Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/natural-language-processing.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/natural-language-processing.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/natural-language-processing.html
Wed Mar 11 08:37:10 2015
@@ -104,136 +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>Natural Language Processing</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>PANACEA addressing the most critical
aspect for Machine Translation (MT).</p>
-<p><a name="panacea"></a></p>
-<h2 id="panacea">PANACEA</h2>
-<p><a href="http://www.panacea-lr.eu/";>PANACEA</a> is a EU funded project
whose objective is to build a factory of Language Resources that automates the
- stages involved in the acquisition, production, updating and maintenance of
language resources required by
- MT systems, and by other applications based on Language Technologies, and
within the time required.
-The architecture of the factory platform is based on deploying NLP tools as
Web Services (WS),
- using the SOAP or REST standards (the aim is to be as interoperable as
possible).
-PANACEA uses <a href="http://soaplab.sourceforge.net/soaplab2/";>Soaplab</a> as
it provides a convenient way to generate WSs for command-line software
- (most NLP tools belong to this type).
-Once the WSs are deployed users may want to combine them to create complex
chains.
-<a href="http://www.taverna.org.uk";>Taverna</a> workflow editor and engine is
the tool used in the platform to combine WSs.
-This tool allows the user to create complex workflows with different kinds of
WSs (SOAP, REST, secure WSs, etc.)
- within a GUI.</p>
-<p>The second version of the platform was presented during the second year
project review which was held on
- February 29, at UPF premises in Barcelona, Spain.
-It was headed by Kimmo Rossi, as EC Project Officer, and by Serge Sharoff
(University of Leeds, U.K.) and
- Gregory Grefenstette (Exalead, France), as project reviewers.
-The project development was positively evaluated and both the project Officer
and the reviewers complimented
- the achievements presented while being constructively detailed in their
remarks.
-In special the review report stated that âThe partners gave an impressive
demonstration of the second versión
- of the integrated platformâ.</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/other.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/other.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/other.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>Other uses of 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><a name="moteur"></a></p>
-<h2 id="moteur">MOTEUR</h2>
-<p><a
href="http://modalis.polytech.unice.fr/softwares/moteur/start";>MOTEUR</a> is a
workflow enactor designed to run
- Taverna 1.x workflows on a grid.<br />
-Its main feature is to enable data, service and workflow parallelism during
execution of the workflow.</p>
-<p>MOTEUR allows the workflows to be run on an Enabling Grids for E-sciencE<br
/>
- (<a href="http://eu-egee-org.web.cern.ch/eu-egee-org/index.html";>EGEE</a>)
or
- <a
href="https://www.grid5000.fr/mediawiki/index.php/Grid5000:Home";>GRIDâ5000</a>
grid.</p>
-<p>The workflows run by MOTEUR must be designed and edited using Taverna.</p>
-<h3 id="publications">Publications</h3>
-<p>MOTEUR is described in the <a
href="http://portal.acm.org/citation.cfm?id=1400050.1400057";>paper</a>
- <em>Flexible and efficient workflow deployement of data-intensive
applications on grids with MOTEUR</em> by Glatard et al.</p>
-<p><a name="simdat"></a></p>
-<h2 id="simdat">SIMDAT</h2>
-<p>The Grids for Industrial Product Development SIMDAT <a
href="http://www.simdat.org/";>project</a>
- involves a large number of European academic and commercial
- <a href="http://www.simdat.org/partners_simdat.html";>partners</a>.</p>
-<p>The SIMDAT project takes industrial product and process development forward
by introducing advanced Grid technology
- in the automotive, aerospace, pharmaceutical and meteorological domains.</p>
-<p>Under the SIMDAT project, a <a href="http://www.gria.org/";>GRIA</a>
- <a
href="http://www.gria.org/documentation/5.2/manual/gria-workflow-plugins-for-taverna/installation/?searchterm=taverna";>plugin</a>
- was developed for Taverna to allow Taverna workflows to access services on
a grid.</p>
-<h3 id="publications_1">Publications</h3>
-<p>Some of the work within SIMDAT is detailed in the
- <a
href="http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=4031069";>paper</a>
- <em>Grid-Enabled Workflows for Industrial Product Design</em> by Ghanem 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/protein-and-proteomics.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/protein-and-proteomics.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/protein-and-proteomics.html
Wed Mar 11 08:37:10 2015
@@ -104,135 +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>Protein and proteomics</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 projects and
researchers for the analysis of proteins and proteomics:</p>
-<ul>
-<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="#prodom">ProDom</a> -running of Taverna workflows behind a portal
to search a protein database</li>
-</ul>
-<p><a name="prodom"></a></p>
-<h2 id="prodom">ProDom</h2>
-<p><a href="http://prodom.prabi.fr/";>ProDom</a> is a comprehensive database of
protein domain families generated
- from the global comparison of all available protein sequences.
-It was developed at the Rhône-Alpes Bioinformatics Center (<a
href="http://www.prabi.fr/";>PRABI</a>).</p>
-<p>ProDom is described in the <a
href="http://dx.doi.org/10.1093/nar/gki034";>paper</a>
- *The ProDom database of protein domain families: more emphasis on 3D * by
Bru et al.</p>
-<p>A Web-based front-end is <a
href="http://prodom.prabi.fr/prodom/current/html/form.php";>available</a>
- to perform searches and comparisons on the content of the database.</p>
-<p>Some of the queries used by the front-end make use of Taverna
- <a
href="http://prodom.prabi.fr/prodom/current/html/webservices.html";>workflows</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-in-use/service-provision.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-provision.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-provision.html
Wed Mar 11 08:37:10 2015
@@ -104,120 +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>Service provision</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"><ul>
-<li>Enable Taverna workflows in a
- <a href="/introduction/related-projects#shared-genomics">Shared
Genomics</a>
- causality workbench as services using the
- <a href="/documentation/server">Taverna Server</a> to run workflows.</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/introduction/taverna-in-use/service-testing.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-testing.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/service-testing.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>Service testing</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>Many projects and individual researchers
develop Web services.<br />
-Taverna is often used as a testbed to evaluate the functionality of the Web
services and also as a workflow editor
- and enactor for the projectâs users.
-These Web service developers include:</p>
-<ul>
-<li><a href="/introduction/related-projects#e-fungi">e-Fungi</a></li>
-<li><a href="/introduction/taverna-in-use/annotation#adoption-by-moby">Moby
consortium</a></li>
-<li><a href="/introduction/taverna-in-use/arts#composition-of-music">Music
composition</a></li>
-<li><a href="/introduction/related-projects#ondex">ONDEX</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/introduction/taverna-in-use/social-sciences.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/social-sciences.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/social-sciences.html
Wed Mar 11 08:37:10 2015
@@ -104,120 +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>Social sciences</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"><ul>
-<li><a href="/introduction/related-projects.html#neiss">NeISS</a>
- project works on developing Taverna workflows for various social
simulations and running them in portals
- using the Taverna Server. The wokflows are going to be used in
population and traffic simulations and for
- drawing of the resulting geo-social maps and help social scientists with
various predictions.</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/introduction/taverna-in-use/systems-biology.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/systems-biology.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/systems-biology.html
Wed Mar 11 08:37:10 2015
@@ -104,139 +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>Systems biology</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 projects and
researchers for investigations into systems biology:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/biology#enfin">ENFIN â Enabling
Systems Biology</a> 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) â a live DVD based on Ubuntu Linux that comes with a
comprehensive list of Systems Biology Software
- (including Taverna)</li>
-<li><a href="#metware">MetWare</a> - applications, databases and workflows for
metabolomics</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="/introduction/taverna-in-use/biology#ccpn">CCPN</a> - Taverna is
used to encapsulate and combine protocols between
- WeNMR (Worldwide e-Infrastructure for NMR and structural biology)
portals and CCPN's
- (Collaborative Computing Project for NMR) software. </li>
-</ul>
-<p><a name="metware"></a></p>
-<h2 id="metware">MetWare</h2>
-<p>The MetWare project provides applications, databases and workflows for
metabolomics.
-The MetWare project is a collaboration between several metabolomics groups in
the Netherlands and Germany.</p>
-<p>The work involving Taverna workflows is done by
- <a
href="http://www.ipb-halle.de/en/research/stress-and-developmental-biology/all-staff/";>Steffen
Neumanns group (Bioinformatics & Mass Spectrometry)</a>.</p>
-<p>They developed a Web-based player of Taverna workflows and also have
uploaded their workflows on myExperiment at
- <a
href="http://www.myexperiment.org/users/937/workflows";>http://www.myexperiment.org/users/937/workflows</a>.</p>
-<p><a
href="http://sourceforge.net/apps/mediawiki/metware/index.php?title=Main_Page";>Software
project page</a> can be found at Sorceforge.</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/what-is-a-workflow-management-system.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/what-is-a-workflow-management-system.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/what-is-a-workflow-management-system.html
Wed Mar 11 08:37:10 2015
@@ -104,122 +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>What is a Workflow Management System?</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>Workflow Management System (WMS) is a
piece of software that provides an infrastructure to setup, execute,
- and monitor <a href="/introduction/why-use-workflows">scientific
workflows</a>.
-In other words, the WMS provide an environment where in
- <a href="/introduction/what-is-in-silico-experimentation">silico
experiments</a> can be defined and executed.</p>
-<p>An important function of an WMS during the workflow execution, or
enactment, is the coordination of operation of individual components that
constitute the workflow â the process also often referred to as
orchestration.</p>
-<p>As research becomes more data-intensive and more reliant on the use of
computers, larger volumes of experimentation data are recorded quicker and with
greater precision. This trend has spurred significant increase in complexity of
scientific simulation software. Many tools only perform a small well-defined
task, thus necessitating that several of them are joined in a pipeline to model
a useful experiment.</p>
-<p>Additional difficulties arise from the need to deal with the
â¨incompatible data formats that various services produce or consume. â¨It is
evident that considerable amount of computer science knowledge is required to
overcome the â¨outlined problems; however, domain scientists across
disciplines do not have sufficient relevant â¨expertise.</p>
-<p>Scientific workflows and WMSs have emerged to solve this problem and
provide an easy-to-use â¨way of specifying the tasks that have to be performed
during a specific in silico experiment. The â¨need to combine several tools
into a single research analysis still holds, but technical details of
â¨workflow execution are now delegated to Workflow Management
Systems.</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/what-is-in-silico-experimentation.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/what-is-in-silico-experimentation.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/what-is-in-silico-experimentation.html
Wed Mar 11 08:37:10 2015
@@ -104,142 +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>What is âin silicoâ experimentation?</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 rapid increase in the processing power
of computers in the past few decades has enabled the emergence
-of in silico experimentation across many domains, where research is conducted
via computer simulations
-with models closely reflecting the real world.</p>
-<p>In silico experimentation provides researchers with a number of significant
advantages:</p>
-<ul>
-<li>higher precision and better quality of experimental data;</li>
-<li>better support for data-intensive research and access to vast sets of</li>
-<li>experimental data generated by scientific communities;</li>
-<li>more accurate simulations through more sophisticated models;</li>
-<li>faster individual experiments;</li>
-<li>higher work productivity.</li>
-</ul>
-<p>In silico experimentation nowadays suffers from an increased complexity of
setting up,
- maintaining and making changes to the experimental simulation systems.
-Such systems often involve a range of heterogeneous components: modules for
preparation,
- extraction and conversion of data, program codes that perform
experiment-related computations,
- and scripts that join the other components and make them work as a coherent
system which is capable
- of displaying desired behaviour.
-Interaction with such a system involves a great amount of purely computing
aspects.</p>
-<p>A regular researcher (for example, a biologist or chemist) may not have
enough background knowledge to
- configure and tune the system to his needs.
-Insufficient computing background â which is natural for scientists as it is
not the focus of their work â
- acts as a strong barrier in adoption and distribution of scientific
applications,
- thus leaving these applications inaccessible for the majority of
researchers.</p>
-<p><a href="/introduction/why-use-workflows">Scientific workflows</a> offer a
solution to this problem.
-They provide an easy-to-use declarative way of specifying the tasks that have
to be performed during
- a specific in silico experiment, whereas the technical details of workflow
execution are now delegated
- to a <a href="/introduction/what-is-a-workflow-management-system">Workflow
Management System</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/why-use-workflows.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/why-use-workflows.html
(original)
+++ websites/staging/taverna/trunk/content/introduction/why-use-workflows.html
Wed Mar 11 08:37:10 2015
@@ -104,178 +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>Why use 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"><h2 id="history">History</h2>
-<p>Workflow, as a concept, was defined in the business domain in 1996 by the
Workflow Management Coalition as:</p>
-<blockquote>
-<p>âThe automation of a business process, in whole or part, during which
documents,
- information or tasks are passed from one participant to another for action,
- according to a set of procedural rules.â</p>
-</blockquote>
-<h2 id="scientific-workflows">Scientific workflows</h2>
-<p>Scientific workflows are widely recognised as a âuseful paradigm to
describe, manage,
- and share complex scientific analysesâ. They are the method often used by
the
- <a href="/introduction/what-is-in-silico-experimentation">in silico
experimentation</a>.</p>
-<p>Scientific workflows have emerged to tackle the problem of excessive
complexity in scientific experiments and
- applications.
-They provide a high-level declarative way of specifying what a particular in
silico experiment modelled
-by a workflow is set to achieve, not how it will be executed.</p>
-<p>Various types of tasks that can be performed within a workflow can be
implemented by local services,
- remote Web services, scripts, and sub-workflows (complete workflows used as
subroutines in larger ones).
-Each component is only responsible for a small fragment of functionality,
- therefore many components need to be chained in a pipeline in order to
obtain a workflow that can perform
- a useful task.</p>
-<p>The process of linking components is known as workflow composition,
- a result of which a conceptual model of the described scientific analysis
is produced.
-This model is often represented as a graph-like structure (example can be seen
in Figure 1 below)
- that defines the flow of data within the workflow â and thus its semantic
meaning.
-Representations of all required heterogeneous resources are integrated into
this single workflow,
- thus abstracting superfluous detail and concentrating on the real goal of
the experiment.</p>
-<p>An example of simple workflow that retrieves a weather forecast for the
specified city</p>
-<p class="text-center">
-<img title="Get weather forecast for a city workflow"
src="/img/get_weather_workflow.png"
- alt="An example of simple workflow that retrieves a weather forecast for
the specified city"
- width="195" height="269" />
-</p>
-
-<p class="text-center">
-Figure 1. An example of a simple workflow that retrieves a weather forecast
for the specified city
-</p>
-
-<p>The use of workflows allows offloading much of the data processing to
remote components and
- makes it feasible to execute even larger and more complex workflows on
regular personal computers.
-This is the reason why Web services are normally chosen to perform most of the
core computation in workflows,
- whereas local services and scripts are used to perform data format
conversion procedures and
- other auxiliary tasks.</p>
-<p>A further advantage of using workflows is the potential to automate highly
repetitive processing stages that
- research work is known to involve. This, in turn, can stimulate the pace of
research and
- the overall productivity of experimentation through evident savings in time
and effort.</p>
-<p>To learn more about scientific workflows and their role in data-intensive
experiments, have a look at:</p>
-<ul>
-<li><a
href="http://research.microsoft.com/en-us/collaboration/fourthparadigm/4th_paradigm_book_part3_goble_deroure.pdf";>âThe
impact of workflow tools on data-centric researchâ</a>
- chapter by Carole Goble and David De Roure of the
- <a
href="http://research.microsoft.com/en-us/collaboration/fourthparadigm/";>âThe
Fourth Paradigm: Data-Intensive Scientific Discoveryâ</a>
- book.</li>
-<li><a
href="http://cnx.org/contents/8fedc2ef-93a4-4f55-9bca-52820a2586b7@3/Scientific_Workflows";>âScientific
workflowsâ</a>
- paper by Katy Wolstencroft, Paul Fisher, David De Roure and Carole
Goble.</li>
-</ul>
-<p>Massive power, minimal complexity</p>
-<p>Because services within a workflow do not normally reside on the machine
you use to create and run the workflow,
- your local machine does not have to be a supercomputer.
-By installing and using the Taverna
- [Workflow Management
System(/introduction/what-is-a-workflow-management-system)
- you can tap into the resources of
- a number of institutes, hundreds of analysis applications and literally
thousands of CPUs worth of
- computational power entirely for free, with no installation or support
hassle for you.</p>
-<p>Of course, if you already have significant resource in house it is a
relatively simple matter to
- integrate these resources in Taverna with those available from other
sites.</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/works-with.html
==============================================================================
--- websites/staging/taverna/trunk/content/introduction/works-with.html
(original)
+++ websites/staging/taverna/trunk/content/introduction/works-with.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
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glyphicon-info-sign" aria-hidden="true"></span>
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-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 directly interfaces with a range
of software tools and systems.
-Currently Taverna works with the following:</p>
-<ul>
-<li><a href="http://www.biomart.org/"; target="_blank">
- <img src="/img/biomart.gif" alt="BioMart" width="61" height="19" /></a>
<br />
-<a href="#biomart">Biomart</a></li>
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- <img src="/img/Rshell.png" alt="RShell" width="29" height="21" /></a>
<br />
-<a href="#r">R</a></a> </li>
-<li><a href="http://www.bioconductor.org/"; target="_blank">
- <img src="/img/logo_bioconductor.gif" alt="Bioconductor" width="130"
height="39" /></a> <br />
-<a href="#bioconductor">Bioconductor</a></a></li>
-<li>A number of <a href="/documentation/plugins">third party plugins</a></li>
-</ul>
-<p><a name="biomart"></a></p>
-<h2 id="biomart">Biomart</h2>
-<ul>
-<li><a href="http://www.biomart.org/"; target="_blank">
- <img src="/img/biomart.gif" alt="BioMart" width="61" height="19" ></a>
</li>
-</ul>
-<p>The <a href="http://www.biomart.org/";>Biomart system</a> is a flexible data
warehouse aimed at complex interlinked biological data sets.
-It enables the retrieval of large amounts of genomic data e.g. from Ensembl
and Sanger, as well as Uniprot,
- MSD datasets and many more.
-The <a href="http://dev.mygrid.org.uk/wiki/display/taverna/Biomart";>Biomart
service</a> is one of the default Taverna services.</p>
-<p><a name="soaplab"></a></p>
-<h2 id="soaplab">SoapLab</h2>
-<ul>
-<li><a href="http://sourceforge.net/p/soaplab/wiki/Home/"; target="_blank">
- <img src="/img/Soaplab.png" alt="SoapLab" width="33" height="25" ></a>
</li>
-</ul>
-<p><a href="http://sourceforge.net/p/soaplab/wiki/Home/";>SoapLab</a> services
are command line applications, wrapped as SOAP services, and served from a
Soaplab server.
-Soaplab is especially well suited for applications with well described input
and output parameters
-(such as EMBOSS sequence analysis)</p>
-<p><a name="sadi"></a></p>
-<h2 id="sadi">SADI</h2>
-<ul>
-<li><a href="/documentation/plugins/#sadi_plugin">
- <img src="/img/sadi-header-small.png" alt="SADI" ></a> <br />
-Semantic Web services described using the SADI framework</li>
-</ul>
-<p><a name="r"></a></p>
-<h2 id="r">R</h2>
-<ul>
-<li><a href="http://www.r-project.org/"; target="_blank">
- <img src="/img/Rshell.png" alt="RShell" width="29" height="21" ></a></li>
-</ul>
-<p><a href="http://www.r-project.org/";>R</a> is a popular scripting language
oriented towards statistical computing.
-The <a
href="http://dev.mygrid.org.uk/wiki/display/taverna23/Rshell";>Rshell</a>
service in Taverna allows your workflow to include services that run R scripts
on an
- R installation.</p>
-<p><a name="bioconductor"></a></p>
-<h2 id="bioconductor">Bioconductor</h2>
-<ul>
-<li><a href="http://www.bioconductor.org/"; target="_blank">
- <img src="/img/logo_bioconductor.gif" alt="Bioconductor" width="130"
height="39" ></a><br /></li>
-</ul>
-<p><a href="http://www.bioconductor.org/";>Bioconductor</a> provides tools for
the analysis and comprehension of high-throughput genomic data.
-Bioconductor uses the R statistical programming language, and is open source
and open development</p></div>
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