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svn commit: r1656729 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/bioinformatics.md
Author: brenninc
Date: Tue Feb 3 13:40:31 2015
New Revision: 1656729
URL: http://svn.apache.org/r1656729
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incubator/taverna/site/trunk/content/introduction/taverna-in-use/bioinformatics.md
Added: incubator/taverna/site/trunk/content/introduction/taverna-in-use/bioinformatics.md
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+Title: Bioinformatics
+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 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.
+<img class="aligncenter"
+ title="Bioinformatics services and resources"
+ src="/img/BioinformaticsResources.png"
+ alt="Bioinformatics services and resources" width="676" height="441" />
+
+Bioinformatics systems/tools using Taverna:
+
+ - [BioWEP][1] - bioinformatics workflow enactment portal
+ - [BioLinux][2] - Ubuntu Linux distribution that includes Taverna and many other bioinformatics programs
+
+### Biodiversity ###
+
+ - [BioVeL][3]
+
+### Gene and genome expression ###
+
+ - [Next Generation Sequencing][4] using Taverna 2 Server on Amazon cloud
+ - [TavernaPBS][5] - 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][6] (CASIMIR) -
+ workflows to associate mouse genome and phenome
+ - [Developmental Gene Expression Map][7] (DGEMap)- analysis of human gene expression during development
+ - [Graves disease][8] - identification of genes responsible
+ - [Examination of gene expression from MicroArray data using R][9] - statistical analysis of gene expression
+ - [SIGENAE][10] - development of workflows to analyse breeding animal data
+ - [Trypanosomiasis][11] - identification of genes responsible for sleeping sickness
+ - [Williams-Beuren syndrome][12] - automation and confirmation of gene characterization
+ - [PLANET][13] - integration of plant genome resources
+ - [Annotation of genomes][14]</a>
+ - [Shared Genomics][15]</a>
+ - [e-Fungi][16] functional genomics in fungal species
+
+###Protein and proteomics###
+
+ - [Analysis of mass spectrometry data in proteomics][17]
+ - [Anthrax analysis][18] - identification of proteins secreted by bacteria
+ - [eFamily][19] - integrating data from different databases
+ - [European Model for Bioinformatics Research And Community Education][20] (EMBRACE) -
+ calling services on a grid; recovering a database
+ - [iSpider][21] - querying multiple data sources
+ - [ProDom][22] - running of Taverna workflows behind a portal to search a protein database
+
+###Biology and systems biology###
+
+ - [ENFIN][23] â Enabling Systems Biology â calling of wrapped tools within workflows
+ - [Manchester Centre for Integrative Systems Biology][24] (MCISB) â modelling metabolomic pathways
+ - [Systems Biology Operational Software][25] (SB.OS) - a live DVD based on Ubuntu Linux that comes with a
+ comprehensive list of Systems Biology Software (including Taverna)
+ - [Tav4SB][26] - Taverna workflows for systems biology,
+ in particular for analysis of the kinetic models of biological systems
+ - [Measuring of enzyme characteristics of yeast][27]
+ - [Automatic Functional Annotation in a distributed Web Service Environment][28] (AFAWE) â
+ protein prediction and annotation by a tool that calls workflows
+ - [PLANET (A Network of European Plant Databases)][29] â calling of workflows from a portal
+
+###Biomedicine and disease-related research###
+
+ - [Fighting dementia][30] (VP-DARE@IT and VPH-SHARE)
+ - [Analysis of the anthrax bacterium][31]
+ - [Study of resistance into trypanosomiasis][32] (sleeping sickness)
+ - [Identification of genes linked to Graves disease][33]
+ - [Characterisation of genes associated with Williams-Beuren syndrome][34]
+ - [caGrid][35] - research into predicting limphoma cancer
+ - [EU-ADR][36] - detecting adverse drug reactions through the exploitation of clinical data from electronic
+ healthcare records
+
+<a name="biowep"></a>
+###BioWEP###
+Researchers at the Italian National Institute for Cancer Research Genoa ([IST][37]) have developed a
+ Bioinformatics Workflow Enactment Portal called [BioWEP][38].
+
+The [portal][39] allows registered users to search for or select from a set of specified Taverna workflows.
+The workflow can be enacted by entering input values into a form.
+During enaction, the user can either wait for the result, or for longer running workflows,
+ visit the portal later. The results of the enactment can be downloaded for external visualization.
+
+####Publications####
+The http://dx.doi.org/10.1186/1471-2105-8-S1-S19 *Biowep: a workflow enactment portal for bioinformatics
+ applications* by Romano et al gives an overview of the intent and design of Biowep.
+
+<a naem="biolinux"></a>
+###BioLinux###
+The UKâs Natural Environment Research Council (NERC) Environmental Bioinformatics [Centre][40] release
+ [BioLinux][41], an installation of Ubuntu Linux that includes many bioinformatics programs.
+
+Among the programs included in the BioLinux distribution is Taverna.
+The suite of programs are also available for installation on pre-existing Linux systems.
+
+<a name="lumc"></a>
+###LUMC###
+People from the Leiden University Medical Center ([LUMC][42]) in the Netherlands are using Taverna for analysis
+ of mass spectrometry data in proteomics.
+
+They presented a [poster][43] at the 2011 ASMS (the American Society for Mass Spectrometry) Conference on
+ Mass Spectrometry and Allied Topics.
+
+Please contact [Dr. Magnus Palmblad][44] for more details.
+
+<a name="measuring-enzyme-characteristics-of-yeast"></a>
+###Measuring enzyme characteristics of yeast###
+The [Manchester Centre for Integrative Systems Biology][45] (MCISB) 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.
+
+####Publications####
+A [poster][46] 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.
+
+Many of the workflows make use of Systems Biology Markup Language ([SBML][47]) as described in the
+ [paper][48] *Automated manipulation of systems biology models using libSBML within Taverna workflows*
+ by Li et al.
+
+An [example workflow][49] using SBML is available on [myExperiment][50].
+
+ [1]: #biowep
+ [2]: #biolinux
+ [3]: /introduction/related-projects/biovel
+ [4]: /introduction/taverna-in-use/genome-and-gene-expression.html#next-generation-sequencing
+ [5]: /introduction/taverna-in-use/genome-and-gene-expression.html#tavernapbs
+ [6]: /introduction/taverna-in-use/genome-and-gene-expression.html#casimir
+ [7]: /introduction/taverna-in-use/genome-and-gene-expression.html#dgemap
+ [8]: /introduction/taverna-in-use/disease-research.html#graves-disease
+ [9]: /introduction/taverna-in-use/bioinformatics.html#gene-expression-from-microarray
+ [10]: /introduction/taverna-in-use/genome-and-gene-expression.html#sigenae
+ [11]: /introduction/taverna-in-use/disease-research.html#trypanosomiasis
+ [12]: /introduction/taverna-in-use/disease-research.html#williams-beuren-syndrome
+ [13]: /introduction/taverna-in-use/biology.html#planet
+ [14]: /introduction/taverna-in-use/annotation.html#annotation-of-genomes
+ [15]: /introduction/related-projects.html#shared-genomics
+ [16]: http://img.cs.man.ac.uk/efungi/
+ [17]: #lumc
+ [18]: /introduction/taverna-in-use/disease-research.html#analysis-of-anthrax-bacterium
+ [19]: /introduction/taverna-in-use/databases.html#efamily
+ [20]: http://www.mygrid.org.uk/mygrid-in-use/adoption-by-embrace
+ [21]: /introduction/related-projects.html#ispider
+ [22]: /introduction/taverna-in-use/protein-and-proteomics.html#prodom
+ [23]: /introduction/taverna-in-use/biology.html#enfin
+ [24]: /introduction/taverna-in-use/biology.html#manchester-centre-for-integrative-systems-biology
+ [25]: /introduction/taverna-in-use/biology.html#sb-os
+ [26]: /introduction/taverna-in-use/biology.html#tav4sb
+ [27]: #measuring-enzyme-characteristics-of-yeast
+ [28]: /introduction/taverna-in-use/annotation.html#afawe
+ [29]: /introduction/taverna-in-use/biology.html#planet
+ [30]: /introduction/taverna-in-use/disease-research.html#vph-dareit
+ [31]: /introduction/taverna-in-use/disease-research.html#analysis-of-anthrax-bacterium
+ [32]: /introduction/taverna-in-use.html#trypanosomiasis
+ [33]: /introduction/taverna-in-use/disease-research.html#graves-disease
+ [34]: /introduction/taverna-in-use/disease-research.html#williams-beuren-syndrome
+ [35]: /introduction/related-projects.html#cagrid
+ [36]: /introduction/taverna-in-use/medicine.html#eu-adr
+ [37]: http://www.istge.it/
+ [38]: http://bioinformatics.istge.it/biowep/index.html
+ [39]: http://bioinformatics.istge.it:8080/biowep/
+ [40]: http://nebc.nox.ac.uk/
+ [41]: http://nebc.nox.ac.uk/biolinux.html
+ [42]: http://www.lumc.nl/home/?setlanguage=English&setcountry=en
+ [43]: /pages/wp-content/uploads/2011/06/Palmblad_ASMS_2011_LUMC.pdf
+ [44]: https://www.lumc.nl/org/proteomics-metabolomics/medewerkers/nmpalmblad
+ [45]: /introduction/taverna-in-use/biology/manchester-centre-for-integrative-systems-biology
+ [46]: http://www.mygrid.org.uk/files/2008/09/peter-li-poster.pdf
+ [47]: http://sbml.org/
+ [48]: http://www.mygrid.org.uk/outreach/publications/li2007/
+ [49]: http://www.myexperiment.org/workflows/79
+ [50]: http://www.myexperiment.org/
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