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Posted to commits@taverna.apache.org by bu...@apache.org on 2015/02/03 15:06:40 UTC
svn commit: r938803 - in /websites/staging/taverna/trunk: cgi-bin/ content/
content/introduction/taverna-in-use/index.html
Author: buildbot
Date: Tue Feb 3 14:06:40 2015
New Revision: 938803
Log:
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@@ -501,208 +501,6 @@ These projects include:</p>
</ul>
<p><a name="by-domain" </a></p>
<h2 id="by-domain">By domain</h2>
-<p>Various domains where scientists have used Taverna so far include:</p>
-<p><a name="annotation"></a></p>
-<h3 id="annotations">Annotations</h3>
-<p>Taverna is used by various tools and projects for the association of metadata with data (annotation).
-These include:
- - <a href="#afawe">Automatic Functional Annotation in a distributed Web service Environment</a>(AFAWE) -
- annotation of plant genes with their functionality
- - <a href="#annotation-of-genomes">Interactive genome annotation pipeline</a></a> - automatic and manual annotation of genes
- - <a href="#taweka">TaWeka</a> - associating biological data with calculated functionality</p>
-<p>In addition, Taverna makes use of the semantic annotation that has been specified for the services provided by
- the <a href="#adoption-by-moby">MOBY consortium</a>.</p>
-<p>Taverna has also been used for the identification of mismatches and possible annotations in workflows by the
- <a href="/introduction/related-projects.html#ispider">iSPIDER</a> project.</p>
-<p><a name="afawe"></a></p>
-<h4 id="afawe">AFAWE</h4>
-<p>The <a href="http://www.mpiz-koeln.mpg.de/2169/en">Max Planck Institute for Plant Breeding Research</a> in Cologne, Germany have developed the
- Automatic Functional Annotation in a distributed Web Service Environment (<a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/">AFAWE</a>).
-AFAWE is a tool for the automatic functional annotation of new genes in plants and other organisms.
-The annotation involves the running of several Web services, and also the execution of a Taverna <a href="http://bioinfo.mpiz-koeln.mpg.de/afawe/help/Tools.html#SIFTER">workflow</a>.</p>
-<p>The annotation workflow is <a href="http://www.myexperiment.org/workflows/95">available</a> on <a href="http://www.myexperiment.org/">myExperiment</a>.</p>
-<h5 id="publications">Publications</h5>
-<p>The <a href="http://dx.doi.org/10.1093/bioinformatics/btn394">paper</a> <em>Protein function prediction and annotation in an integrated environment powered by web services
- (AFAWE)</em> by Joecker et al describes the concepts and implementation of AFAWE.</p>
-<p><a name="annotation-of-genomes"></a></p>
-<h3 id="annotation-of-genomes">Annotation of genomes</h3>
-<p>A collaboration between <a href="http://www.mygrid.org.uk/about-us/people/previous-members/thomas-oinn/">Tom Oinn</a> from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
- Pal Puntervoll from the <a href="http://www.uib.no/en">University of Bergen</a>, Norway, has produced an interactive genome annotation
- pipeline.</p>
-<p>Sequencing, characterising and annotating a genome are the first steps to understanding its function.
-Important stages in this include gene prediction, comparative genomics and function prediction of genes and
- gene products.
-With workflows all of these stages can be automate, requiring little human interaction.
-However, manual inspection can be required at certain points in the process.</p>
-<h4 id="publications_1">Publications</h4>
-<p><a href="http://www.mygrid.org.uk/bibsearch-results/?bibliography_subject=genome-annotation">Articles and papers</a> about the success of Taverna for genome annotation are available on-line.</p>
-<p><a name="taweka"></a></p>
-<h4 id="taweka">TaWeka</h4>
-<p><a href="http://homepages.inf.ed.ac.uk/ldeferra/">Luna De Ferrari</a> from the Computational Systems Biology &
- <a href="http://www.bioinformatics.ed.ac.uk/">Bioinformatics group at the University of Edinburgh</a> has developed <a href="http://mook.inf.ed.ac.uk/twiki/bin/view.cgi/PublicCSB/TaWeka">TaWeka</a>,</p>
-<blockquote>
-<p>a rapid prototyping tool for biological classifiers.</p>
-</blockquote>
-<p>TaWeka uses Taverna workflows to store data retrieved from webservices, e.g. queries of biological data,
- into a database.
-<a href="http://www.cs.waikato.ac.nz/ml/weka/">Weka</a> is then used to run machine learning experiments on the data in order to evaluate and improve
- biological classification functions.</p>
-<h5 id="publications_2">Publications</h5>
-<p>A poster <a href="http://mook.inf.ed.ac.uk/twiki/pub/PublicCSB/TaWekaPosters/colourA4_16.pdf"><em>TaWeka: from biological web services to data mining</em></a> by De Ferrara and Goryanin describes the
- purpose and implementation of TaWeka.</p>
-<p><a name="adoption-by-moby"></a></p>
-<h4 id="adoption-by-the-moby-consortium">Adoption by the Moby consortium</h4>
-<p>The <a href="http://biomoby.open-bio.org/">Moby</a> project develops a system for interoperability between biological data hosts and
- analytical services.
-Their relationship with Taverna is multiple:</p>
-<ul>
-<li>The Moby team actively collaborate with myGrid in the development of the ontologies used to describe their
- services.
- Service descriptions are then used by Taverna to find services to use in workflows.</li>
-<li>The services published on Moby are a large proportion of the services often used in Taverna workflows</li>
-<li>People wishing to combine Moby services commonly use Taverna Workbench as a platform</li>
-<li>Specific support for Moby services is available within Taverna.</li>
-</ul>
-<h5 id="publications_3">Publications</h5>
-<p>The <a href="http://dx.doi.org/10.1093/bib/bbn003">paper</a> <em>Interoperability with Moby 1.0âItâs better than sharing your toothbrush!</em> by the
- Moby consortium gives an overview of Moby and their activities.</p>
-<p><a name="arts"></a></p>
-<h3 id="arts">Arts</h3>
-<p>Taverna has been used for the <a href="#composition-of-music">composition of music</a> using Web services for synthesis.</p>
-<p><a name="composition-of-music"></a></p>
-<h4 id="composition-of-music">Composition of music</h4>
-<p><a href="http://en.wikipedia.org/wiki/John_ffitch">John Ffitch</a> and others at the University of Bath have developed a service-oriented composition environment
- for music.
-The environment consists of three main components:
- - A suite of synthesis Web services that incorporate a selection of the basic atomic components required for
- sound creation and processing</li>
- - A tool that gives a description of music in terms of the construction of the instruments
- (parameters, connections) and the score they will play on>
- - An âenvironment of useâ that allows the connection and enactment of the synthesis services</p>
-<p>Both <a href="http://www.trianacode.org/">Triana</a> and Taverna have been tested as the environment of use.</p>
-<h5 id="publications_4">Publications</h5>
-<p>This work is described in the <a href="http://opus.bath.ac.uk/5290/">paper</a> <em>Composition with Sound Web Services and Workflows</em> by Ffitch et al.</p>
-<p><a name="astronomy"></a></p>
-<h3 id="astronomy">Astronomy</h3>
-<p>Taverna and <a href="http://www.myexperiment.org">myExperiment</a> are being used for astronomy research by several projects:</p>
-<ul>
-<li><a href="#astrogrid">AstroGrid</a> - plugin to allow AstroGrid utilities within Taverna 1.x</li>
-<li><a href="/introduction/related-projects.html#helio">HELIO</a> - workflows including heliophysical services</li>
-<li><a href="#sampo">SAMPO</a> - development of a workflow system based upon Taverna</li>
-</ul>
-<p><a name="astrogrid"></a></p>
-<h4 id="astrogrid">AstroGrid</h4>
-<p>The UKâs <a href="http://www.astrogrid.org/">AstroGrid</a> is a ~£14M (over the period 2001-2009) project aimed at building a data-grid for UK
- astronomy, which will form the UK contribution to a global VirtualObservatory.</p></p>
-<p>A <a href="http://wiki.astrogrid.org/bin/view/Astrogrid/VoWorkflowsWithTaverna">Taverna 1.x processor</a> has been written to enable client-site AstroGrid utilities to be included within
- Taverna workflows.</p>
-<h5 id="publications_5">Publications</h5>
-<p>A book chapter "AstroGrid and the Virtual Observatory", Walton, N. A., Gonzalez-Solareson, E., Springer,
- Lecture Notes in Physic, vol. 791, pp. 81-113, 2009. <br />
-<a href="http://www.springerlink.com/content/yk36404544k778g8">http://www.springerlink.com/content/yk36404544k778g8</a></p>
-<p>AstroGrid: Taverna in the Virtual Observatory, Benson, K. M., Walton, N. A., Memorie della Società Astronomica
- Italiana, vol. 80, p.574, 2009 <br />
-<a href="http://adsabs.harvard.edu/abs/2009MmSAI..80..574B">http://adsabs.harvard.edu/abs/2009MmSAI..80..574B</a></p>
-<p>Taverna and Workflows in the Virtual Observatory, Walton, N. A.; Witherwick, D. K.; Oinn, T.; Benson, K. M.,
- Proceedings of the Astronomical Data Analysis Software and Systems ASP Conference Series, London, UK.
-Edited by Robert W. Argyle, Peter S. Bunclark, and James R. Lewis., p.309, 2008. <br />
-<a href="http://adsabs.harvard.edu/abs/2008ASPC..394..309W">http://adsabs.harvard.edu/abs/2008ASPC..394..309W</a></p>
-<p><a name="sampo"></a></p>
-<h4 id="sampo">SAMPO</h4>
-<p>The SAMPO <a href="http://www.eso.org/sci/data-processing/software/sampo/">project</a> was part of the ongoing Finnish contribution to the <a href="http://www.eso.org/">European Southern Observatory</a>.</p>
-<p>Based upon Taverna, the SAMPO project developed the Recipe Flexible Execution workflow system <a href="http://www.eso.org/sci/data-processing/software/sampo/reflex/">ESO Reflex</a>.
-ESO Refex allows users to connect together C programs that reduce the raw data produced by ESO instruments.</p>
-<h5 id="publications_6">Publications</h5>
-<p>The <a href="http://www.springerlink.com/content/p67480k2w7311315/">paper</a> <em>ESO Reflex: A Graphical Workflow Engine for Running Recipes</em> by Hook et al, describes the
- ESO Reflex workbench.</p>
-<p><a name="biodiversity"></a></p>
-<h3 id="biodiversity">Biodiversity</h3>
-<p><a href="/introduction/related-projects.html#biovel">BioVel</a> - establishing an international e-Laboratory to allow biodiversity scientists to jointly tackle
- diverse research challenges using Taverna, myExperiment and BioCatalogue</p>
-<p><a name="bioinformatics"></a></p>
-<h3 id="bioinformatics">Bioinformatics</h3>
-<p><p>Taverna can connect to a wide variety of bioinformatics resources and has been successfully applied to a number of bioinformatics problems, listed below according to their sub-domains.<span id="more-2073"></span></p>
-<p style="text-align: center;"><img class="aligncenter" title="Bioinformatics services and resources" src="/pages/wp-content/uploads/2011/03/BioinformaticsResources.png" alt="Bioinformatics services and resources" width="676" height="441" /></p>
-<p>Bioinformatics systems/tools using Taverna:</p>
-<ul>
-<li><a href="/introduction/taverna-in-use/bioinformatics/biowep/">BioWEP</a> – bioinformatics workflow enactment portal</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics/biolinux/">BioLinux</a> – Ubuntu Linux distribution that includes Taverna and many other bioinformatics programs</li>
-</ul>
-<h3>Biodiversity</h3>
-<ul>
-<li><a href="/introduction/related-projects/biovel">BioVeL</a></li>
-</ul>
-<h3>Gene and genome expression</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression/next-generation-sequencing">Next Generation Sequencing</a> using Taverna 2 Server on Amazon cloud</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression/tavernapbs/">TavernaPBS</a> – next generation sequencing analysis using a computational cluster that uses a PBS queuing system and Taverna 2 Workbench</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression/casimir/">Coordination and Sustainability of International Mouse Informatics Resources</a> (CASIMIR) – workflows to associate mouse genome and phenome</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression/dgemap/">Developmental Gene Expression Map</a> (DGEMap)- analysis of human gene expression during development</li>
-<li><a href="/introduction/taverna-in-use/disease-research/graves-disease/">Graves disease</a> – identification of genes responsible</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics/gene-expression-from-microarray/">Examination of gene expression from MicroArray data using R</a> – statistical analysis of gene expression</li>
-<li><a href="/introduction/taverna-in-use/genome-and-gene-expression/sigenae/">SIGENAE</a> – development of workflows to analyse breeding animal data</li>
-<li><a href="/introduction/taverna-in-use/disease-research/trypanosomiasis/">Trypanosomiasis</a> – identification of genes responsible for sleeping sickness</li>
-<li><a href="/introduction/taverna-in-use/disease-research/williams-beuren-syndrome/">Williams-Beuren syndrome</a> – automation and confirmation of gene characterization</li>
-<li><a href="/introduction/taverna-in-use/biology/planet/">PLANET</a> – integration of plant genome resources</li>
-<li><a href="/introduction/taverna-in-use/annotation/annotation-of-genomes/">Annotation of genomes</a></li>
-<li><a href="/introduction/related-projects/shared-genomics/">Shared Genomics</a></li>
-<li><a href="http://img.cs.man.ac.uk/efungi/" target="_blank">e-Fungi</a> – functional genomics in fungal species</li>
-</ul>
-<h3>Protein and proteomics</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/bioinformatics/lumc/">Analysis of mass spectrometry data in proteomics</a></li>
-<li><a href="/introduction/taverna-in-use/disease-research/analysis-of-anthrax-bacterium/">Anthrax analysis</a> – identification of proteins secreted by bacteria</li>
-<li><a href="/introduction/taverna-in-use/databases/efamily/">eFamily</a> – integrating data from different databases</li>
-<li><a href="http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace/">European Model for Bioinformatics Research And Community Education</a> (EMBRACE) – calling services on a grid; recovering a database</li>
-<li><a href="/introduction/related-projects/ispider/">iSpider</a> – querying multiple data sources</li>
-<li><a href="/introduction/taverna-in-use/protein-and-proteomics/prodom/">ProDom</a> – running of Taverna workflows behind a portal to search a protein database</li>
-</ul>
-<h3>Biology and systems biology</h3>
-<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) – a live DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software (including Taverna)</li>
-<li><span><a href="/introduction/taverna-in-use/biology/tav4sb/">Tav4SB</a> -</span> Taverna workflows for systems biology, in particular for analysis of the kinetic models of biological systems</li>
-<li><a href="/introduction/taverna-in-use/bioinformatics/measuring-enzyme-characteristics-of-yeast/">Measuring of enzyme characteristics of yeast</a></li>
-<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="/introduction/taverna-in-use/biology/planet/">PLANET (A Network of European Plant Databases)</a> â calling of workflows from a portal</li>
-</ul>
-<h3>Biomedicine and disease-related research</h3>
-<ul>
-<li><a href="/introduction/taverna-in-use/disease-research/vph-dareit/">Fighting dementia</a> (VP-DARE@IT and VPH-SHARE)</li>
-<li><a href="/introduction/taverna-in-use/disease-research/analysis-of-anthrax-bacterium/">Analysis of the anthrax bacterium</a></li>
-<li><a href="/introduction/taverna-in-use/trypanosomiasis/">Study of resistance into trypanosomiasis</a> (sleeping sickness)</li>
-<li><a href="/introduction/taverna-in-use/disease-research/graves-disease/">Identification of genes linked to Graves disease</a></li>
-<li><a href="/introduction/taverna-in-use/disease-research/williams-beuren-syndrome/">Characterisation of genes associated with Williams-Beuren syndrome</a></li>
-<li><a href="/introduction/related-projects/cagrid/">caGrid</a> – research into predicting limphoma cancer</li>
-<li><a href="/introduction/taverna-in-use/medicine/eu-adr/">EU-ADR</a> – detecting adverse drug reactions through the exploitation of clinical data from electronic healthcare records</li>
-</ul></p>
-<p><a name="chemistry"></a></p>
-<h3 id="chemistry">Chemistry</h3>
-<p><a name="data-and-text-mining"></a></p>
-<h3 id="data-and-text-mining">Data and text mining</h3>
-<p><a name="databases"></a></p>
-<h3 id="databases">Databases</h3>
-<p><a name="document-analysis"></a></p>
-<h3 id="document-and-image-analysis-digital-preservation">Document and image analysis (digital preservation)</h3>
-<p><a name="education"></a></p>
-<h3 id="education">Education</h3>
-<p><a name="engineering"></a></p>
-<h3 id="engineering">Engineering</h3>
-<p><a name="geoinformatics"></a></p>
-<h3 id="geoinformatics">Geoinformatics</h3>
-<p><a name="information-quality"></a></p>
-<h3 id="information-quality">Information quality</h3>
-<p><a name="multimedia"></a></p>
-<h3 id="multimedia">Multimedia</h3>
-<p><a name="natural-language-processing"></a></p>
-<h3 id="natural-language-processingwzxhzdk254wzxhzdk255">Natural language processing</a></li></h3>
-<p><a name="service-provision"></a></p>
-<h3 id="service-provision">Service provision</h3>
-<p><a name="service-testing"></a></p>
-<h3 id="service-testing">Service testing</h3>
-<p><a name="social-sciences"></a></p>
-<h3 id="social-sciences">Social sciences</h3>
<p>==</p>
<p><a name="chronology"<a/></p></div>