Annotation
of genomes</a></a></li>
-<li><a href="/introduction/related-projects#shared-genomics">Shared
Genomics</a></a></li>
-<li><a href="http://img.cs.man.ac.uk/efungi/";>e-Fungi</a> functional genomics
in fungal species</li>
-</ul>
-<h3 id="protein-and-proteomics">Protein and proteomics</h3>
-<ul>
-<li><a href="#lumc">Analysis of mass spectrometry data in proteomics</a></li>
-<li><a
href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Anthrax
analysis</a> - identification of proteins secreted by bacteria</li>
-<li><a href="/introduction/taverna-in-use/databases#efamily">eFamily</a> -
integrating data from different databases</li>
-<li><a
href="http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace";>European
Model for Bioinformatics Research And Community Education</a> (EMBRACE) -
- calling services on a grid; recovering a database</li>
-<li><a href="/introduction/related-projects#ispider">iSpider</a> - querying
multiple data sources</li>
-<li><a
href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a> -
running of Taverna workflows behind a portal to search a protein database</li>
-</ul>
-<h3 id="biology-and-systems-biology">Biology and systems biology</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/biology#enfin">ENFIN</a> â
Enabling Systems Biology â calling of wrapped tools within workflows</li>
-<li><a
href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">Manchester
Centre for Integrative Systems Biology</a> (MCISB) â modelling metabolomic
pathways</li>
-<li><a href="/introduction/taverna-in-use/biology#sb-os">Systems Biology
Operational Software</a> (SB.OS) - a live DVD based on Ubuntu Linux that comes
with a
- comprehensive list of Systems Biology Software (including Taverna)</li>
-<li><a href="/introduction/taverna-in-use/biology#tav4sb">Tav4SB</a> - Taverna
workflows for systems biology,
- in particular for analysis of the kinetic models of biological
systems</li>
-<li><a href="#measuring-enzyme-characteristics-of-yeast">Measuring of enzyme
characteristics of yeast</a></li>
-<li><a href="/introduction/taverna-in-use/annotation.html#afawe">Automatic
Functional Annotation in a distributed Web Service Environment</a> (AFAWE) â
- protein prediction and annotation by a tool that calls workflows</li>
-<li><a href="/introduction/taverna-in-use/biology#planet">PLANET (A Network of
European Plant Databases)</a> â calling of workflows from a portal</li>
-</ul>
-<h3 id="biomedicine-and-disease-related-research">Biomedicine and
disease-related research</h3>
-<ul>
-<li><a
href="/introduction/taverna-in-use/disease-research#vph-dareit">Fighting
dementia</a> (VP-DARE@IT and VPH-SHARE)</li>
-<li><a
href="/introduction/taverna-in-use/disease-research#analysis-of-anthrax-bacterium">Analysis
of the anthrax bacterium</a></li>
-<li><a href="/introduction/taverna-in-use#trypanosomiasis">Study of resistance
into trypanosomiasis</a> (sleeping sickness)</li>
-<li><a
href="/introduction/taverna-in-use/disease-research#graves-disease">Identification
of genes linked to Graves disease</a></li>
-<li><a
href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Characterisation
of genes associated with Williams-Beuren syndrome</a></li>
-<li><a href="/introduction/related-projects#cagrid">caGrid</a> - research into
predicting limphoma cancer</li>
-<li><a href="/introduction/taverna-in-use/medicine#eu-adr">EU-ADR</a> -
detecting adverse drug reactions through the exploitation of clinical data from
electronic
- healthcare records</li>
-</ul>
-<p><a name="biowep"></a></p>
-<h3 id="biowep">BioWEP</h3>
-<p>Researchers at the Italian National Institute for Cancer Research Genoa (<a
href="http://www.istge.it/";>IST</a>) have developed a
- Bioinformatics Workflow Enactment Portal called <a
href="http://bioinformatics.istge.it/biowep/index.html";>BioWEP</a>.</p>
-<p>The <a href="http://bioinformatics.istge.it:8080/biowep/";>portal</a> allows
registered users to search for or select from a set of specified Taverna
workflows.
-The workflow can be enacted by entering input values into a form.
-During enaction, the user can either wait for the result, or for longer
running workflows,
- visit the portal later. The results of the enactment can be downloaded for
external visualization.</p>
-<h4 id="publications">Publications</h4>
-<p>The http://dx.doi.org/10.1186/1471-2105-8-S1-S19 <em>Biowep: a workflow
enactment portal for bioinformatics
- applications</em> by Romano et al gives an overview of the intent and
design of Biowep.</p>
-<p><a naem="biolinux"></a></p>
-<h3 id="biolinux">BioLinux</h3>
-<p>The UKâs Natural Environment Research Council (NERC) Environmental
Bioinformatics <a href="http://nebc.nox.ac.uk/";>Centre</a> release
- <a href="http://nebc.nox.ac.uk/biolinux.html";>BioLinux</a>, an installation
of Ubuntu Linux that includes many bioinformatics programs.</p>
-<p>Among the programs included in the BioLinux distribution is Taverna.<br />
-The suite of programs are also available for installation on pre-existing
Linux systems.</p>
-<p><a name="lumc"></a></p>
-<h3 id="lumc">LUMC</h3>
-<p>People from the Leiden University Medical Center (<a
href="https://www.lumc.nl/";>LUMC</a> in the Netherlands are using Taverna for
analysis
- of mass spectrometry data in proteomics.</p>
-<p>They presented a <a
href="http://www.taverna.org.uk/pages/wp-content/uploads/2011/06/Palmblad_ASMS_2011_LUMC.pdf";>poster</a>
at the 2011 ASMS (the American Society for Mass Spectrometry) Conference on
- Mass Spectrometry and Allied Topics.</p>
-<p>Please contact <a
href="https://www.lumc.nl/org/proteomics-metabolomics/medewerkers/nmpalmblad";>Dr.
Magnus Palmblad</a> for more details.</p>
-<p><a name="measuring-enzyme-characteristics-of-yeast"></a></p>
-<h3 id="measuring-enzyme-characteristics-of-yeast">Measuring enzyme
characteristics of yeast</h3>
-<p>The <a
href="/introduction/taverna-in-use/biology#manchester-centre-for-integrative-systems-biology">Manchester
Centre for Integrative Systems Biology</a> (MCISB) is in the process of
measuring the
- kinetic and binding constants associated with enzyme reactions in metabolic
pathways in the yeast,
- Saccharomyces cerevisiae.
-Quantitative models of these metabolic pathways are being integrated with
transcriptomic, proteomic and
- metabolomic data by workflows that have been constructed and enacted using
Taverna.</p>
-<h4 id="publications_1">Publications</h4>
-<p>A <a
href="http://www.mygrid.org.uk/files/2008/09/peter-li-poster.pdf";>poster</a> by
Peter Li describing the systems biology workflows was presented at the
International
- Conference of Systems Biology 2006 and he has written several publications
about the work.</p>
-<p>Many of the workflows make use of Systems Biology Markup Language (<a
href="http://sbml.org/";>SBML</a>) as described in the
- <a
href="http://bioinformatics.oxfordjournals.org/content/24/2/287.full.pdf";>paper</a>
- <em>Automated manipulation of systems biology models using libSBML within
Taverna workflows</em>
- by Li et al.</p>
-<p>An <a href="http://www.myexperiment.org/workflows/79";>example workflow</a>
using SBML is available on <a
href="http://www.myexperiment.org/";>myExperiment</a>.</p></div>
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