ProbabilisticModelCheckingPMCcomputeresultsresultsXmltext/xml2011-07-19 13:50:32.113 CESTconstantNameListtext/plain2011-07-19 13:50:32.113 CESTpropertiesUrlvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityhttp://bioputer.mimuw.edu.pl/tav4sb/models/enzyme.cslnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokevarNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeinitValuesvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity12;1:3:19net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemodelUrlvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityhttp://bioputer.mimuw.edu.pl/tav4sb/models/enzyme_stoch.xmlnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeconstNamevalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityp_MAXnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeinitValuesSepvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivity;net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerewardsUrlvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityhttp://bioputer.mimuw.edu.pl/tav4sb/models/enzyme.rewnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametrizePrismModelconstList1initList1inModel0outModel00paramList11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivityinModel0'text/plain'java.lang.StringtrueconstList1l('text/plain')java.lang.StringtrueinitList1l('text/plain')java.lang.StringtrueinitSufix0'text/plain'java.lang.StringtrueoutModel0'text/plain'0paramList1l('text/plain')1workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetConstantsStrvalueList1nameList1constantsStr00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivitynameList1l('text/plain')java.lang.StringtruevalueList1l('text/plain')java.lang.StringtrueconstantsStr0'text/plain'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeinitvalues2Liststring0regex0split11net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivitystring0'text/plain'java.lang.Stringtrueregex0'text/plain'java.lang.Stringtruesplit1l('text/plain')1workfloworg.embl.ebi.escience.scuflworkers.java.SplitByRegexnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeappendRewardsstring10string20output00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivitystring10'text/plain'java.lang.Stringtruestring20'text/plain'java.lang.Stringtrueoutput0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringConcatnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePrismconstants0model0properties0resultsXml00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeSbml2PrismmaxAmount0sbmlModel0warnings11error00prismModel00net.sf.taverna.t2.activitiesdataflow-activity1.3net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokemaxAmountvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetModelfileurl0encoding0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivityfileurl0'text/plain'java.lang.Stringtrueencoding0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0workflownet.sourceforge.taverna.scuflworkers.io.TextFileReadernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefileEncodingvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.3net.sf.taverna.t2.activities.stringconstant.StringConstantActivityUTF-8net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetRewardsfileurl0encoding0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivityfileurl0'text/plain'java.lang.Stringtrueencoding0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0workflownet.sourceforge.taverna.scuflworkers.io.TextFileReadernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokegetPropertiesfileurl0encoding0filecontents00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivityfileurl0'text/plain'java.lang.Stringtrueencoding0'text/plain'java.lang.Stringtruefilecontents0'text/plain'0workflownet.sourceforge.taverna.scuflworkers.io.TextFileReadernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeparametrizePrismModelconstListparametrizePrismModelinitListparametrizePrismModelinModelsetConstantsStrvalueListsetConstantsStrnameListinitvalues2Liststringinitvalues2ListregexappendRewardsstring1appendRewardsstring2PrismconstantsPrismmodelPrismpropertiesSbml2PrismmaxAmountSbml2PrismsbmlModelgetModelfileurlgetModelencodinggetRewardsfileurlgetRewardsencodinggetPropertiesfileurlgetPropertiesencodingresultsXmlconstantNameList2011-07-19 13:50:32.613 CESTProbabilistic Model Checking (PMC): compute results2011-07-19 13:50:32.613 CEST6cffab9c-ee3f-4ff1-b9a9-0f90007ae2782011-07-19 13:57:09.628 CESTbc2a51de-7592-4f86-b003-f373e443b0f62011-07-19 13:56:09.305 CEST2011-07-19 13:50:32.613 CESTsbml2PrismWebservicesbmlModel00String with the SBML model compatible with Level 2 Version 1 of the SBML specification. Attention: it has to be a 'stochastic' version of the model, i.e. with initial amounts not initial concentrations.2011-07-19 13:50:32.600 CESTtext/plain2011-07-19 13:50:32.600 CESTmaxAmount00text/plain2011-07-19 13:50:32.600 CESTOptional upper bound for amount of each species (to ensure a finite state space). By default translator uses an upper bound of 100. ATTENTION: for that case you should provide input value with empty string.2011-07-19 13:50:32.600 CESTprismModeltext/plain2011-07-19 13:50:32.600 CESTwarningstext/plain2011-07-19 13:50:32.600 CESTerrortext/plain2011-07-19 13:50:32.600 CESTsbml2Prismsbml2PrismParams0attachmentList11sbml2PrismResult00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://bioputer.mimuw.edu.pl/tav4sb/services/wsdlsbml2Prismnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesbml2PrismParamsXMLmaxAmount0sbmlModel0output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitysbmlModel0'text/plain'java.lang.StringtruemaxAmount0'text/plain'java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="sbml2PrismParams" name="sbml2PrismParams" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}sbml2PrismParams"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="sbmlModel" qname=">sbml2PrismParams>sbmlModel" /><s:basetype optional="true" unbounded="false" typename="integer" name="maxAmount" qname=">sbml2PrismParams>maxAmount" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesbml2PrismResultXMLinput0error00prismModel00warnings11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.StringtrueprismModel0'text/plain'0warnings1l('text/plain')1error0'text/plain'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="sbml2PrismResult" name="sbml2PrismResult" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}sbml2PrismResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="prismModel" qname=">sbml2PrismResult>prismModel" /><s:arraytype optional="true" unbounded="true" wrapped="true" typename="string" name="warnings" qname=">sbml2PrismResult>warnings"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="" qname="{http://www.w3.org/2001/XMLSchema}string" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="error" qname=">sbml2PrismResult>error" /></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesbml2Prismsbml2PrismParamssbml2PrismParamsXMLmaxAmountsbml2PrismParamsXMLsbmlModelsbml2PrismResultXMLinputprismModelwarningserrorsbml2Prism Web service2011-07-19 13:50:32.611 CESTMikołaj Rybiński2011-07-19 13:50:32.611 CESTFor example of the SBML to PRISM translation and the description of its details see http://www.prismmodelchecker.org/manual/RunningPRISM/SupportForSBML .2011-07-19 13:50:32.611 CEST13546ace-ae6a-4a5f-827e-1a32cf6851f12011-07-19 13:56:09.607 CESTprismWebservicemodel00PRISM model file content.
Reference: http://www.prismmodelchecker.org/manual/ThePRISMLanguage/PRISMLanguageFiles
Example value:
// Enzymatic reaction model
ctmc
// Reaction rates constants
const double k1 = 0.184;
const double k2 = 0.016;
const double k3 = 0.211;
// Species s (Substrate)
const int s_MAX;
module s
s : [0..s_MAX] init s_MAX;
// r1 (ES-complex association)
[r1] s > 0 -> (s'=s-1);
// r2 (ES-complex dissociation)
[r2] s <= s_MAX-1 -> (s'=s+1);
endmodule
// Species e (Enzyme)
const int e_MAX;
module e
e : [0..e_MAX] init e_MAX;
// r1 (ES-complex association)
[r1] e > 0 -> (e'=e-1);
// r2 (ES-complex dissociation)
[r2] e <= e_MAX-1 -> (e'=e+1);
// r3 (Product creation)
[r3] e <= e_MAX-1 -> (e'=e+1);
endmodule
// Species es (ES-complex)
const int es_MAX = min(s_MAX, e_MAX);
module es
es : [0..es_MAX] init 0;
// r1 (ES-complex association)
[r1] es <= es_MAX-1 -> (es'=es+1);
// r2 (ES-complex dissociation)
[r2] es > 0 -> (es'=es-1);
// r3 (Product creation)
[r3] es > 0 -> (es'=es-1);
endmodule
// Species p (Product)
const int p_MAX = s_MAX;
module p
p : [0..p_MAX] init 0;
// r3 (Product creation)
[r3] p <= p_MAX-1 -> (p'=p+1);
endmodule
// Reaction rates
module reaction_rates
// r1 (ES-complex association)
[r1] (k1*s*e) > 0 -> (k1*s*e) : true;
// r2 (ES-complex dissociation)
[r2] (k2*es) > 0 -> (k2*es) : true;
// r3 (Product creation)
[r3] (k3*es) > 0 -> (k3*es) : true;
endmodule
// A expected number of enzyme-substrate complex association reactions.
rewards "r1"
[r1] true : 1;
endrewards2011-07-19 13:50:32.529 CESTtext/plain2011-07-19 13:50:32.528 CESTtext/x-taverna-web-url2011-07-19 13:50:32.528 CESTproperties00text/plain2011-07-19 13:50:32.529 CESTtext/x-taverna-web-url2011-07-19 13:50:32.529 CESTPRISM properties file content.
Reference:
http://www.prismmodelchecker.org/manual/PropertySpecification/PropertiesFiles
Example value:
// How many times on average a enzyme-substrate complex association reaction have to occure before the amount of product reaches 50% of it's maximum? Corresponds to EC50 coefficient.
// Attention: for this formula to make sense, the maximum amount of product must be known and set to the appropriate value; in this particular case it means that p_MAX must be equal to sum of initial amounts of all species, except of enzyme e.
R{"r1"}=? [ F (p >= 0.5 * p_MAX) ]2011-07-19 13:50:32.529 CESTconstants00text/plain2011-07-19 13:50:32.529 CESTOptional constants and their values in the format of PRISM '-const' switch, i.e. comma separated definitons of constants: name=start:[step:]stop, where step is optional and by default equal to 1.
Reference:
http://www.prismmodelchecker.org/manual/RunningPRISM/Experiments
Example value:
e_MAX=1:2:15,s_MAX=1:102011-07-19 13:50:32.529 CESTresultsXmltext/xml2011-07-19 13:50:32.529 CESTsetConstantCompactXmlListinput0output11net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivityinput0'text/plain'java.lang.Stringtrueoutput1l('text/xml')1workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokewrapWithResultsTagstr0wrapped00net.sf.taverna.t2.activitiesbeanshell-activity1.3net.sf.taverna.t2.activities.beanshell.BeanshellActivitystr0'text/plain'java.lang.Stringtruename0'text/plain'java.lang.Stringtruewrapped0'text/xml'0workflownet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprismprismParamsCompact0attachmentList11prismResult00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.WSDLActivityhttp://bioputer.mimuw.edu.pl/tav4sb/services/wsdlprismnet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeMerge_string_list_to_stringstringlist1concatenated00net.sf.taverna.t2.activitieslocalworker-activity1.3net.sf.taverna.t2.activities.localworker.LocalworkerActivitystringlist1l('text/plain')java.lang.Stringtrueseperator0'text/plain'java.lang.Stringtrueconcatenated0'text/plain'0workfloworg.embl.ebi.escience.scuflworkers.java.StringListMergenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprismParamsCompactXMLproperties0model0constantCompact1output00net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivitymodel0'text/plain'java.lang.Stringtrueproperties0'text/plain'java.lang.StringtrueconstantCompact1l('text/xml')java.lang.Stringtrueoutput0'text/xml'0<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="prismParamsCompact" name="prismParamsCompact" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/wsdl}prismParamsCompact"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="model" qname=">prismParamsCompact>model" /><s:basetype optional="false" unbounded="false" typename="string" name="properties" qname=">prismParamsCompact>properties" /><s:arraytype optional="true" unbounded="true" wrapped="false" typename="FiniteValues" name="constantCompact" qname=">prismParamsCompact>constantCompact"><s:elementtype><s:complextype optional="false" unbounded="false" typename="FiniteValues" name="" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/wsdl}FiniteValues"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="name" qname="FiniteValues>name" /><s:arraytype optional="false" unbounded="true" wrapped="false" typename="decimal" name="value" qname="FiniteValues>value"><s:elementtype><s:basetype optional="false" unbounded="false" typename="decimal" name="" qname="{http://www.w3.org/2001/XMLSchema}decimal" /></s:elementtype></s:arraytype></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeprismResultXMLinput0result11net.sf.taverna.t2.activitieswsdl-activity1.3net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivityinput0'text/xml'java.lang.Stringtrueresult1l('text/xml')1<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="prismResult" name="prismResult" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}prismResult"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="ResultValue" name="result" qname=">prismResult>result"><s:elementtype><s:complextype optional="false" unbounded="false" typename="ResultValue" name="" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}ResultValue"><s:elements><s:arraytype optional="true" unbounded="true" wrapped="false" typename="FiniteValue" name="constant" qname="ResultValue>constant"><s:elementtype><s:basetype optional="false" unbounded="false" typename="string" name="FiniteValue" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}FiniteValue" /></s:elementtype></s:arraytype><s:arraytype optional="true" unbounded="true" wrapped="false" typename="Value" name="property" qname="ResultValue>property"><s:elementtype><s:basetype optional="false" unbounded="false" typename="double" name="Value" qname="{http://bioputer.mimuw.edu.pl/tav4sb/services/xsd/prism}Value" /></s:elementtype></s:arraytype><s:basetype optional="true" unbounded="false" typename="string" name="error" qname="ResultValue>error" /></s:elements></s:complextype></s:elementtype></s:arraytype></s:elements></s:complextype></s:extensions>net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0000net.sf.taverna.t2.coreworkflowmodel-impl1.3net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesetConstantCompactXmlListinputwrapWithResultsTagstrprismprismParamsCompactMerge_string_list_to_stringstringlistprismParamsCompactXMLpropertiesprismParamsCompactXMLmodelprismParamsCompactXMLconstantCompactprismResultXMLinputresultsXmlprism Web service2011-07-19 13:50:32.597 CESTPRISM model checking (http://www.prismmodelchecker.org/manual/RunningPRISM/ModelChecking). The '-fixdl' switch is used, which means that all deadlock states in model are fixed by addition of self-loops.2011-07-19 13:50:32.597 CESTMikołaj Rybiński2011-07-19 13:50:32.597 CEST04a7e63c-9a6b-4bd4-afb0-0e1d905e7b0b2011-07-19 13:56:09.689 CEST