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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/24 18:34:11 UTC
svn commit: r941361 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/taverna-in-use/genome-and-gene-expression/
content/introduction/taverna-in-use/genome-and-gene-expression/index.html
Author: buildbot
Date: Tue Feb 24 17:34:10 2015
New Revision: 941361
Log:
Staging update by buildbot for taverna
Added:
websites/staging/taverna/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/
websites/staging/taverna/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.html
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+ <h1>Genome and gene expression</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 being used by various projects and researchers for the analysis of genomes and gene expression.<br />
+These include:</p>
+<ul>
+<li><a href="#next-generation-sequencing">Next Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
+<li><a href="#tavernapbs">TavernaPBS</a> - next generation sequencing analysis using a computational cluster that
+ uses a PBS queuing system and Taverna 2 Workbench</li>
+<li><a href="#casimir">Coordination and Sustainability of International Mouse Informatics Resources</a>
+ (CASIMIR) -workflows to associate mouse genome and phenome</li>
+<li><a href="#dgemap">Developmental Gene Expression Map</a> (DGEMap)- analysis of human gene expression during development</li>
+<li><a href="/introduction/taverna-in-use/disease-research#graves-disease">Graves disease</a> - identification of genes responsible</li>
+<li><a href="/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray">MicroArray analysis using R</a> -
+ statistical analysis of gene expression</li>
+<li><a href="#sigenae">SIGENAE</a> - development of workflows to analyse breeding animal data</li>
+<li><a href="/introduction/taverna-in-use/disease-research#trypanosomiasis">Trypanosomiasis</a> -
+ identification of genes responsible for sleeping sickness</li>
+<li><a href="/introduction/taverna-in-use/disease-research#williams-beuren-syndrome">Williams-Beuren syndrome</a> -
+ automation and confirmation of gene characterization</li>
+<li><a href="/introduction/taverna-in-use/bioinformatics#planet">Integration of plant genome resources</a> (PLANET)</li>
+<li><a href="/introduction/taverna-in-use/annotation#annotation-of-genomes">Annotation of genomes</a></li>
+<li><a href="/introduction/related-projects#shared-genomics">Shared Genomics</a></li>
+<li><a href="http://www.cs.man.ac.uk/~cornell/eFungi/">e-Fungi</a> - functional genomics in fungal species</li>
+</ul>
+<p><a name="next-generation-sequencing"</a></p>
+<h2 id="next-generation-sequencing">Next generation sequencing</h2>
+<p>Next generation sequencing presents new challenges in large scale data processing.
+In collaboration with the University of Liverpoolâs
+ <a href="http://www.liv.ac.uk/infection-and-global-health/research/animal-health-and-welfare/">Animal Sciences & Physiology Research group</a>,
+ in particular <a href="http://www.liv.ac.uk/integrative-biology/staff/harry-noyes/">Dr Harry Noyes</a>,<br />
+ we combined Taverna scientific workflows with computing power from the Amazon cloud to create
+ a powerful next generation sequencing application for whole genome Single Nucleotide Polymorphism (SNP) analysis.</p>
+<p>Through a Web portal, the application allows scientists to upload their input data,
+ fire off a number of parallel cloud instances for the analysis,
+ monitor progress and collect results (see figure below).</p>
+<p><img alt="" src="/img/NextGenSequencing-Figure.png" /></p>
+<p>Preliminary work on the genetic variation of African cattle showed we can run a whole genome of ~22 million SNPs
+ in a matter of hours.
+This work focuses on the response to trypanomiasis infection (sleeping sickness) in different cattle species.</p>
+<p>The application was demonstrated at the European Conference of Computational Biology (ECCB) 2010, Ghent, Belgium,
+ under the title âSoftware for the Data-Driven Researcher of the Futureâ â see the
+ <a href="http://www.mygrid.org.uk/files/presentations/ECCB_Tech_Talk.ppt">slides</a> and
+ <a href="http://www.youtube.com/watch?v=eR_iPWNYb48">video</a> (no audio or subtitles yet!) from the talk.</p>
+<p>This cloud application was based on the next generation sequencing work done presented at
+ Bioinformatics Open Source Conference (BOSC) 2010, Boston, USA, under the title
+ âAnalysing African and European cattle with Taverna 2.2â³.
+ See the <a href="http://www.mygrid.org.uk/files/presentations/BOSC2010.ppt">slides</a> from the talk.</p>
+<p><a name="tavernapbs></a></p>
+<h2 id="tavernapbs">TavernaPBS</h2>
+<p><a href="http://obx.cphg.virginia.edu/mackey/?page_id=1348">TavernaPBS</a>
+ is a plugin for Taverna developed by the
+ <a href="http://obx.cphg.virginia.edu/mackey/">Mackey Lab</a>,
+ Center for Public Health Genomics, University of Virginia, US.
+It allows a user to define workflows that can then be run using a computational cluster that uses a PBS queuing system.
+The workflows represent next generation sequencing analysis pipelines.</p>
+<p>To most efficiently make use of their myriad of UNIX command line tools, the project has developed a custom
+ <a href="/documentation/glossary#beanshell">Beanshell</a> -
+ based library to enable workflows composed of UNIX command line invocations. Furthermore, they have abstracted the command execution such that each step could be executed as an independent “job” on a remote high performance computing or grid environment. By doing so, they have essentially turned Taverna into a distributed workflow “compiler”.</p></p>
+<p>You can download the code from the project's
+ <a href="http://sourceforge.net/projects/tavernapbs/">pages at SourceForge</a>.</p>
+<p><a name="casimir"></a></p>
+<h2 id="casimir">CASIMIR</h2>
+<p>The Coordination and Sustainability of International Mouse Informatics Resources (CASIMIR)
+ <a href="http://www.casimir.org.uk/">project</a> carried out a
+ <a href="http://www.casimir.org.uk/fullstory.php?storyid=50">pilot study</a>
+ that demonstrated how (parts of) existing databases can be made accessible in a standardized way and
+ data processed using the
+ <a href="http://molgenis.sourceforge.net/">MOLGENIS toolkit</a>,
+ <a href="http://www.biomart.org/">BioMART</a> and Taverna.</p>
+<p>The MOLGENIS toolkit was used to generate WSDL services to access the databases.
+These were then included in a Taverna workflow along with BioMart processors.</p>
+<p>An example <a href="http://www.myexperiment.org/workflows/126">workflow</a> can be found on
+ <a href="http://www.myexperiment.org">myExperiment</a>.</p>
+<p><a name="dgemap"></a></p>
+<h2 id="dgemap">DGEMap</h2>
+<p>The Developmental Gene Expression Map (DGEMap)
+ <a href="http://www.dgemap.org/">project</a>
+ is an EU-funded study to design a pan-European infrastructure to support gene expression studies in early human development.</p>
+<p>The DGEMap team <a href="http://www.inf.ed.ac.uk/research/ICTreviewEPSRC20061207/posters/HumanDev.pdf">plan</a>
+ to use Taverna workflows to link human spatio-temporal gene expression data with other bioinformatics resources.</p>
+<p><a name="sigenae"></a></p>
+<h2 id="sigenae">SIGENAE</h2>
+<p>The <a href="http://www.sigenae.org/">Systeme dâInformation des GENomes des animaux âElevage</a>
+ (SIGENAE) is the Information System of Analysis of Breeding Animalsâ Genome
+ (<a href="http://www.inra.fr/agenae/">AGENAE</a>) program.
+They are a group of French bioinformaticians providing services to biologists working on four mammal and one fish species.
+They are funded by the French National Institute for Agricultural Research
+ (<a href="http://www.international.inra.fr/">INRA</a>).<br />
+They not only use Taverna Workbench to support e-Science
+ but have been very active in promoting its adoption throughout the French bioinformatics community.</p>
+<p>Some of the workflows developed by the Sigenae community have been made available for
+ <a href="http://www.sigenae.org/index.php?id=84#408">sharing</a>.</p></div>
+
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