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Posted to commits@taverna.apache.org by br...@apache.org on 2015/02/26 10:41:36 UTC
svn commit: r1662398 -
/incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
Author: brenninc
Date: Thu Feb 26 09:41:36 2015
New Revision: 1662398
URL: http://svn.apache.org/r1662398
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Added previous sub pages
Added:
incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
Added: incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md
URL: http://svn.apache.org/viewvc/incubator/taverna/site/trunk/content/introduction/taverna-in-use/biology.md?rev=1662398&view=auto
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+Title: Biology
+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 used by various projects and researchers for investigations into systems biology:
+
+ - [ENFIN â Enabling Systems Biology](#enfin) â calling of wrapped tools within workflows
+ - [Manchester Centre for Integrative Systems Biology](#manchester-centre-for-integrative-systems-biology)
+ (MCISB) â modelling metabolomic pathways
+ - [Systems Biology Operational Software](sb-os) (SB.OS) -
+ a live DVD based on Ubuntu Linux that comes with a comprehensive list of Systems Biology Software (including Taverna)
+ - [Tav4SB](#tav4sb) - Taverna workflows for systems biology,
+ in particular for analysis of the kinetic models of biological systems
+
+Taverna is also used for analysis of plant biology:
+
+ - [Automatic Functional Annotation in a distributed Web Service Environment](/introduction/taverna-in-use/annotation#afawe)
+ (AFAWE) â protein prediction and annotation by a tool that calls workflows
+ - [PLANET (A Network of European Plant Databases](#planet) â calling of workflows from a portal
+
+
+<a name="enfin"<a>
+##ENFIN
+
+The partners within the ENFIN - Enabling Systems Biology [project](http://www.enfin.org/)
+ developed a suite of Systems Biology tools (ENSUITE).
+These tools are also available as normal WSDL services and their possible use within workflows has been
+ demonstrated by use of Taverna.
+
+###Publications
+The [paper](http://www.springerlink.com/content/hw667700pm2170j4/)
+ *ENFIN - An Integrative Structure for Systems Biology*
+ by Reisinger et al. describes the overall design and structure of ENFIN.
+
+<a name="manchester-centre-for-integrative-systems-biology"></a>
+##Manchester Centre for Integrative Systems Biology
+
+The [BBSRC](http://www.bbsrc.ac.uk/) and [EPSRC](http://www.epsrc.ac.uk/) have awarded £6.3m to the
+ [Manchester Centre for Integrative Systems Biology](http://www.mcisb.org/)
+ (MCISB) based at the [Manchester Interdisciplinary Biocentre](http://www.mib.ac.uk/) (MIB).
+The award is to pioneer the development of new experimental and computational technologies in Systems Biology,
+ and their exploitation.
+
+The MCISB is intended to provide a hub for cutting-edge systems biology research in the Manchester area,
+ acting as a focal point for the creation of the necessary ideas and infrastructure,
+ and for establishing new methods and routines.
+
+The co-investigators in the project Professor [Norman Paton](http://www.manchester.ac.uk/research/norman.paton),
+ Professor [Douglas Kell](http://www.manchester.ac.uk/research/Douglas.kell) et al.
+It ran from May 2005 to April 2010.
+
+###Metabolomic Pathways
+
+The Manchester Centre for Integrative Systems Biology 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](http://www.mygrid.org.uk/files/2008/09/peter-li-poster.pdf) 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](http://sbml.org/)) as described in the
+ [paper](http://www.mygrid.org.uk/outreach/publications/li2007/)
+ *Automated manipulation of systems biology models using libSBML within Taverna workflows* by Li et al.
+
+An example [workflow](http://www.myexperiment.org/workflows/79) using SBML is available on
+ [myExperiment](http://www.myexperiment.org).
+
+<a name="sb-os"></a>
+##Systems Biology Operational Software (SB.OS)
+
+[SB.OS](http://www.sbos.eu/doku.php) is a live DVD based on Ubuntu Linux that comes with
+ a comprehensive list of Systems Biology Software.
+Text and video documentation material,
+ as well as an offline copy of the BioModels.net database and Taverna 2.1, are included.
+
+<a name="tav4sb"></a>
+##Tav4SB
+
+[Tav4SB project](http://bioputer.mimuw.edu.pl/tav4sb/) provides a grid environment with a set of Web services,
+ bundled together in Taverna workflows.
+Target application area is the system biology field,
+ in particular analysis of the kinetic models of biological systems.
+
+<a name="planet"></a>
+##PLANET
+
+As part of the [PLANET](http://www.eu-plant-genome.net/) (A Network of European Plant Databases) project,
+ [URGI](http://www.breedwheat.fr/institutions.php?id=6)
+ (Unité de Recherche Génomique-Info) developed BioFloWeb.
+
+BioFloWeb is a stand-alone Web application processing Web services.
+A given user can choose among predefined workflows or define their own with Taverna.
+BioFloWeb has been [demonstrated](http://biofloweb.sourceforge.net/)
+ for retrieval of information about Arabidopsis genes from several European databases.
+
+BioFloWeb makes extensive use of [BioMoby](/introduction/taverna-in-use/annotation#adoption-by-moby) services.
+