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svn commit: r1656737 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md
Author: brenninc
Date: Tue Feb 3 14:06:35 2015
New Revision: 1656737
URL: http://svn.apache.org/r1656737
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incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md
Modified: incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md
URL: http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md?rev=1656737&r1=1656736&r2=1656737&view=diff
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--- incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md (original)
+++ incubator/taverna/site/trunk/content/introduction/taverna-in-use/index.md Tue Feb 3 14:06:35 2015
@@ -388,249 +388,6 @@ Several packages include Taverna as part
<a name="by-domain" </a>
##By domain##
-Various domains where scientists have used Taverna so far include:
-
-<a name="annotation"></a>
-###Annotations###
-Taverna is used by various tools and projects for the association of metadata with data (annotation).
-These include:
- - [Automatic Functional Annotation in a distributed Web service Environment][49](AFAWE) -
- annotation of plant genes with their functionality
- - [Interactive genome annotation pipeline][50]</a> - automatic and manual annotation of genes
- - [TaWeka][51] - associating biological data with calculated functionality
-
-In addition, Taverna makes use of the semantic annotation that has been specified for the services provided by
- the [MOBY consortium][52].
-
-Taverna has also been used for the identification of mismatches and possible annotations in workflows by the
- [iSPIDER][53] project.
-
-<a name="afawe"></a>
-####AFAWE####
-
-The [Max Planck Institute for Plant Breeding Research][54] in Cologne, Germany have developed the
- Automatic Functional Annotation in a distributed Web Service Environment ([AFAWE][55]).
-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 [workflow][56].
-
-The annotation workflow is [available][57] on [myExperiment][58].
-
-#####Publications#####
-The [paper][59] *Protein function prediction and annotation in an integrated environment powered by web services
- (AFAWE)* by Joecker et al describes the concepts and implementation of AFAWE.
-
-<a name="annotation-of-genomes"></a>
-###Annotation of genomes###
-A collaboration between [Tom Oinn][60] from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and
- Pal Puntervoll from the [University of Bergen][61], Norway, has produced an interactive genome annotation
- pipeline.
-
-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.
-
-####Publications####
-[Articles and papers][62] about the success of Taverna for genome annotation are available on-line.
-
-<a name="taweka"></a>
-####TaWeka####
-[Luna De Ferrari][63] from the Computational Systems Biology &
- [Bioinformatics group at the University of Edinburgh][64] has developed [TaWeka][65],
-
-> a rapid prototyping tool for biological classifiers.
-
-TaWeka uses Taverna workflows to store data retrieved from webservices, e.g. queries of biological data,
- into a database.
-[Weka][66] is then used to run machine learning experiments on the data in order to evaluate and improve
- biological classification functions.
-
-#####Publications#####
-A poster [*TaWeka: from biological web services to data mining*][67] by De Ferrara and Goryanin describes the
- purpose and implementation of TaWeka.
-
-<a name="adoption-by-moby"></a>
-####Adoption by the Moby consortium####
-The [Moby][68] project develops a system for interoperability between biological data hosts and
- analytical services.
-Their relationship with Taverna is multiple:
-
- - 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.
- - The services published on Moby are a large proportion of the services often used in Taverna workflows
- - People wishing to combine Moby services commonly use Taverna Workbench as a platform
- - Specific support for Moby services is available within Taverna.
-
-#####Publications#####
-The [paper][69] *Interoperability with Moby 1.0âItâs better than sharing your toothbrush!* by the
- Moby consortium gives an overview of Moby and their activities.
-
-<a name="arts"></a>
-###Arts###
-Taverna has been used for the [composition of music][70] using Web services for synthesis.
-
-<a name="composition-of-music"></a>
-####Composition of music####
-[John Ffitch][71] 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
-
-Both [Triana][72] and Taverna have been tested as the environment of use.
-#####Publications#####
-This work is described in the [paper][73] *Composition with Sound Web Services and Workflows* by Ffitch et al.
-
-<a name="astronomy"></a>
-###Astronomy###
-Taverna and [myExperiment][74] are being used for astronomy research by several projects:
-
- - [AstroGrid][75] - plugin to allow AstroGrid utilities within Taverna 1.x
- - [HELIO][76] - workflows including heliophysical services
- - [SAMPO][77] - development of a workflow system based upon Taverna
-
-<a name="astrogrid"></a>
-####AstroGrid####
-The UKâs [AstroGrid][78] 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>
-
-A [Taverna 1.x processor][79] has been written to enable client-site AstroGrid utilities to be included within
- Taverna workflows.
-
-#####Publications#####
-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.
-[http://www.springerlink.com/content/yk36404544k778g8][80]
-
-AstroGrid: Taverna in the Virtual Observatory, Benson, K. M., Walton, N. A., Memorie della Società Astronomica
- Italiana, vol. 80, p.574, 2009
-[http://adsabs.harvard.edu/abs/2009MmSAI..80..574B][81]
-
-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.
-[http://adsabs.harvard.edu/abs/2008ASPC..394..309W][82]
-
-<a name="sampo"></a>
-####SAMPO####
-The SAMPO [project][83] was part of the ongoing Finnish contribution to the [European Southern Observatory][84].
-
-Based upon Taverna, the SAMPO project developed the Recipe Flexible Execution workflow system [ESO Reflex][85].
-ESO Refex allows users to connect together C programs that reduce the raw data produced by ESO instruments.
-
-#####Publications#####
-The [paper][86] *ESO Reflex: A Graphical Workflow Engine for Running Recipes* by Hook et al, describes the
- ESO Reflex workbench.
-
-<a name="biodiversity"></a>
-###Biodiversity###
-[BioVel][87] - establishing an international e-Laboratory to allow biodiversity scientists to jointly tackle
- diverse research challenges using Taverna, myExperiment and BioCatalogue
-
-<a name="bioinformatics"></a>
-###Bioinformatics###
-<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>
-
-
-<a name="chemistry"></a>
-###Chemistry###
-
-<a name="data-and-text-mining"></a>
-###Data and text mining###
-
-<a name="databases"></a>
-###Databases###
-
-<a name="document-analysis"></a>
-###Document and image analysis (digital preservation)###
-
-<a name="education"></a>
-###Education###
-
-<a name="engineering"></a>
-###Engineering###
-
-<a name="geoinformatics"></a>
-###Geoinformatics###
-
-<a name="information-quality"></a>
-###Information quality###
-
-<a name="multimedia"></a>
-###Multimedia###
-
-<a name="natural-language-processing"></a>
-###Natural language processing</a></li>
-
-<a name="service-provision"></a>
-###Service provision###
-
-<a name="service-testing"></a>
-###Service testing###
-
-<a name="social-sciences"></a>
-###Social sciences###
-
==
@@ -685,42 +442,3 @@ The [paper][86] *ESO Reflex: A Graphical
[46]: http://www.omii.ac.uk/wiki/SoftwareOverview
[47]: #sb-os
[48]: http://code.google.com/p/calctav/
- [49]: #afawe
- [50]: #annotation-of-genomes
- [51]: #taweka
- [52]: #adoption-by-moby
- [53]: /introduction/related-projects.html#ispider
- [54]: http://www.mpiz-koeln.mpg.de/2169/en
- [55]: http://bioinfo.mpiz-koeln.mpg.de/afawe/
- [56]: http://bioinfo.mpiz-koeln.mpg.de/afawe/help/Tools.html#SIFTER
- [57]: http://www.myexperiment.org/workflows/95
- [58]: http://www.myexperiment.org/
- [59]: http://dx.doi.org/10.1093/bioinformatics/btn394
- [60]: http://www.mygrid.org.uk/about-us/people/previous-members/thomas-oinn/
- [61]: http://www.uib.no/en
- [62]: http://www.mygrid.org.uk/bibsearch-results/?bibliography_subject=genome-annotation
- [63]: http://homepages.inf.ed.ac.uk/ldeferra/
- [64]: http://www.bioinformatics.ed.ac.uk/
- [65]: http://mook.inf.ed.ac.uk/twiki/bin/view.cgi/PublicCSB/TaWeka
- [66]: http://www.cs.waikato.ac.nz/ml/weka/
- [67]: http://mook.inf.ed.ac.uk/twiki/pub/PublicCSB/TaWekaPosters/colourA4_16.pdf
- [68]: http://biomoby.open-bio.org/
- [69]: http://dx.doi.org/10.1093/bib/bbn003
- [70]: #composition-of-music
- [71]: http://en.wikipedia.org/wiki/John_ffitch
- [72]: http://www.trianacode.org/
- [73]: http://opus.bath.ac.uk/5290/
- [74]: http://www.myexperiment.org
- [75]: #astrogrid
- [76]: /introduction/related-projects.html#helio
- [77]: #sampo
- [78]: http://www.astrogrid.org/
- [79]: http://wiki.astrogrid.org/bin/view/Astrogrid/VoWorkflowsWithTaverna
- [80]: http://www.springerlink.com/content/yk36404544k778g8
- [81]: http://adsabs.harvard.edu/abs/2009MmSAI..80..574B
- [82]: http://adsabs.harvard.edu/abs/2008ASPC..394..309W
- [83]: http://www.eso.org/sci/data-processing/software/sampo/
- [84]: http://www.eso.org/
- [85]: http://www.eso.org/sci/data-processing/software/sampo/reflex/
- [86]: http://www.springerlink.com/content/p67480k2w7311315/
- [87]: /introduction/related-projects.html#biovel
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