Construction_of_skeleton_SBML_modelyeast_orfs00 YAL038W,YGR254W,YKL060C,YKL152C,YFR053C,YLR044C,YGR240C,YMR205C,YBR196C,YCR012W,YJL052W,YDR050C 2010-03-26 08:21:04.919 GMT A list of yeast orf numbers. 2010-03-26 08:20:46.424 GMT sbml_model An SBML model 2010-03-26 08:22:00.764 GMT sbml_graph A png image of a graph representing the SBML model generated by this workflow 2010-03-26 08:21:38.533 GMT splitregex0string0split11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.SplitByRegex workflow java.lang.String true string 0 'text/plain' java.lang.String true regex 0 'text/plain' 1 split 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeregexvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity , net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterOrfsorfs1filterOrfsReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl filterOrfs net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetReactionIdsByOrforf0getReactionIdsByOrfReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getReactionIdsByOrf net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeflatteninputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetReactantsByReactionIdreactionId0getReactantsByReactionIdReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getReactantsByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetProductsByReactionIdreactionId0getProductsByReactionIdReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getProductsByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetModifiersByReactionIdreactionId0getModifiersByReactionIdReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getModifiersByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokemergereactants2products2modifiers2speciesIds11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true reactants 2 text/plain java.lang.String true products 2 text/plain java.lang.String true modifiers 2 text/plain 1 speciesIds 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetCompartmentIdBySpeciesIdspeciesId0getCompartmentIdBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getCompartmentIdBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeremoveDuplicateCompIdsstringlist1strippedlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates workflow java.lang.String true stringlist 1 l('text/plain') 1 strippedlist 1 l('text/plain') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemergeCompIdscompIds1outsideCompIds1finalCompIds11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true compIds 1 text/plain java.lang.String true outsideCompIds 1 text/plain 1 finalCompIds 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateCompartmentscompMetaId0compName0outsideCompId0compSboTerm0compGoId0compId0compartment00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateCompMetaIdcompId0compMetaId00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true compId 0 text/plain 0 compMetaId 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetCompNameByIdcompartmentId0getCompartmentNameByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getCompartmentNameById net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetOutsideCompByIdcompartmentId0getOutsideCompartmentByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getOutsideCompartmentById net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSboTermByCompIdcompartmentId0getSboTermByCompartmentIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getSboTermByCompartmentId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetGOIdcompartmentId0getGOIdByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getGOIdById net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateModelmodelName0modelId0modelMetaId0model00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoketagvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity glycolysis net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemodelIdvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity taverna1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemetaIdvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity taverna1a net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddCompartmentToModelmodelIn0compartments1net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSpecieskegg0chebi0inchi0speciesSboTerm0speciesId0sgd0speciesName0speciesMetaId0speciesCompId0uniprot0species00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetKeggBySpIdspeciesId0getKeggBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getKeggBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetChebiIdBySpIdspeciesId0getChebiIdBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getChebiIdBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetInchiBySpIdspeciesId0getInchiBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getInchiBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSpSboTermspeciesId0getSBOTermByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getSBOTermById net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterSboTermsboTermIn0sboTermOut00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true sboTermIn 0 text/plain 0 sboTermOut 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSgdBySpIdspeciesId0getSgdBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getSgdBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNameByIdspeciesId0getSpeciesNameByIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getSpeciesNameById net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSpMetaIdspeciesId0speciesMetaId00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true speciesId 0 text/plain 0 speciesMetaId 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetUniprotBySpIdspeciesId0getUniprotBySpeciesIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getUniprotBySpeciesId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddSpeciesobject0s0net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a copy of the given Species object to this Model. org.sbml.libsbml.Model addSpecies s 0 org.sbml.libsbml.Species void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateReactionid0name0sboTerm0ec_code0pubmedId0reaction00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNameByReactionIdreactionId0getNameByReactionIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getNameByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetSboTermByReactionIdreactionId0getSboTermByReactionIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getSboTermByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterSboTermForReactionsboTermIn0sboTermOut00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true sboTermIn 0 text/plain 0 sboTermOut 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetECNumberByReactionIdreactionId0getECNumberByReactionIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getECNumberByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPubMedByReactionIdreactionId0getPubMedByReactionIdReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getPubMedByReactionId net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNumberOfReactantsreactionId0getNumberOfReactantsReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getNumberOfReactants net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokewrapWithList1input1reactantNumber1output22net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 1 text/plain java.lang.String true reactantNumber 1 text/plain 2 output 2 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetReactantStoichreactionId0speciesId0getStoichiometryReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getStoichiometry net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateReactantSpeciesRefspeciesId0stoich0speciesRef00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddReactantToReactionreactantSpeciesRef1reactionIn0net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetNumberOfProductsreactionId0getNumberOfProductsReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getNumberOfProducts net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokewrapWithList2reactantNumber1input1output22net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true input 1 text/plain java.lang.String true reactantNumber 1 text/plain 2 output 2 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetProductStoichspeciesId0reactionId0getStoichiometryReturn00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getStoichiometry net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateProductSpeciesRefspeciesId0stoich0speciesRef00net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddProductToReactionreactionIn0productSpeciesRef1net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateModifierSpeciesRefspeciesId1modifierSpeciesRef11net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddModifierToReactionreactionIn0modifierSpeciesRef1net.sf.taverna.t2.activitiesdataflow-activity1.0.1net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddReactionToModelr0object0net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a copy of the given Reaction object to this Model. org.sbml.libsbml.Model addReaction r 0 org.sbml.libsbml.Reaction void 0 false false workflow net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSBMLDocumentobject00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new SBMLDocument, optionally with given values for the SBML Level and Version. org.sbml.libsbml.SBMLDocument createSBMLDocument org.sbml.libsbml.SBMLDocument 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetModelToDocumentobject0m0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the Model for this SBMLDocument to a copy of the given Model. org.sbml.libsbml.SBMLDocument setModel m 0 org.sbml.libsbml.Model void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSBMLWriterobject00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new SBMLWriter. org.sbml.libsbml.SBMLWriter createSBMLWriter org.sbml.libsbml.SBMLWriter 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokewriteToStringobject0d0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Writes the given SBML document to an in-memory string and returns a pointer to it. org.sbml.libsbml.SBMLWriter writeToString d 0 org.sbml.libsbml.SBMLDocument java.lang.String 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateDotsbml0dot00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity system graphviz-api-1.0.jar libsbmlj.jar java.lang.String true sbml 0 text/plain 0 dot 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokedisplaydot0out00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true dot 0 text/plain 0 out 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetOutsideCompartmentIdscompartmentId0getOutsideCompartmentIdsReturn11net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity http://dbk-ed.mib.man.ac.uk:8080/YeastMetabolicNetwork/services/YeastMetabolicNetwork?wsdl getOutsideCompartmentIds net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeflatten2inputlist2outputlist11net.sf.taverna.t2.activitieslocalworker-activity1.0net.sf.taverna.t2.activities.localworker.LocalworkerActivity org.embl.ebi.escience.scuflworkers.java.FlattenList workflow [B true inputlist 2 l(l('')) 1 outputlist 1 l('') net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplitregexregexvaluesplitstringyeast_orfsfilterOrfsorfssplitsplitgetReactionIdsByOrforffilterOrfsfilterOrfsReturnflatteninputlistgetReactionIdsByOrfgetReactionIdsByOrfReturngetReactantsByReactionIdreactionIdflattenoutputlistgetProductsByReactionIdreactionIdflattenoutputlistgetModifiersByReactionIdreactionIdflattenoutputlistmergereactantsgetReactantsByReactionIdgetReactantsByReactionIdReturnmergeproductsgetProductsByReactionIdgetProductsByReactionIdReturnmergemodifiersgetModifiersByReactionIdgetModifiersByReactionIdReturngetCompartmentIdBySpeciesIdspeciesIdmergespeciesIdsremoveDuplicateCompIdsstringlistgetCompartmentIdBySpeciesIdgetCompartmentIdBySpeciesIdReturnmergeCompIdscompIdsremoveDuplicateCompIdsstrippedlistmergeCompIdsoutsideCompIdsgetOutsideCompartmentIdsgetOutsideCompartmentIdsReturncreateCompartmentscompMetaIdcreateCompMetaIdcompMetaIdcreateCompartmentscompNamegetCompNameByIdgetCompartmentNameByIdReturncreateCompartmentsoutsideCompIdgetOutsideCompByIdgetOutsideCompartmentByIdReturncreateCompartmentscompSboTermgetSboTermByCompIdgetSboTermByCompartmentIdReturncreateCompartmentscompGoIdgetGOIdgetGOIdByIdReturncreateCompartmentscompIdflatten2outputlistcreateCompMetaIdcompIdflatten2outputlistgetCompNameByIdcompartmentIdflatten2outputlistgetOutsideCompByIdcompartmentIdflatten2outputlistgetSboTermByCompIdcompartmentIdflatten2outputlistgetGOIdcompartmentIdflatten2outputlistcreateModelmodelNametagvaluecreateModelmodelIdmodelIdvaluecreateModelmodelMetaIdmetaIdvalueaddCompartmentToModelmodelIncreateModelmodeladdCompartmentToModelcompartmentscreateCompartmentscompartmentcreateSpecieskegggetKeggBySpIdgetKeggBySpeciesIdReturncreateSpecieschebigetChebiIdBySpIdgetChebiIdBySpeciesIdReturncreateSpeciesinchigetInchiBySpIdgetInchiBySpeciesIdReturncreateSpeciesspeciesSboTermfilterSboTermsboTermOutcreateSpeciesspeciesIdmergespeciesIdscreateSpeciessgdgetSgdBySpIdgetSgdBySpeciesIdReturncreateSpeciesspeciesNamegetNameByIdgetSpeciesNameByIdReturncreateSpeciesspeciesMetaIdcreateSpMetaIdspeciesMetaIdcreateSpeciesspeciesCompIdgetCompartmentIdBySpeciesIdgetCompartmentIdBySpeciesIdReturncreateSpeciesuniprotgetUniprotBySpIdgetUniprotBySpeciesIdReturngetKeggBySpIdspeciesIdmergespeciesIdsgetChebiIdBySpIdspeciesIdmergespeciesIdsgetInchiBySpIdspeciesIdmergespeciesIdsgetSpSboTermspeciesIdmergespeciesIdsfilterSboTermsboTermIngetSpSboTermgetSBOTermByIdReturngetSgdBySpIdspeciesIdmergespeciesIdsgetNameByIdspeciesIdmergespeciesIdscreateSpMetaIdspeciesIdmergespeciesIdsgetUniprotBySpIdspeciesIdmergespeciesIdsaddSpeciesobjectcreateModelmodeladdSpeciesscreateSpeciesspeciescreateReactionidflattenoutputlistcreateReactionnamegetNameByReactionIdgetNameByReactionIdReturncreateReactionsboTermfilterSboTermForReactionsboTermOutcreateReactionec_codegetECNumberByReactionIdgetECNumberByReactionIdReturncreateReactionpubmedIdgetPubMedByReactionIdgetPubMedByReactionIdReturngetNameByReactionIdreactionIdflattenoutputlistgetSboTermByReactionIdreactionIdflattenoutputlistfilterSboTermForReactionsboTermIngetSboTermByReactionIdgetSboTermByReactionIdReturngetECNumberByReactionIdreactionIdflattenoutputlistgetPubMedByReactionIdreactionIdflattenoutputlistgetNumberOfReactantsreactionIdflattenoutputlistwrapWithList1inputflattenoutputlistwrapWithList1reactantNumbergetNumberOfReactantsgetNumberOfReactantsReturngetReactantStoichreactionIdwrapWithList1outputgetReactantStoichspeciesIdgetReactantsByReactionIdgetReactantsByReactionIdReturncreateReactantSpeciesRefspeciesIdgetReactantsByReactionIdgetReactantsByReactionIdReturncreateReactantSpeciesRefstoichgetReactantStoichgetStoichiometryReturnaddReactantToReactionreactantSpeciesRefcreateReactantSpeciesRefspeciesRefaddReactantToReactionreactionIncreateReactionreactiongetNumberOfProductsreactionIdflattenoutputlistwrapWithList2reactantNumbergetNumberOfProductsgetNumberOfProductsReturnwrapWithList2inputflattenoutputlistgetProductStoichspeciesIdgetProductsByReactionIdgetProductsByReactionIdReturngetProductStoichreactionIdwrapWithList2outputcreateProductSpeciesRefspeciesIdgetProductsByReactionIdgetProductsByReactionIdReturncreateProductSpeciesRefstoichgetProductStoichgetStoichiometryReturnaddProductToReactionreactionIncreateReactionreactionaddProductToReactionproductSpeciesRefcreateProductSpeciesRefspeciesRefcreateModifierSpeciesRefspeciesIdgetModifiersByReactionIdgetModifiersByReactionIdReturnaddModifierToReactionreactionIncreateReactionreactionaddModifierToReactionmodifierSpeciesRefcreateModifierSpeciesRefmodifierSpeciesRefaddReactionToModelrcreateReactionreactionaddReactionToModelobjectcreateModelmodelsetModelToDocumentobjectcreateSBMLDocumentobjectsetModelToDocumentmcreateModelmodelwriteToStringobjectcreateSBMLWriterobjectwriteToStringdsetModelToDocumentobjectcreateDotsbmlwriteToStringresultdisplaydotcreateDotdotgetOutsideCompartmentIdscompartmentIdremoveDuplicateCompIdsstrippedlistflatten2inputlistmergeCompIdsfinalCompIdssbml_modelwriteToStringresultsbml_graphdisplayout Peter Li 2010-03-03 10:22:31.592 GMT Construction of skeleton SBML model 2010-03-03 10:22:47.742 GMT This workflow generates a skeleton SBML model consisting of the metabolic reactions for a given list of yeast enzymes ORF numbers 2010-03-03 10:24:59.587 GMT Workflow29productSpeciesRef11reactionIn00reactionaddProductobject0sr0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a given SpeciesReference object as a product in this Reaction. org.sbml.libsbml.Reaction addProduct sr 0 org.sbml.libsbml.SpeciesReference void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddProductobjectreactionInaddProductsrproductSpeciesRefreactionaddProductobjectWorkflow22speciesId11modifierSpeciesRefcreateModifierSpeciesReferencespecies0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new ModiferSpeciesReference, optionally with its 'species' attribute set. org.sbml.libsbml.ModifierSpeciesReference createModifierSpeciesReferenceBySpecies species 0 java.lang.String org.sbml.libsbml.ModifierSpeciesReference 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateModifierSpeciesReferencespeciesspeciesIdmodifierSpeciesRefcreateModifierSpeciesReferenceobjectWorkflow21speciesId00stoich00speciesRefcreateSpeciesReferenceBySpeciesspecies0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new SpeciesReference, optionally setting its species values. org.sbml.libsbml.SpeciesReference createSpeciesReferenceBySpecies species 0 java.lang.String org.sbml.libsbml.SpeciesReference 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetStoichiometryobject0value0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'stoichiometry' attribute of this SpeciesReference. org.sbml.libsbml.SpeciesReference setStoichiometry value 0 double void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSpeciesReferenceBySpeciesspeciesspeciesIdsetStoichiometryobjectcreateSpeciesReferenceBySpeciesobjectsetStoichiometryvaluestoichspeciesRefsetStoichiometryobjectWorkflow13ec_code00name00id00sboTerm00pubmedId00reactioncreateMetaIdspeciesId0metaId00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity workflow java.lang.String true speciesId 0 text/plain 0 metaId 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateReactionByIdsid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new Reaction, optionally with the given identifier. org.sbml.libsbml.Reaction createReactionById sid 0 java.lang.String org.sbml.libsbml.Reaction 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetMetaIdobject0metaid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'metaid' attribute of this object. org.sbml.libsbml.SBase setMetaId metaid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetNameobject0name0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'name' attribute of this SBML object. org.sbml.libsbml.SBase setName name 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetSBOTermobject0value0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'sboTerm' attribute. org.sbml.libsbml.SBase setSBOTerm value 0 int void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetECec0r0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Reaction with a given ec code uri uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setEC r ec 0 0 org.sbml.libsbml.Reaction java.lang.String org.sbml.libsbml.Reaction 0 true false system libsbml_helpers.jar libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetPubMedIdpubmed0r0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Reaction with a given pubmed uri uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setPubMedId r pubmed 0 0 org.sbml.libsbml.Reaction java.lang.String org.sbml.libsbml.Reaction 0 true false system libsbmlj.jar libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateMetaIdspeciesIdidcreateReactionByIdsididsetMetaIdobjectcreateReactionByIdobjectsetMetaIdmetaidcreateMetaIdmetaIdsetNameobjectsetMetaIdobjectsetNamenamenamesetSBOTermobjectsetNameobjectsetSBOTermvaluesboTermsetECecec_codesetECrsetSBOTermobjectsetPubMedIdpubmedpubmedIdsetPubMedIdrsetECresultreactionsetPubMedIdresultWorkflow15speciesId00speciesMetaId00speciesName00speciesCompId00speciesSboTerm00inchi00chebi00kegg00sgd00uniprot00speciessetMetaIdmetaid0object0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'metaid' attribute of this object. org.sbml.libsbml.SBase setMetaId metaid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateSpeciesid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new Species, optionally with the given <code>id</code> and <code>name</code> attribute values. org.sbml.libsbml.Species createSpeciesById id 0 java.lang.String org.sbml.libsbml.Species 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetNameobject0name0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'name' attribute of this SBML object. org.sbml.libsbml.SBase setName name 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetCompartmentobject0sid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the 'compartment' attribute of this Species. org.sbml.libsbml.Species setCompartment sid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetSBOTermobject0value0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'sboTerm' attribute. org.sbml.libsbml.SBase setSBOTerm value 0 int void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetInchiStrings0inchi0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Species with a given inchi string uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setInchiString s inchi 0 0 org.sbml.libsbml.Species java.lang.String org.sbml.libsbml.Species 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetChebiIds0chebiId0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Species with a given chebi id uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setChebiId s chebiId 0 0 org.sbml.libsbml.Species java.lang.String org.sbml.libsbml.Species 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetKeggIds0keggId0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Species with a given kegg id uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setKeggId s keggId 0 0 org.sbml.libsbml.Species java.lang.String org.sbml.libsbml.Species 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetSgdIds0sgdId0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Species with a given SGD id uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setSgdId s sgdId 0 0 org.sbml.libsbml.Species java.lang.String org.sbml.libsbml.Species 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetUniprotIds0uniprot0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Species with a given uniprot id uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setUniprotId s uniprot 0 0 org.sbml.libsbml.Species java.lang.String org.sbml.libsbml.Species 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetMetaIdmetaidspeciesMetaIdsetMetaIdobjectcreateSpeciesobjectcreateSpeciesidspeciesIdsetNameobjectsetMetaIdobjectsetNamenamespeciesNamesetCompartmentobjectsetNameobjectsetCompartmentsidspeciesCompIdsetSBOTermobjectsetCompartmentobjectsetSBOTermvaluespeciesSboTermsetInchiStringssetSBOTermobjectsetInchiStringinchiinchisetChebiIdssetInchiStringresultsetChebiIdchebiIdchebisetKeggIdssetChebiIdresultsetKeggIdkeggIdkeggsetSgdIdssetKeggIdresultsetSgdIdsgdIdsgdsetUniprotIdssetSgdIdresultsetUniprotIduniprotuniprotspeciessetUniprotIdresultWorkflow29reactantSpeciesRef11reactionIn00reactionaddReactantsr0object0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a given SpeciesReference object as a reactant in this Reaction. org.sbml.libsbml.Reaction addReactant sr 0 org.sbml.libsbml.SpeciesReference void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddReactantsrreactantSpeciesRefaddReactantobjectreactionInreactionaddReactantobjectWorkflow3modelName00modelMetaId00modelId00modelcreateModelid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Creates a new Model, optionally with a given identifier and name. org.sbml.libsbml.Model Model id 0 java.lang.String org.sbml.libsbml.Model 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetMetaIdobject0metaid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'metaid' attribute of this object. org.sbml.libsbml.SBase setMetaId metaid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetNamename0object0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'name' attribute of this SBML object. The string in <code>name</code> is copied. org.sbml.libsbml.SBase setName name 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateModelidmodelIdsetMetaIdobjectcreateModelobjectsetMetaIdmetaidmodelMetaIdsetNamenamemodelNamesetNameobjectsetMetaIdobjectmodelsetNameobjectWorkflow28modifierSpeciesRef11reactionIn00reactionaddModifierobject0msr0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a given ModifierSpeciesReference object as a product in this Reaction. org.sbml.libsbml.Reaction addModifier msr 0 org.sbml.libsbml.ModifierSpeciesReference void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddModifierobjectreactionInaddModifiermsrmodifierSpeciesRefreactionaddModifierobjectWorkflow9compartments11modelIn00modelOutaddCompobject0c0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Adds a copy of the given Compartment object to this Model. org.sbml.libsbml.Model addCompartment c 0 org.sbml.libsbml.Compartment void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeaddCompobjectmodelInaddCompccompartmentsmodelOutaddCompobjectWorkflow10compSboTerm00outsideCompId00compMetaId00compId00compName00compGoId00compartmentcreateCompartmentname0id0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libsbml-3.1.0-hacked No description Creates a new Compartment, optionally with the given <code>id</code> and <code>name</code> attribute values. org.sbml.libsbml.Compartment Compartment id name 0 0 java.lang.String java.lang.String org.sbml.libsbml.Compartment 0 false true system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetCompMetaIdobject0metaid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'metaid' attribute of this object. org.sbml.libsbml.SBase setMetaId metaid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetOutsideCompobject0sid0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the 'outside' attribute of this Compartment. org.sbml.libsbml.Compartment setOutside sid 0 java.lang.String void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetCompSboTermobject0value0object00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity libSBML 3.1.0 API for taverna This is API description for libSBML 3.1.0 for use in taverna workflows Sets the value of the 'sboTerm' attribute. org.sbml.libsbml.SBase setSBOTerm value 0 int void 0 false false system libsbmlj.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetCompGOIdc0goId0result00net.sf.taverna.t2.activitiesapiconsumer-activity1.0net.sf.taverna.t2.activities.apiconsumer.ApiConsumerActivity No name No description Annotates an SBML Compartment with a given Gene Ontology identifer uk.ac.mcisb.libsbml.helpers.MIRIAMAnnotationHelper setCompartmentGOId c goId 0 0 org.sbml.libsbml.Compartment java.lang.String org.sbml.libsbml.Compartment 0 true false system libsbml_helpers.jar net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokecreateCompartmentnamecompNamecreateCompartmentidcompIdsetCompMetaIdobjectcreateCompartmentobjectsetCompMetaIdmetaidcompMetaIdsetOutsideCompobjectsetCompMetaIdobjectsetOutsideCompsidoutsideCompIdsetCompSboTermobjectsetOutsideCompobjectsetCompSboTermvaluecompSboTermsetCompGOIdcsetCompSboTermobjectsetCompGOIdgoIdcompGoIdcompartmentsetCompGOIdresult