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Mapping microarray data onto metabolic pathways

Workflow Entry: Mapping microarray data onto metabolic pathways

Created at: 14/11/07 @ 16:51:26 Last updated: 22/11/07 @ 10:39:32

Version 1 (of 1)

Version created on: 14/11/07 @ 16:51:26 by: Peter Li | Revision comments Expand

Last edited on: 22/11/07 @ 10:39:32 by: Peter Li

Title: Mapping microarray data onto metabolic pathways

Type: Taverna 1

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Mapping_microarray_data_onto_metabolic_pathways_3766

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Description

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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Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/79/download?version=1
[ More Info Expand ]

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

Outputs (2)

Name	Description
sbml
image

Links (18)

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

Coordinations (0)

Taverna 1 workflow

Information Original Uploader

Peter Li

Information License

All versions of this Workflow are licensed under the Creative Commons Attribution-Share Alike 3.0 License.

Information Credits (1)

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Peter Li

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Information Tags (5)

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Information Statistics

1012 viewings

1177 downloads

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

Earliest Version:
[1] - Mapping microarray data onto metabolic pathways

Created on: Wednesday 14 November 2007 @ 16:51:26 (GMT)

Created by: Peter Li

Last edited on: Thursday 22 November 2007 @ 10:39:32 (GMT)

Last edited by: Peter Li

Revision comments:

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This Workflow only has one version.