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Posted to commits@taverna.apache.org by br...@apache.org on 2015/02/24 18:34:01 UTC
svn commit: r1662038 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.md
Author: brenninc
Date: Tue Feb 24 17:34:01 2015
New Revision: 1662038
URL: http://svn.apache.org/r1662038
Log:
added DGEMap and SIGENAE
Added:
incubator/taverna/site/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.md
Added: incubator/taverna/site/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.md
URL: http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/taverna-in-use/genome-and-gene-expression/index.md?rev=1662038&view=auto
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+Title: Genome and gene expression
+Notice: Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied. See the License for the
+ specific language governing permissions and limitations
+ under the License.
+
+Taverna is being used by various projects and researchers for the analysis of genomes and gene expression.
+These include:
+
+ - [Next Generation Sequencing](#next-generation-sequencing) using Taverna 2 Server on Amazon cloud
+ - [TavernaPBS](#tavernapbs) - next generation sequencing analysis using a computational cluster that
+ uses a PBS queuing system and Taverna 2 Workbench
+ - [Coordination and Sustainability of International Mouse Informatics Resources](#casimir)
+ (CASIMIR) -workflows to associate mouse genome and phenome
+ - [Developmental Gene Expression Map](#dgemap) (DGEMap)- analysis of human gene expression during development
+ - [Graves disease](/introduction/taverna-in-use/disease-research#graves-disease) - identification of genes responsible
+ - [MicroArray analysis using R](/introduction/taverna-in-use/bioinformatics#gene-expression-from-microarray) -
+ statistical analysis of gene expression
+ - [SIGENAE](#sigenae) - development of workflows to analyse breeding animal data
+ - [Trypanosomiasis](/introduction/taverna-in-use/disease-research#trypanosomiasis) -
+ identification of genes responsible for sleeping sickness
+ - [Williams-Beuren syndrome](/introduction/taverna-in-use/disease-research#williams-beuren-syndrome) -
+ automation and confirmation of gene characterization
+ - [Integration of plant genome resources](/introduction/taverna-in-use/bioinformatics#planet) (PLANET)
+ - [Annotation of genomes](/introduction/taverna-in-use/annotation#annotation-of-genomes)
+ - [Shared Genomics](/introduction/related-projects#shared-genomics)
+ - [e-Fungi](http://www.cs.man.ac.uk/~cornell/eFungi/) - functional genomics in fungal species
+
+<a name="next-generation-sequencing"</a>
+##Next generation sequencing
+
+Next generation sequencing presents new challenges in large scale data processing.
+In collaboration with the University of Liverpoolâs
+ [Animal Sciences & Physiology Research group](http://www.liv.ac.uk/infection-and-global-health/research/animal-health-and-welfare/),
+ in particular [Dr Harry Noyes](http://www.liv.ac.uk/integrative-biology/staff/harry-noyes/),
+ 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.
+
+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).
+
+
+
+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.
+
+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
+ [slides](http://www.mygrid.org.uk/files/presentations/ECCB_Tech_Talk.ppt) and
+ [video](http://www.youtube.com/watch?v=eR_iPWNYb48) (no audio or subtitles yet!) from the talk.
+
+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 [slides](http://www.mygrid.org.uk/files/presentations/BOSC2010.ppt) from the talk.
+
+<a name="tavernapbs></a>
+##TavernaPBS
+
+[TavernaPBS](http://obx.cphg.virginia.edu/mackey/?page_id=1348)
+ is a plugin for Taverna developed by the
+ [Mackey Lab](http://obx.cphg.virginia.edu/mackey/),
+ 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.
+
+To most efficiently make use of their myriad of UNIX command line tools, the project has developed a custom
+ [Beanshell](/documentation/glossary#beanshell) -
+ 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>
+
+You can download the code from the project's
+ [pages at SourceForge](http://sourceforge.net/projects/tavernapbs/).
+
+<a name="casimir"></a>
+##CASIMIR
+
+The Coordination and Sustainability of International Mouse Informatics Resources (CASIMIR)
+ [project](http://www.casimir.org.uk/) carried out a
+ [pilot study](http://www.casimir.org.uk/fullstory.php?storyid=50)
+ that demonstrated how (parts of) existing databases can be made accessible in a standardized way and
+ data processed using the
+ [MOLGENIS toolkit](http://molgenis.sourceforge.net/),
+ [BioMART](http://www.biomart.org/) and Taverna.
+
+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.
+
+An example [workflow](http://www.myexperiment.org/workflows/126) can be found on
+ [myExperiment](http://www.myexperiment.org).
+
+<a name="dgemap"></a>
+##DGEMap
+
+The Developmental Gene Expression Map (DGEMap)
+ [project](http://www.dgemap.org/)
+ is an EU-funded study to design a pan-European infrastructure to support gene expression studies in early human development.
+
+The DGEMap team [plan](http://www.inf.ed.ac.uk/research/ICTreviewEPSRC20061207/posters/HumanDev.pdf)
+ to use Taverna workflows to link human spatio-temporal gene expression data with other bioinformatics resources.
+
+<a name="sigenae"></a>
+##SIGENAE
+
+The [Systeme dâInformation des GENomes des animaux âElevage](http://www.sigenae.org/)
+ (SIGENAE) is the Information System of Analysis of Breeding Animalsâ Genome
+ ([AGENAE](http://www.inra.fr/agenae/)) 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
+ ([INRA](http://www.international.inra.fr/)).
+They not only use Taverna Workbench to support e-Science
+ but have been very active in promoting its adoption throughout the French bioinformatics community.
+
+Some of the workflows developed by the Sigenae community have been made available for
+ [sharing](http://www.sigenae.org/index.php?id=84#408).
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