Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/biology.html
Wed Mar 11 08:37:10 2015
@@ -104,257 +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>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="#enfin">ENFIN â Enabling Systems Biology</a> â calling of
wrapped tools within workflows</li>
-<li><a href="#manchester-centre-for-integrative-systems-biology">Manchester
Centre for Integrative Systems Biology</a>
- (MCISB) â modelling metabolomic pathways</li>
-<li><a href="#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="#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>Taverna is also used for analysis of plant biology:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/annotation#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="#planet">PLANET (A Network of European Plant Databases)</a> â
calling of workflows from a portal</li>
-</ul>
-<p><a name="enfin"></a></p>
-<h2 id="enfin">ENFIN</h2>
-<p>The partners within the ENFIN - Enabling Systems Biology <a
href="http://www.enfin.org/";>project</a>
- developed a suite of Systems Biology tools (ENSUITE).
-These tools are also available as normal WSDL services and their possible use
within workflows has been
- demonstrated by use of Taverna.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a
href="http://www.springerlink.com/content/hw667700pm2170j4/";>paper</a>
- <em>ENFIN - An Integrative Structure for Systems Biology</em>
- by Reisinger et al. describes the overall design and structure of ENFIN.</p>
-<p><a name="manchester-centre-for-integrative-systems-biology"></a></p>
-<h2 id="manchester-centre-for-integrative-systems-biology">Manchester Centre
for Integrative Systems Biology</h2>
-<p>The <a href="http://www.bbsrc.ac.uk/";>BBSRC</a> and <a
href="http://www.epsrc.ac.uk/";>EPSRC</a> have awarded £6.3m to the
- <a href="http://www.mcisb.org/";>Manchester Centre for Integrative Systems
Biology</a>
- (MCISB) based at the <a href="http://www.mib.ac.uk/";>Manchester
Interdisciplinary Biocentre</a> (MIB).
-The award is to pioneer the development of new experimental and computational
technologies in Systems Biology,
- and their exploitation.</p>
-<p>The MCISB is intended to provide a hub for cutting-edge systems biology
research in the Manchester area,
- acting as a focal point for the creation of the necessary ideas and
infrastructure,
- and for establishing new methods and routines.</p>
-<p>The co-investigators in the project Professor <a
href="http://www.manchester.ac.uk/research/norman.paton";>Norman Paton</a>,
- Professor <a
href="http://www.manchester.ac.uk/research/Douglas.kell";>Douglas Kell</a> et
al.<br />
-It ran from May 2005 to April 2010.</p>
-<h3 id="metabolomic-pathways">Metabolomic Pathways</h3>
-<p>The Manchester Centre for Integrative Systems Biology 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>
-<h3 id="publications_1">Publications</h3>
-<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 example <a href="http://www.myexperiment.org/workflows/79";>workflow</a>
using SBML is available on
- <a href="http://www.myexperiment.org";>myExperiment</a>.</p>
-<p><a name="sb-os"></a></p>
-<h2 id="systems-biology-operational-software-sbos">Systems Biology Operational
Software (SB.OS)</h2>
-<p><a href="http://www.sbos.eu/doku.php";>SB.OS</a> is a live DVD based on
Ubuntu Linux that comes with
- a comprehensive list of Systems Biology Software.
-Text and video documentation material,
- as well as an offline copy of the BioModels.net database and Taverna 2.1,
are included.</p>
-<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>
-<p><a name="tav4sb"></a></p>
-<h2 id="tav4sb">Tav4SB</h2>
-<p><a href="http://bioputer.mimuw.edu.pl/tav4sb/";>Tav4SB project</a> provides
a grid environment with a set of Web services,
- bundled together in Taverna workflows.
-Target application area is the system biology field,
- in particular analysis of the kinetic models of biological systems.</p>
-<p><a name="ccpn"></a></p>
-<h2 id="ccpn">CCPN</h2>
-<p><strong>CCPN use of Taverna</strong>
-by Rasmus Fogh [email protected], Feb 2013</p>
-<p><a href="http://www.wenmr.eu/";>WeNMR</a> (Worldwide e-Infrastructure for
NMR and structural biology)
- is a virtual research community project that is funded as part of the 7th
EU framework.
-The infrastructure lies within the fields of structural biology, NMR and SAXS.
-Its purpose is twofold: It provides an infrastructure for sharing
documentation, outreach and communications.<br />
-It also offers web portals where structural biology programs can be run,
supports a grid infrastructure
- for running associated relevant jobs and provides software that presents
programs on the web portals and
- pipes data between them for uploading and downloading.</p>
-<p>Our contribution to the WeNMR project is the development of a dual use
Workflow Management System (WMS) as shown in Fig.1.
-Its two methods of use are as a:</p>
-<ul>
-<li>
-<p>means to launch, manage, and gather results generated by structural biology
calculations,
- making use of programs present on the WeNMR portals,
- in effect to serve as an entry port for WeNMR and associated
calculations in general.</p>
-</li>
-<li>
-<p>data tracking, management and access control system for structural biology
laboratories.</p>
-</li>
-</ul>
-<p><img alt="CCPN Use of Taverna" src="/img/CCPNuse.png" /></p>
-<p align="center">Fig. 1</p>
-
-<p>Taverna is being used to encapsulate and combine protocols on our system,
- so that the systems are available to, and can be combined with,
- workflow components from other sources,
- and to combine different protocols on our system into pipelines.
-The current test project is to develop a system to run four different
structure calculation programs
- from a single job start specification and collating the results into a
single combined data source.</p>
-<p>Whether Taverna is being used in a scientific role is down to the
definition of its role within the project.
-We are developing scientific software,
- which will be used to perform actual scientific research and analysis by
end users â
- we tend to categorise our role as that of methods developers for structural
biology.
-Whether that categorises the role as computer science, structural biology,
- or software engineering depends on the point of view.</p>
-<p>The <em>methods</em> are established programs for calculating (mainly)
macromolecular structures
- from Nuclear Magnetic Resonance data, and are therefore used as the primary
process for obtaining results.
-These types of calculation require the use of several different programs,
sequentially, to process them.
-Passing the data and results from one program to another has been a problem
for many years.
-CCPN has long been working on data exchange standards, data conversion
software and integration with different programs,
- and is now working explicitly on setting up pipelines.
-There is an ever-increasing demand for high-throughput calculations that allow
the use of alternative programs and
- that inexperienced users are able to utilise with ease.
-It is to meet these demands that Taverna is being used as a tool that enables
the setup of flexible,
- easy-to-use pipelines.</p>
-<p>About me:</p>
-<p>I am currently working at the University of Cambridge, Department of
Biochemistry,
- under Professor Ernest Laue.
-As part of my role I am attached to the <a href="http://www.ccpn.ac.uk/";>CCPN
project</a>,
- led by Professor Vuister (University of Leicester), formerly led by
Professor Laue.</p>
-<p><a name="planet"></a></p>
-<h2 id="planet">PLANET</h2>
-<p>As part of the <a href="http://www.eu-plant-genome.net/";>PLANET</a> (A
Network of European Plant Databases) project,
- <a href="http://www.breedwheat.fr/institutions.php?id=6";>URGI</a>
- (Unité de Recherche Génomique-Info) developed BioFloWeb.</p>
-<p>BioFloWeb is a stand-alone Web application processing Web services.
-A given user can choose among predefined workflows or define their own with
Taverna.
-BioFloWeb has been <a
href="http://biofloweb.sourceforge.net/";>demonstrated</a>
- for retrieval of information about Arabidopsis genes from several European
databases.</p>
-<p>BioFloWeb makes extensive use of <a
href="/introduction/taverna-in-use/annotation#adoption-by-moby">BioMoby</a>
services.</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,
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-
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- $(this).find('.dropdown-menu').first().stop(true,
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-
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-
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- location.href = this.href;
- });
-
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- });
-</script>
-
-
- </body>
-</html>
\ No newline at end of file
Modified:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/chemistry.html
Wed Mar 11 08:37:10 2015
@@ -104,152 +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>Chemistry</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 for
the creation of chemistry workflows. These include:</p>
-<ul>
-<li><a href="#chemistry-development-kit">Chemistry Development Kit</a> (CDK) -
integration of a chemistry-specific toolkit with Taverna</li>
-<li><a
href="#chemical-informatics-and-cyberinfrastructure-collaboratory">Chemical
Informatics and Cyberinfrastructure Collaboratory</a> (CICC) -use of Taverna
for workflow creation</li>
-</ul>
-<p><a name ="chemistry-development-kit"></a></p>
-<h2 id="chemistry-development-kit">Chemistry Development Kit</h2>
-<p>The Chemistry Development Kit (CDK) <a
href="http://sourceforge.net/projects/cdk";>project</a> have developed a
- <a href="/documentation/plugins#cdk">plugin</a>
- to allow their tools to be used within Taverna workflows.</p></p>
-<p>There is a myExperiment <a
href="http://www.myexperiment.org/groups/105";>group</a></a> for workflows using
the CDK-Taverna plugin.</p></p>
-<p>This work has been described in the <a
href="http://dx.doi.org/10.1186/1752-153X-2-S1-P27";>poster</a>
- <em>Creating chemo- & bioinformatics workflows, further developments
within the CDK-Taverna Project</em>
- by Kuhn et al.</p>
-<p>The latest posts from the CDK Taverna <a
href="http://cdktaverna.wordpress.com/";>Web site</a> are:</p>
-<ul>
-<li><a
href="https://cdktaverna.wordpress.com/2011/07/29/cdk-taverna-2-0-final-version-released/";>CDK-Taverna
2.0 Final version released</a></li>
-<li><a
href="https://cdktaverna.wordpress.com/2011/02/15/cdk-taverna-2-0-released/";>CDK-Taverna
2.0 released</a> </li>
-<li><a
href="http://cdktaverna.wordpress.com/2010/01/18/cdk-taverna-installation-instruction/";>CDK-Taverna
installation instructions</a></li>
-<li><a
href="http://cdktaverna.wordpress.com/2010/01/17/cdk-taverna-version-0-5-1-1-released/";>CDK-Taverna
Version 0.5.1.1 released</a></li>
-<li><a
href="http://cdktaverna.wordpress.com/2008/09/07/time-evaluation-for-calculating-molecular-descriptors-using-the-cdk/";>Time
evaluation for calculating molecular descriptors using the cdk</a></li>
-<li><a
href="http://cdktaverna.wordpress.com/2008/09/06/atom-typing-on-natural-products-with-the-cdk/";>Atom
typing on natural products with the cdk</a></li>
-<li><a
href="http://cdktaverna.wordpress.com/2008/08/29/myexperimentorg-plug-in-for-taverna/";>myExperiment.org
plug-in for Taverna</a></li>
-</ul>
-<p><a name
="chemical-informatics-and-cyberinfrastructure-collaboratory"></a></p>
-<h2 id="chemical-informatics-and-cyberinfrastructure-collaboratory">Chemical
Informatics and Cyberinfrastructure Collaboratory</h2>
-<p>Within the Chemical Informatics and Cyberinfrastructure Collaboratory
(CICC) project</p>
-<blockquote>
-<p>uses modern Grid technology to allow convenient integration of
-distributed chemistry tools, simulations, documents and databases
-among themselves and with similar biological resources.</p>
-</blockquote>
-<p>The members of the CICC are developing Taverna workflows</p>
-<blockquote>
-<p>which encapsulate important processes in chemoinformatics and drug
-design, use diverse kinds of information together in novel ways,<br />
-and which are of demonstrated scientific merit.</p>
-</blockquote></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>
-
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- 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/data-and-text-mining.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/data-and-text-mining.html
Wed Mar 11 08:37:10 2015
@@ -104,143 +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>Data and text mining</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 for the automation of data
and text mining by various projects and researchers.<br />
-These include:</p>
-<ul>
-<li><a href="/introduction/related-projects#e-lico">e-Lico</a> - building a
virtual e-science laboratory for interdisciplinary collaborative research in
data mining
- and data-intensive sciences</li>
-<li><a href="#aid">Adaptive Information Disclosure (AID) workflows</a> -
workflows to extract knowledge and data to
- associate proteins and diseases</li>
-<li><a href="/introduction/taverna-in-use/multimedia#course-generator">Course
generator</a></a> - workflow to create a course based upon user
requirements</li>
-<li><a href="/introduction/related-projects#refine">REFINE</a> - representing
evidence for interacting network elements</li>
-<li><a href="#open-software-development-workflows">Open software development
workflows</a> - modelling the development of open software projects</li>
-<li><a href="/introduction/taverna-in-use/annotation#taweka">TaWeka</a> -
mining databases for subsequent machine learning</li>
-</ul>
-<p><a name="aid"></a></p>
-<h2 id="aid">AID</h2>
-<p>Taverna is used by researchers at <a
href="http://www.mygrid.org.uk/outreach/collaboration/collaboration-with-nbic/";>NBIC</a>
as an enactment platform for <a
href="http://www.adaptivedisclosure.org/aida/workflows";>BioAID</a> workflows
from
- the AIDA (Adaptive Information Disclosure Application) toolkit developed by
<a href="http://www.vl-e.nl/";>VL-e</a>
- that offers services for knowledge extraction, text mining and knowledge
management.</p>
-<p>There is a myExperiment <a
href="http://www.myexperiment.org/groups/42";>group</a> for AID workflows.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a
href="https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CDMQFjAA&url=https%3A%2F%2Fbioinformatics.cs.vt.edu%2F~murali%2Fconference-fayfaars%2F2007-ismb-eccb%2FISMBECCB07%2FDemos%2Froos_20070511110510.pdf&ei=aBrSVPmcJYqS7AarnIG4BA&usg=AFQjCNFxsZFPdqYu7OqkwPd_-KIX4xQXPw&sig2=jqEU3XVUPOOgp0HTNVekxw&bvm=bv.85076809,d.ZGU";>presentation</a>
<em>My BioAID: personalised text mining with Web services from the AIDA
toolbox</em>
- by Marco Roos describes the use of the AIDA toolkit and Taverna.</p>
-<p><a name="open-software-development-workflows"></a></p>
-<h2 id="open-software-development-workflows">Open software development
workflows</h2>
-<p>Taverna has been used to model the research community developing open
source software together with
- the software itself.
-This work, done by the Free/Libre Open Source Software Research community is
described on the <a href="http://floss.syr.edu/";>Web site</a>,
- in particular their <a
href="http://floss.syr.edu/papers";>publications</a>.</p>
-<p>There is a myExperiment <a
href="http://www.myexperiment.org/groups/64";>group</a> for researchers studying
open source software development.<br />
-The myExperiment group share some of their Taverna <a
href="http://www.myexperiment.org/users/384/workflows";>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/databases.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/databases.html
Wed Mar 11 08:37:10 2015
@@ -104,169 +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>Databases</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>Various projects and researchers use
Taverna to access, collate and manipulate data from databases:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/multimedia#echase">Electronic
Cultural Heritage made Accessible for Sustainable Exploitation</a> (eCHASE)</li>
-<li><a href="#efamily">eFamily</a></li>
-<li><a href="#embrace">European Model for Bioinformatics Research And
Community Education</a> (EMBRACE)</li>
-<li><a href="/introduction/related-projects#ispider">iSpider</a></li>
-<li><a href="#omixed">omixed</a></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>
-<p><a name="efamily"></a></p>
-<h2 id="efamily">eFamily</h2>
-<p>The <a href="http://www.ebi.ac.uk/pdbe/docs/sifts/efamily.html";>eFamily
project</a> was designed to integrate the information contained in five major
protein databases.
- The project developed webservices to allow the calculation of results based
upon the content of
- several databases, and upon annotation of the data.</p>
-<p>The project made use of Taverna workflows to integrate the webservices,
- both those provided by the eFamily project and those developed
externally.</p>
-<h3 id="publications">Publications</h3>
-<p>Some details of this work are given in the
http://www.allhands.org.uk/2004/proceedings/papers/211.pdf
- <em>eFamily: Bridging Sequence and Structure</em> by Finn et al.</p>
-<p><a name="embrace"></a></p>
-<h2 id="embrace">EMBRACE</h2>
-<p><a href="http://www.embracegrid.info/";>EMBRACE</a> is the European Model
for Bioinformatics Research And Community Education (EMBRACE).
-It consists of a large number of partners throughout Europe</p>
-<blockquote>
-<p>The objective of EMBRACE is to draw together a wide group of experts
-throughout Europe who are involved in the use of information
-technology in the biomolecular sciences.<br />
-The EMBRACE Network of Excellence will optimise informatics and information
exploitation by
-pure and applied biological scientists in both the academic and commercial
sectors.</p>
-</blockquote>
-<p>The <a href="http://www.manchester.ac.uk/";>University of Manchester</a> is
a member of the EMBRACE project,
- and the Taverna Workbench has been adopted by EMBRACE as its workflow
system of choice.</p>
-<p>The suitability of Taverna Workbench has been confirmed by its use in
several test cases:</p>
-<ul>
-<li>The use of Taverna to access Grid Protein Sequence Analysis (GPSA) Web
services as described by
- Blanchet et al. in the <a
href="http://dx.doi.org/10.1007/11946465_22";>paper</a>
- <em>Web Services Interface to Run Protein Sequence Tools on Grid,
Testcase of Protein Sequence Alignment</em>.
- This includes the running of the Web services on <a
href="https://eu-egee-org.web.cern.ch/eu-egee-org/index.html";>EGEE</a>
grid.</li>
-<li>Taverna has been used to automate the cleaning up and extraction of data
by the EMBRACE project from the
- tGRAP database of mutated G-protein coupled receptors.</li>
-<li>The ProDom-based protein family analyses test case includes the use of
Taverna within <a
href="/introduction/taverna-in-use/protein-and-proteomics#prodom">ProDom</a>.</li>
-</ul>
-<p>The tGRAP work is described in the <a
href="http://www.myexperiment.org/files/29";>document</a> <em>The reincarnation
of the tGRAP database</em> by Vroling.</p>
-<p>Use of Taverna allows the members of EMBRACE to have ready access to the
existing bioinformatics services and
- also to the myGrid teamâs expertise in this area. Correspondingly, the
members of EMBRACE represent
- a diverse group of users with different backgrounds and infrastructure.</p>
-<p><a name="omixed"></a></p>
-<h2 id="omixed">omixed</h2>
-<p><a href="http://nebc.nerc.ac.uk/tools/omixed/overview";>omixed</a></a> is a
âcustomisable storage system for scientific data, completely managed via web
servicesâ.
-Its developers have written a Taverna 1.7.x <a
href="http://www.omixed.org/documentation/omixed%20taverna%20plugin";>plugin</a>
to allow users to access data.</p>
-<p>The plugin âprovides two endpoints giving full control of omixed
resources.
-The first endpoint, known as the server endpoint, is designed for most users
who want to browse, download,
- or add to or modify existing resources.
-The second point, known as the admin endpoint, is designed for administrators
to create and delete resources,
- assign schema to them, and modify user privileges.â</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/disease-research.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/disease-research.html
Wed Mar 11 08:37:10 2015
@@ -104,248 +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>Disease-related research</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 various diseases:</p>
-<ul>
-<li><a href="#vph-dareit">Dementia</a> (VPH-DARE@IT and VPH-SHARE)</li>
-<li><a href="#analysis-of-anthrax-bacterium">Analysis of the anthrax
bacterium</a></li>
-<li><a href="#trypanosomiasis">Study of resistance into trypanosomiasis</a>
(sleeping sickness)</li>
-<li><a href="#graves-disease">Identification of genes linked to Graves
disease</a></li>
-<li><a href="#williams-beuren-syndrome">Characterisation of genes associated
with Williams-Beuren syndrome</a></li>
-<li><a href="/introduction/related-projects#cagrid">Cancer research</a>
(caGrid)</li>
-</ul>
-<p><a name="vph-dareit"></a></p>
-<h2 id="vph-dareit">VPH-DARE@IT</h2>
-<p>The Center for Computational Imaging and Simulation Technologies in
Biomedicine at the
- <a href="http://sheffield.ac.uk/";>University of Sheffield</a>, is leading
the âVirtual Physiological Human:
- DementiA Research Enabled by ITâ (<a
href="http://www.vph-dare.eu/";>VPH-DARE@IT</a>) project,
- which aims to provide a systematic,
- multifactorial and multiscale modelling approach to understanding dementia
onset and
- progression and enable more objective, earlier,
- predictive and individualised diagnoses and prognoses of dementias to cope
with the challenge of an ageing European society.
- See <a href="http://www.vph-dare.eu/";>http://www.vph-dare.eu/</a> for more
details.</p>
-<p>The project will use <a href="http://vph-share.eu/";>VPH-SHARE</a>
infrastructure and
- the GIMIAS software along with Taverna Workbench and Taverna Server
technology for the execution and
- composition of medical simulation workflows.
-These workflows will be focused on the analysis of medical data from thousands
of individuals and populations;
- as well as genetic, biochemical and metabolic pathway models.
-The results of the analysis aim to support highly innovative clinical decision
systems for
- fighting the colossal health and societal burden resulting from
dementias.</p>
-<p><a name="analysis-of-anthrax-bacterium"></a></p>
-<h2 id="analysis-of-anthrax-bacterium">Analysis of anthrax bacterium</h2>
-<p>Taverna has been used by Anil Wipat and others to automate a series of
analyses on all the proteins
- produced by a bacterium to create, by a process of selection and
elimination,
- a list of secreted proteins and their properties.</p>
-<p>The secreted proteins explain why anthrax can grow in animal hosts but not
in soil.</p>
-<h3 id="publications">Publications</h3>
-<p>The <a
href="http://www.allhands.org.uk/2006/proceedings/papers/709.pdf";>paper</a>
- <em>e-Science Tools For The Genomic Scale Characterisation Of Bacterial
Secreted Proteins</em>
- by Craddock et al. gives an overview of this work.</p>
-<p><a name="trypanosomiasis"></a></p>
-<h2 id="trypanosomiasis-sleeping-sickness">Trypanosomiasis (sleeping
sickness)</h2>
-<p>One of the major goals of biology, and consequently bioinformatics,
- is to successfully bridge the gap between genotype and phenotype.
-Microarray and Quantitative Trait Loci data are increasingly used to aid in
the discovery of candidate genes
- that might be responsible for phenotypic differences.
-In previous years, studies into genotype-phenotype correlations have been
conducted manually.
-This has led to problems with regards to the identification of functional
candidate genes,
- primarily due to the scale of data being investigated and the reliance on
specific expertise,
- which may bias the investigations outcome.</p>
-<p>With the development and connection of Web services into workflows,
however,
- these large scale datasets can be processed systematically enabling
detailed information to be gathered,
- published and subsequently re-investigated,
- enhancing the possibility of bridging the gap between genotype and
phenotype using pathways.</p>
-<p>So far this investigation has highlighted the issues facing the manual
analysis of microarray and QTL data,
- and how automated approaches provide a systematic means to investigate
genotype-phenotype correlations.
-We were able to illustrate how the large scale analysis of microarray gene
expression and quantitative trait data,
- investigated at the level of biological pathways,
- enables links between genotype and phenotype to be successfully
established.</p>
-<p>An example of a workflow used to gather pathway information for candidate
genes from a QTL region is shown below.
-These workflows have so far been applied to two different genotype-phenotype
problems:</p>
-<ul>
-<li>The study of resistance to African Trypanosomiasis in mice, infected with
Trypanosoma congolen</li>
-<li>The study of immunological effects and parasite expulsion in mice infected
with Trichuris muris</li>
-</ul>
-<p>Using this systematic,
- pathway driven approach, we were able to successfully identify a candidate
gene and
- biological pathway believed to be strongly associated with resistance to
African Trypanosomiasis.</p>
-<p>The workflow for performing this analysis is available on
- <a href="http://www.myexperiment.org/workflows/16";>myExperiment</a>.</p>
-<p><a href="http://www.myexperiment.org/workflows/16";><img
alt="pathways_and_gene_annotations_for_qtl_phenotype_28303_3"
src="/img/trypanosomiasis.jpg" /></a></p>
-<h3>Publications</h3>
-
-<p><a
href="http://scholar.google.co.uk/scholar?hl=en&q=Taverna+trypanosomiasis";>Articles
and papers</a>
- about the success of Taverna for trypanosomiasis (sleeping sickness)
research.</p>
-<p><a name="graves-disease"></a></p>
-<h2 id="graves-disease">Graves disease</h2>
-<h3 id="graves-disease-scenario">Graves disease scenario</h3>
-<p>The aim of this scenario is to identify and characterise genes which are
located in regions on human chromosomes
- which show linkage to Graves disease (GD) (shown in figure below).
-GD is an autoimmune disease of the thyroid in which the immune system of an
individual attacks cells
- in the thyroid gland resulting in hyperthyroidism.
-This is caused by the stimulation of the thyrotrophin receptor by
thyroid-stimulating autoantibodies secreted by
- lymphocytes of the immune system.</p>
-<p><a href="/img/gravesdiseasescenario_1.png">
- <img title="gravesdiseasescenario_1" src="/img/gravesdiseasescenario_1.png"
- alt="Graves Disease Scenario" width="249" height="300" /></a></p>
-<h3 id="affymetrix-microarray-studies">Affymetrix microarray studies</h3>
-<p>The GD candidate genes were identified by microarray analysis.
-Affymetrix U95A arrays were probed with RNA extracted from CD4 positive
lymphocytes from four GD patients
- and four healthy controls.
-The four GD microarray datasets were then compared to the four control
datasets using
- the Affymetrix data mining tool to identify differentially expressed
genes.</p>
-<h3 id="annotation-pipeline">Annotation pipeline</h3>
-<p>Over 50 genes were found to be differentially-expressed in CD4 positive
lymphocytes from GD patients.
-In order to understand why these genes were expressed in lymphocytes from GD
patients but not in healthy individuals,
- the GD biologist would like to use myGrid to query public databases such as
- EMBL, GO, HGVBASE and MEDLINE to view information about gene structure and
function,
- chromosome location, the presence of single nucleotide polymorphisms
(SNPs),
- expression control features and association with other genetic diseases.
-The experimental conditions and diseases in which the expression of the
candidate genes
- are significantly altered also need to be identified from OMIM.</p>
-<h3 id="genotype-assay-design-system">Genotype assay design system</h3>
-<p>SNPs are small (single base pair) changes genetic variations which are
found in the genome amongst individuals.
-The differential expression of the candidate genes in GD individuals may be
due or related to the presence of
- SNPs associated with GD.
-The GD biologist is interested in identifying and determining the frequency of
those SNPs which are found in her GD patients.</p>
-<p>Restriction fragment length polymorphism (RFLP) assays are developed to
genotype SNPs in her candidate genes.
-A region flanking either side of the SNP is amplified using polymerase chain
reaction (PCR).
-The amplified PCR product is digested with a suitable restriction enzyme
- (i.e. one that will cut at one SNP allele and not the other)
- and the products are run on agarose gels to view product size and determine
the genotype.</p>
-<p>The GD biologist would like to use myGrid to:</p>
-<ul>
-<li>Query databases to retrieve SNP information associated with candidate
genes.</li>
-<li>Aid in the design of primers
- (bits of DNA which signify the start and end points of the section of the
DNA sequence which she wants to amplify)
- for the PCR experiment.</li>
-<li>Select the restriction enzyme that is specific to a particular SNP for the
RFLP experiment.</li>
-</ul>
-<h3
id="3d-protein-structure-wzxhzdk12-effect-of-coding-snp-on-protein-active-site">3D
protein structure & effect of coding SNP on protein active site</h3>
-<p>Any SNPs occurring in the coding regions of a candidate gene may
potentially give rise to
- a change in the amino acid sequence of the protein encoded by the gene.
-The GD biologist would like to use myGrid to:</p>
-<ul>
-<li>Query a protein structure database, e.g. PDB or MSD,
- to determine whether a structure of the protein encoded by her candidate
gene is available.
- If so, view the protein structure to study how it relates to the function
of the protein.</li>
-<li>Obtain information about the protein, e.g. its function and functional
domains, by querying SWISS-PROT and InterPro.
- Use Sheffieldâs AMBIT Web service to retrieve information about an active
site whose characteristics
- may be altered due to the presence of a coding SNP which has affected a
change in the amino acid sequence
- of the protein where the active site is encoded.</li>
-</ul>
-<p>The <a href="http://www.myexperiment.org/workflows/28";>workflow</a>
- for the Graves Disease analysis is published on <a
href="http://www.myexperiment.org/";>myExperiment</a>.</p>
-<h3 id="publications_1">Publications</h3>
-<p><a
href="http://scholar.google.co.uk/scholar?q=Taverna+Graves+Disease";>Articles
and papers</a>
- about the success of Taverna for Graves Disease research.</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/document-analysis.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/document-analysis.html
Wed Mar 11 08:37:10 2015
@@ -104,156 +104,3 @@
<li><a
href="/documentation/#tools">Tools and Services</a></li>
</ul>
</li>
- <li class="dropdown">
- <a href="/download"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Download<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="/download">Which Taverna
to use</a></li>
- <li><a
href="/download/workbench">TavernaWorkbench</a></li>
- <li><a
href="/download/language">Taverna's SCUFL2 Language</a></li>
- <li><a
href="/download/command-line-tool">Taverna Command Line</a></li>
- <li><a
href="/download/server">Taverna Server</a></li>
- <li><a
href="/documentation/plugins">Plugins</a></li>
- <li><a href="/download/code">Source
Code</a></li>
- <li><a href="/download/maven">Maven
Repository</a></li>
- <li><a
href="/download/system-requirements">System Requirements</a></li>
- <li><a
href="/download/pre-apache">Taverna 2.x (Pre-Apache)</a></li>
- </ul>
- </li>
- <li class="dropdown">
- <a href="/community"
class="dropdown-toggle" data-toggle="dropdown" role="button"
aria-expanded="false">Community<span class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a
href="/community/lists">Mailing Lists</a></li>
- <li><a href="/community/irc">IRC
chat</a></li>
- <li><a
href="/community#contribute">Contribute</a></li>
- <li><a
href="/community#reportbugs">Report a Bug</a></li>
- <li><a href="/community/edit">Edit
website</a></li>
- </ul>
- </li>
- </ul>
-
- <form >
-
-
- <!--<input type="submit" id="submit" value="Search">-->
- </form>
-
- <form class="navbar-form navbar-right" role="search"
- name="search" id="search"
action="http://www.google.com/search"; method="get">
- <input value="taverna.incubator.apache.org"
name="sitesearch" type="hidden"/>
- <div class="form-group input-group">
- <input type="text" name="q" id="query"
placeholder="Search" class="form-control">
- <span class="input-group-btn">
- <button type="submit" class="btn
btn-default">Search</button>
- </span>
- </div>
- </form>
-
- <ul class="nav navbar-nav navbar-right">
- <li class="dropdown">
- <a href="http://www.apache.org/"; class="dropdown-toggle"
data-toggle="dropdown" role="button" aria-expanded="false">ASF<span
class="caret"></span></a>
- <ul class="dropdown-menu" role="menu">
- <li><a href="http://www.apache.org/";>Apache Software
Foundation</a></li>
- <li><a
href="http://www.apache.org/foundation/how-it-works.html";>How it works</a></li>
- <li><a
href="http://www.apache.org/foundation/thanks.html";>Thanks</a></li>
- <li><a
href="http://www.apache.org/foundation/sponsorship.html";>Become a
Sponsor</a></li>
- <li><a
href="http://incubator.apache.org/projects/taverna.html";>Taverna Incubation
Status</a></li>
- </ul>
- </li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container-->
- </nav>
-
-
- <div id="page" class="container">
- <h1>Document and image analysis</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="#islandora">Islandora</a> - an open-source software framework
designed to help institutions and organizations and
- their audiences collaboratively manage, and discover digital assets using a
best-practices framework.</li>
-<li><a href="/introduction/related-projects#scape">SCAPE</a> â large scale
and computation intense automated digital preservation and quality assurance
workflows
- on a cloud infrastructure</li>
-<li><a href="#dae">DAE</a> - Document analysis algorithm contributions in
end-to-end applications</li>
-<li><a href="/introduction/taverna-in-use/social-sciences#impact">IMPACT</a>
project works on improving access to historical texts and digitisation of
European cultural
- heritage using Taverna and <a
href="http://www.myexperiment.org/";>myExperiment</a></li>
-</ul>
-<p><a name="islandora"></a></p>
-<h2 id="islandora">Islandora</h2>
-<p><a href="http://islandora.ca/";>Islandora</a> is an open-source software
framework designed to help institutions and organizations and their
- audiences collaboratively manage, and discover digital assets using a
best-practices framework.</p>
-<p>Islandora connects the <a href="http://drupal.org/";>Drupal</a> and <a
href="http://www.fedora-commons.org/";>Fedora</a> open software applications,
acting as a kind of glue between
- the content management and presentation capabilities of Drupal with the
long term preservation features of
- Fedora.</p>
-<p>In an <a
href="http://blogs.loc.gov/digitalpreservation/2013/03/islandoras-open-source-ecosystem-and-digital-preservation-an-interview-with-mark-leggott/";>interview</a>
with http://loomware.typepad.com/about.html, the University Librarian at the
University of
- Prince Edward Island, Mark explains how Taverna workflows are utilized by
the Islandora framework to
- call local Python scripts remotely via Web services&' wrappers.
-This allowed for extreme agility within the Islandora ecosystem and has
allowed the integration of a wide range
- of open source (and proprietary where desirable) software systems in
relatively quick order.
-Read the <a
href="http://blogs.loc.gov/digitalpreservation/2013/03/islandoras-open-source-ecosystem-and-digital-preservation-an-interview-with-mark-leggott/";>full
interview</a> with Mark Leggott.</p>
-<p><a name="dae"></a></p>
-<h2 id="dae">DAE</h2>
-<p>The <a href="http://dae.cse.lehigh.edu/DAE/";>DAE project</a> (Document
Analysis Algorithm Contributions in End-to-End Applications) provides the
- <a
href="http://sourceforge.net/apps/mediawiki/daeplatform/index.php?title=Platform_Architecture";>DAE
Platform</a> to give access to a collection of resources and applications
related to machine perception
- and document analysis.
- Applications include binarization, text segmentation, OCR (Optical
Character Recognition),
- named entity detection, etc.</p>
-<p>The DAE Platform is accessible though a Web portal which provides a series
of services related to document
- analysis research of which the most prominent are the access to a wide
range of reference datasets,
- as well as their annotations, ground-truths or interpretations; a
catalogue of state of the art algorithms
- that can be executed on hosted or otherwise provided data, as well as the
uploading and execution of
- complex workflows combining those algorithms.</p>
-<p>One of the more advanced contributions of the DAE Platform is to provide
an open and very flexible framework to
- add, run, evaluate and contribute algorithms. These algorithms are
provided as Web services and can be
- invoked from anywhere.
-Because of its open architecture users can very easily contribute and convert
their own algorithms to this
- framework, without necessarily disclosing their source code, and without
the need to port their code to
- a particular technical environment.</p>
-<p>The Platform is integrated with the <a
href="http://sourceforge.net/apps/mediawiki/daeplatform/index.php?title=Platform_Architecture#Web_Service_Orchestration";>Taverna
Web Service Orchestration</a> to provide the opportunity to
- design, host and execute complete and complex workflows of combined and
distributed algorithms.</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/education.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/education.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>Education</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 has been used in education (as
well as for teaching purposes) for the
- <a
href="/introduction/taverna-in-use/multimedia.html#course-generator">creation
of courses from individual learning activities and resources</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/engineering.html
==============================================================================
---
websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html
(original)
+++
websites/staging/taverna/trunk/content/introduction/taverna-in-use/engineering.html
Wed Mar 11 08:37:10 2015
@@ -104,132 +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>Engineering</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 has been used in engineering
projects:</p>
-<p><a href="#jpl">Jet Propusion Laboratory</a> (JPL) -using Taverna as the Web
services-based infrastructure for their
- Observing Systems Simulation Experiments (OSSE) project (modelling how
mission design objectives impact science)</li></p>
-<p><a name="jpl"></a></p>
-<h2 id="jpl">JPL</h2>
-<p>NASAâs <a href="http://www.jpl.nasa.gov/";>Jet Propulsion Laboratory</a>
(JPL), based at the California Institute of Technology,
- created the first American satellite,
- sent the first robotic craft to the moon and currently has twenty
spacecraft on active missions.
-The JPL have been involved in yet another giant leap for mankind: they have
adopted Taverna as the Web services -
- based infrastructure for their Observing Systems Simulation Experiments
(OSSE) project.
-The JPL are applying OSSE in the study of science algorithms as part of a
proposed hyper-spectral imaging mission.</p>
-<p>JPL considered a number of different research and commercial workflow
systems and finally settled on Taverna.
-"The thing that really sold us on Taverna was the dynamic WSDL introspection
and presentation of the
- WSDL interface as ports of a process component" - said Hook Hua,
- a member of the High Capability Computing and Modeling Group at JPL.
-Taverna's recent overhaul appears to have helped their decision too, as Hook
Hua describes
- "one of the initial reasons we chose to use Taverna was its polished look
and feel when compared to
- other workflow engines".</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
