Mapping microarray data onto metabolic pathways

Created: 2007-11-14 16:51:26 Last updated: 2007-11-22 10:39:32

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This workflow maps microarray data onto metabolic pathway diagrams represented as SBML models drawn using Cell Designer. To run this workflow requires libsbml to be installed into taverna - see http://www.mcisb.org/software/taverna/libsbml/index.html

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Workflow Components

Inputs (0)

Processors (13)

Name	Type	Description
FileLocation	stringconstant	URL of the SBML file of the glycolysis pathway
createDictionary	beanshell	Creates a mapping of yeast gene names with affymetrix probe set identifiers
swapAffyIds	beanshell
extractExpressData	beanshell
addColorToValues	beanshell
merge	beanshell
calcExpressionRange	beanshell
getSBMLFile	local
queryMaxd	arbitrarywsdl	Will take a list of Gene names, a list of Measurement names and a list of Column Types and produce a table. All values are coloured in relation to the a reference. In the list of Measurement names, the first Measurement listed is taken to be the reference. Formatted as text.
extractGeneNames	workflow	A sub workflow that reads the gene names used by labelling enzymes in the SBML model
writeSBML	workflow	Creates a new SBML model containing new colours for how the enzymes should coloured according to gene expression level
createImage	arbitrarywsdl	Renders an image of the new SBML model
getAffyIds	arbitrarywsdl

Beanshells (8)

Name	Description	Inputs	Outputs
extractGeneNames		NumOfSpecies listOfSpecies	geneNames
writeAnnotation		annotation ExpressionValues	NewSBMLFile
createDictionary	Creates a mapping of yeast gene names with affymetrix probe set identifiers	AffyIds GeneNames	AffyIdGeneNameMap
swapAffyIds		affyIdGeneNameMap expressionValues	NewExpressionValues
extractExpressData		maxdBrowseXMLOutput	ExpressionValues
addColorToValues		colorcode expressionValues	ColorCodedExpressionValues
merge		ids	mergedIds
calcExpressionRange		expressionValues	colorcode

Outputs (2)

Name	Description
sbml
image

Links (18)

Source	Sink
FileLocation:value	getSBMLFile:url
addColorToValues:ColorCodedExpressionValues	writeSBML:colouredExpressionValues
calcExpressionRange:colorcode	addColorToValues:colorcode
createDictionary:AffyIdGeneNameMap	swapAffyIds:affyIdGeneNameMap
createImage:createImageReturn	image
extractExpressData:ExpressionValues	swapAffyIds:expressionValues
extractGeneNames:geneNames	createDictionary:GeneNames
extractGeneNames:geneNames	getAffyIds:geneName
getAffyIds:getAffyIdReturn	createDictionary:AffyIds
getAffyIds:getAffyIdReturn	merge:ids
getSBMLFile:contents	extractGeneNames:sbmlString
getSBMLFile:contents	writeSBML:sbmlString
merge:mergedIds	queryMaxd:GeneNames
queryMaxd:return	extractExpressData:maxdBrowseXMLOutput
swapAffyIds:NewExpressionValues	addColorToValues:expressionValues
swapAffyIds:NewExpressionValues	calcExpressionRange:expressionValues
writeSBML:newSBMLString	createImage:sbml
writeSBML:newSBMLString	sbml

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Peter Li

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Information Version 1 (of 1)

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Peter Li

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Information Statistics

8301 viewings

4067 downloads

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Citations (1)

1. Peter Li, Tom Oinn, Stian Soiland and Douglas B. Kell, Automated manipulation of systems biology models using libSBML within Taverna workflows, Bioinformatics (In press), 29 November 2007, http://www.mcisb.org/software/taverna/libsbml/index.html

Version History

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Mapping microarray data onto metabolic pathways

Created by Peter Li on Wednesday 14 November 2007 16:51:26 (UTC)

Last edited by Peter Li on Thursday 22 November 2007 10:39:32 (UTC)

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