Workflow Entry: Construction of skeleton SBML model using a list of yeast ORF numbers

Created at: 26/03/10 @ 17:08:13 Last updated: 26/03/10 @ 17:13:15

Version 1 (of 1)

Version created on: 26/03/10 @ 17:08:13 by: Peter Li | Revision comments Expand

Last edited on: 26/03/10 @ 17:13:19 by: Peter Li

Title: Construction of skeleton SBML model using a list of yeast ORF numbers

Type: Taverna 2

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Description

This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Inputs (1)

Name	Description
yeast_orfs	A list of yeast orf numbers.

Processors (61)

Name	Type	Description
split	localworker
regex	stringconstant
filterOrfs	wsdl
getReactionIdsByOrf	wsdl
flatten	localworker
getReactantsByReactionId	wsdl
getProductsByReactionId	wsdl
getModifiersByReactionId	wsdl
merge	beanshell
getCompartmentIdBySpeciesId	wsdl
removeDuplicateCompIds	localworker
mergeCompIds	beanshell
createCompartments	workflow
createCompMetaId	beanshell
getCompNameById	wsdl
getOutsideCompById	wsdl
getSboTermByCompId	wsdl
getGOId	wsdl
createModel	workflow
tag	stringconstant
modelId	stringconstant
metaId	stringconstant
addCompartmentToModel	workflow
createSpecies	workflow
getKeggBySpId	wsdl
getChebiIdBySpId	wsdl
getInchiBySpId	wsdl
getSpSboTerm	wsdl
filterSboTerm	beanshell
getSgdBySpId	wsdl
getNameById	wsdl
createSpMetaId	beanshell
getUniprotBySpId	wsdl
addSpecies	apiconsumer
createReaction	workflow
getNameByReactionId	wsdl
getSboTermByReactionId	wsdl
filterSboTermForReaction	beanshell
getECNumberByReactionId	wsdl
getPubMedByReactionId	wsdl
getNumberOfReactants	wsdl
wrapWithList1	beanshell
getReactantStoich	wsdl
createReactantSpeciesRef	workflow
addReactantToReaction	workflow
getNumberOfProducts	wsdl
wrapWithList2	beanshell
getProductStoich	wsdl
createProductSpeciesRef	workflow
addProductToReaction	workflow
createModifierSpeciesRef	workflow
addModifierToReaction	workflow
addReactionToModel	apiconsumer
createSBMLDocument	apiconsumer
setModelToDocument	apiconsumer
createSBMLWriter	apiconsumer
writeToString	apiconsumer
createDot	beanshell
display	beanshell
getOutsideCompartmentIds	wsdl
flatten2	localworker

Beanshells (11)

Name	Inputs	Outputs
merge	reactants products modifiers	speciesIds
mergeCompIds	compIds outsideCompIds	finalCompIds
createCompMetaId	compId	compMetaId
filterSboTerm	sboTermIn	sboTermOut
createSpMetaId	speciesId	speciesMetaId
filterSboTermForReaction	sboTermIn	sboTermOut
wrapWithList1	input reactantNumber	output
wrapWithList2	input reactantNumber	output
createDot	sbml	dot
display	dot	out
createMetaId	speciesId	metaId

Outputs (2)

Name	Description
sbml_model	An SBML model
sbml_graph	A png image of a graph representing the SBML model generated by this workflow

Datalinks (95)

Source	Sink
regex:value	split:regex
yeast_orfs	split:string
split:split	filterOrfs:orfs
filterOrfs:filterOrfsReturn	getReactionIdsByOrf:orf
getReactionIdsByOrf:getReactionIdsByOrfReturn	flatten:inputlist
flatten:outputlist	getReactantsByReactionId:reactionId
flatten:outputlist	getProductsByReactionId:reactionId
flatten:outputlist	getModifiersByReactionId:reactionId
getReactantsByReactionId:getReactantsByReactionIdReturn	merge:reactants
getProductsByReactionId:getProductsByReactionIdReturn	merge:products
getModifiersByReactionId:getModifiersByReactionIdReturn	merge:modifiers
merge:speciesIds	getCompartmentIdBySpeciesId:speciesId
getCompartmentIdBySpeciesId:getCompartmentIdBySpeciesIdReturn	removeDuplicateCompIds:stringlist
removeDuplicateCompIds:strippedlist	mergeCompIds:compIds
getOutsideCompartmentIds:getOutsideCompartmentIdsReturn	mergeCompIds:outsideCompIds
createCompMetaId:compMetaId	createCompartments:compMetaId
getCompNameById:getCompartmentNameByIdReturn	createCompartments:compName
getOutsideCompById:getOutsideCompartmentByIdReturn	createCompartments:outsideCompId
getSboTermByCompId:getSboTermByCompartmentIdReturn	createCompartments:compSboTerm
getGOId:getGOIdByIdReturn	createCompartments:compGoId
flatten2:outputlist	createCompartments:compId
flatten2:outputlist	createCompMetaId:compId
flatten2:outputlist	getCompNameById:compartmentId
flatten2:outputlist	getOutsideCompById:compartmentId
flatten2:outputlist	getSboTermByCompId:compartmentId
flatten2:outputlist	getGOId:compartmentId
tag:value	createModel:modelName
modelId:value	createModel:modelId
metaId:value	createModel:modelMetaId
createModel:model	addCompartmentToModel:modelIn
createCompartments:compartment	addCompartmentToModel:compartments
getKeggBySpId:getKeggBySpeciesIdReturn	createSpecies:kegg
getChebiIdBySpId:getChebiIdBySpeciesIdReturn	createSpecies:chebi
getInchiBySpId:getInchiBySpeciesIdReturn	createSpecies:inchi
filterSboTerm:sboTermOut	createSpecies:speciesSboTerm
merge:speciesIds	createSpecies:speciesId
getSgdBySpId:getSgdBySpeciesIdReturn	createSpecies:sgd
getNameById:getSpeciesNameByIdReturn	createSpecies:speciesName
createSpMetaId:speciesMetaId	createSpecies:speciesMetaId
getCompartmentIdBySpeciesId:getCompartmentIdBySpeciesIdReturn	createSpecies:speciesCompId
getUniprotBySpId:getUniprotBySpeciesIdReturn	createSpecies:uniprot
merge:speciesIds	getKeggBySpId:speciesId
merge:speciesIds	getChebiIdBySpId:speciesId
merge:speciesIds	getInchiBySpId:speciesId
merge:speciesIds	getSpSboTerm:speciesId
getSpSboTerm:getSBOTermByIdReturn	filterSboTerm:sboTermIn
merge:speciesIds	getSgdBySpId:speciesId
merge:speciesIds	getNameById:speciesId
merge:speciesIds	createSpMetaId:speciesId
merge:speciesIds	getUniprotBySpId:speciesId
createModel:model	addSpecies:object
createSpecies:species	addSpecies:s
flatten:outputlist	createReaction:id
getNameByReactionId:getNameByReactionIdReturn	createReaction:name
filterSboTermForReaction:sboTermOut	createReaction:sboTerm
getECNumberByReactionId:getECNumberByReactionIdReturn	createReaction:ec_code
getPubMedByReactionId:getPubMedByReactionIdReturn	createReaction:pubmedId
flatten:outputlist	getNameByReactionId:reactionId
flatten:outputlist	getSboTermByReactionId:reactionId
getSboTermByReactionId:getSboTermByReactionIdReturn	filterSboTermForReaction:sboTermIn
flatten:outputlist	getECNumberByReactionId:reactionId
flatten:outputlist	getPubMedByReactionId:reactionId
flatten:outputlist	getNumberOfReactants:reactionId
flatten:outputlist	wrapWithList1:input
getNumberOfReactants:getNumberOfReactantsReturn	wrapWithList1:reactantNumber
wrapWithList1:output	getReactantStoich:reactionId
getReactantsByReactionId:getReactantsByReactionIdReturn	getReactantStoich:speciesId
getReactantsByReactionId:getReactantsByReactionIdReturn	createReactantSpeciesRef:speciesId
getReactantStoich:getStoichiometryReturn	createReactantSpeciesRef:stoich
createReactantSpeciesRef:speciesRef	addReactantToReaction:reactantSpeciesRef
createReaction:reaction	addReactantToReaction:reactionIn
flatten:outputlist	getNumberOfProducts:reactionId
getNumberOfProducts:getNumberOfProductsReturn	wrapWithList2:reactantNumber
flatten:outputlist	wrapWithList2:input
getProductsByReactionId:getProductsByReactionIdReturn	getProductStoich:speciesId
wrapWithList2:output	getProductStoich:reactionId
getProductsByReactionId:getProductsByReactionIdReturn	createProductSpeciesRef:speciesId
getProductStoich:getStoichiometryReturn	createProductSpeciesRef:stoich
createReaction:reaction	addProductToReaction:reactionIn
createProductSpeciesRef:speciesRef	addProductToReaction:productSpeciesRef
getModifiersByReactionId:getModifiersByReactionIdReturn	createModifierSpeciesRef:speciesId
createReaction:reaction	addModifierToReaction:reactionIn
createModifierSpeciesRef:modifierSpeciesRef	addModifierToReaction:modifierSpeciesRef
createReaction:reaction	addReactionToModel:r
createModel:model	addReactionToModel:object
createSBMLDocument:object	setModelToDocument:object
createModel:model	setModelToDocument:m
createSBMLWriter:object	writeToString:object
setModelToDocument:object	writeToString:d
writeToString:result	createDot:sbml
createDot:dot	display:dot
removeDuplicateCompIds:strippedlist	getOutsideCompartmentIds:compartmentId
mergeCompIds:finalCompIds	flatten2:inputlist
writeToString:result	sbml_model
display:out	sbml_graph

Coordinations (6)

Controller	Target
addCompartmentToModel	addSpecies
addReactantToReaction	addProductToReaction
addModifierToReaction	addReactionToModel
addSpecies	addReactionToModel
addReactionToModel	setModelToDocument
addProductToReaction	addModifierToReaction