Time_course_simulation_of_SBML_model_using_CopasiWSsbml00
A parameterised SBML model
2010-03-25 17:10:21.859 GMT
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">
<model metaid="COPASI1" id="Model_1" name="Test model">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml"/>
</notes>
<listOfFunctionDefinitions>
<functionDefinition id="function_1" name="function_4_fructose-bisphosphate aldolase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> Et </ci>
</bvar>
<bvar>
<ci> Ks </ci>
</bvar>
<bvar>
<ci> M_276 </ci>
</bvar>
<bvar>
<ci> kcat </ci>
</bvar>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> kcat </ci>
<ci> Et </ci>
<ci> M_276 </ci>
</apply>
<apply>
<plus/>
<ci> Ks </ci>
<ci> M_276 </ci>
</apply>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_4_phosphofructokinase" name="function_4_phosphofructokinase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_172 </ci>
</bvar>
<bvar>
<ci> M_273 </ci>
</bvar>
<bvar>
<ci> k0 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k0 </ci>
<ci> M_172 </ci>
<ci> M_273 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_2" name="function_4_glucose-6-phosphate isomerase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> I </ci>
</bvar>
<bvar>
<ci> Ki </ci>
</bvar>
<bvar>
<ci> Km </ci>
</bvar>
<bvar>
<ci> M_292 </ci>
</bvar>
<bvar>
<ci> Vmax </ci>
</bvar>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> Vmax </ci>
<ci> M_292 </ci>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> Km </ci>
<apply>
<plus/>
<cn> 1 </cn>
<apply>
<divide/>
<ci> I </ci>
<ci> Ki </ci>
</apply>
</apply>
</apply>
<ci> M_292 </ci>
</apply>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_3" name="function_4_phosphoglycerate kinase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> E_670 </ci>
</bvar>
<bvar>
<ci> Km </ci>
</bvar>
<bvar>
<ci> M_57 </ci>
</bvar>
<bvar>
<ci> kcat </ci>
</bvar>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> E_670 </ci>
<ci> kcat </ci>
<ci> M_57 </ci>
</apply>
<apply>
<plus/>
<ci> Km </ci>
<ci> M_57 </ci>
</apply>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_4_enolase" name="function_4_enolase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> Km </ci>
</bvar>
<bvar>
<ci> M_36 </ci>
</bvar>
<bvar>
<ci> Vmax </ci>
</bvar>
<apply>
<divide/>
<apply>
<divide/>
<apply>
<times/>
<ci> Vmax </ci>
<ci> M_36 </ci>
</apply>
<apply>
<plus/>
<ci> Km </ci>
<ci> M_36 </ci>
</apply>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_4" name="function_4_glyceraldehyde-3-phosphate dehydrogenase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_289 </ci>
</bvar>
<bvar>
<ci> M_411 </ci>
</bvar>
<bvar>
<ci> M_454 </ci>
</bvar>
<bvar>
<ci> k1 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k1 </ci>
<ci> M_289 </ci>
<ci> M_411 </ci>
<ci> M_454 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_5" name="function_4_hexokinase (D-glucose:ATP)">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_172 </ci>
</bvar>
<bvar>
<ci> M_304 </ci>
</bvar>
<bvar>
<ci> k2 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k2 </ci>
<ci> M_172 </ci>
<ci> M_304 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_6" name="function_4_phosphoglycerate mutase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_57 </ci>
</bvar>
<bvar>
<ci> k3 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k3 </ci>
<ci> M_57 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_7" name="function_4_pyruvate kinase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_135 </ci>
</bvar>
<bvar>
<ci> M_329 </ci>
</bvar>
<bvar>
<ci> M_446 </ci>
</bvar>
<bvar>
<ci> k4 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k4 </ci>
<ci> M_135 </ci>
<ci> M_329 </ci>
<ci> M_446 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="function_8" name="function_4_pyruvate decarboxylase">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> C_1 </ci>
</bvar>
<bvar>
<ci> M_329 </ci>
</bvar>
<bvar>
<ci> M_483 </ci>
</bvar>
<bvar>
<ci> k5 </ci>
</bvar>
<apply>
<divide/>
<apply>
<times/>
<ci> k5 </ci>
<ci> M_329 </ci>
<ci> M_483 </ci>
</apply>
<ci> C_1 </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
<compartment metaid="COPASI2" id="C_1" name="Cytoplasm" size="1">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI2">
<CopasiMT:is rdf:resource="urn:miriam:obo.go:GO:0005737"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI2">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="COPASI3" id="C_10" name="Plasma membrane" size="1">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI3">
<CopasiMT:is rdf:resource="urn:miriam:obo.go:GO:0005886"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI3">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
<compartment metaid="COPASI4" id="C_2" name="Extracellular" size="1">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI4">
<CopasiMT:is rdf:resource="urn:miriam:obo.go:GO:0005576"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI4">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="COPASI5" id="M_276" name="D-Fructose 1,6-bisphosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI5">
<bqbiol:is rdf:resource="#meta_M_276"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:16905"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI5">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI6" id="M_172" name="ATP" compartment="C_1" initialConcentration="3.5">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI6">
<bqbiol:is rdf:resource="#meta_M_172"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:15422"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI6">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI7" id="M_273" name="D-Fructose 6-phosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI7">
<bqbiol:is rdf:resource="#meta_M_273"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:15946"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI7">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI8" id="M_292" name="D-Glucose 6-phosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI8">
<bqbiol:is rdf:resource="#meta_M_292"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:15954"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI8">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI9" id="M_4" name="3-Phospho-D-glyceroyl phosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI9">
<bqbiol:is rdf:resource="#meta_M_4"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:16001"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI9">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI10" id="M_135" name="ADP" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI10">
<bqbiol:is rdf:resource="#meta_M_135"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:16761"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI10">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI11" id="M_36" name="D-Glycerate 2-phosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI11">
<bqbiol:is rdf:resource="#meta_M_36"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:17835"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI11">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI12" id="M_289" name="Glyceraldehyde 3-phosphate" compartment="C_1" initialConcentration="0">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI12">
<bqbiol:is rdf:resource="#meta_M_289"/>
<CopasiMT:is rdf:resource="urn:miriam:obo.chebi:CHEBI:29052"/>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI12">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="COPASI13" id="M_411" name="Nicotinamide adenine dinucleotide" compartment="C_1" initialConcentration="4">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI13">
<bqbiol:is rdf:resource="#meta_M_411"/>
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_172"/>
<speciesReference species="M_304"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_135"/>
<speciesReference species="M_292"/>
<speciesReference species="M_329"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="E_502"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> C_1 </ci>
<apply>
<ci> function_5 </ci>
<ci> C_1 </ci>
<ci> M_172 </ci>
<ci> M_304 </ci>
<ci> k2 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k2" name="k2" value="1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI42" id="R_1655" name="phosphoglycerate mutase">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI42">
<dcterms:bibliographicCitation>
<rdf:Bag>
<rdf:li>
<rdf:Description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:ec-code:5.4.2.1"/>
</rdf:Description>
</rdf:li>
<rdf:li>
<rdf:Description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:pubmed:3033435"/>
</rdf:Description>
</rdf:li>
</rdf:Bag>
</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI42">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_57"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_36"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="E_336"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> C_1 </ci>
<apply>
<ci> function_6 </ci>
<ci> C_1 </ci>
<ci> M_57 </ci>
<ci> k3 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k3" name="k3" value="1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI43" id="R_1680" name="pyruvate kinase">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI43">
<dcterms:bibliographicCitation>
<rdf:Bag>
<rdf:li>
<rdf:Description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:ec-code:2.7.1.40"/>
</rdf:Description>
</rdf:li>
<rdf:li>
<rdf:Description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:pubmed:6185493"/>
</rdf:Description>
</rdf:li>
</rdf:Bag>
</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI43">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_135"/>
<speciesReference species="M_329"/>
<speciesReference species="M_446"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_172"/>
<speciesReference species="M_483"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="E_726"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> C_1 </ci>
<apply>
<ci> function_7 </ci>
<ci> C_1 </ci>
<ci> M_135 </ci>
<ci> M_329 </ci>
<ci> M_446 </ci>
<ci> k4 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k4" name="k4" value="1"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="COPASI44" id="R_1681" name="pyruvate decarboxylase">
<annotation>
<COPASI xmlns="http://www.copasi.org/static/sbml">
<rdf:RDF xmlns:CopasiMT="http://www.copasi.org/RDF/MiriamTerms#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#COPASI44">
<dcterms:bibliographicCitation>
<rdf:Description>
<CopasiMT:isDescribedBy rdf:resource="urn:miriam:ec-code:4.1.1.1"/>
</rdf:Description>
</dcterms:bibliographicCitation>
</rdf:Description>
</rdf:RDF>
</COPASI>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#COPASI44">
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:unknown:"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="M_329"/>
<speciesReference species="M_483"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="M_121"/>
<speciesReference species="M_203"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="E_24"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> C_1 </ci>
<apply>
<ci> function_8 </ci>
<ci> C_1 </ci>
<ci> M_329 </ci>
<ci> M_483 </ci>
<ci> k5 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="k5" name="k5" value="1"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
2010-03-25 15:32:46.380 GMT
A parameteried SBML model
2010-03-25 15:33:01.946 GMT
sbrml
The results of the time course simulation in SBRML format
2010-02-26 16:15:08.243 GMT
plot
A png image of the plot of the time simulation results from Copasi
2010-02-26 16:14:44.612 GMT
stepnumbervalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
10
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.InvokeparseSbrmlsbrml0species0selectedSpeciesNames1output00net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
sbrml
0
text/plain
java.lang.String
true
species
0
text/plain
java.lang.String
true
selectedSpeciesNames
1
text/plain
0
output
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.InvokevisualiseResultscsv0graph_image00net.sf.taverna.t2.activitiesrshell-activity1.0net.sf.taverna.t2.activities.rshell.RshellActivity
false
localhost
6311
false
false
csv
TEXT_FILE
graph_image
PNG_FILE
false
csv
0
0
graph_image
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.Invokedurationvalue00net.sf.taverna.t2.activitiesstringconstant-activity1.0net.sf.taverna.t2.activities.stringconstant.StringConstantActivity
50
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.InvokerunTimeCourseSimduration0stepNumber0sbml0sbrml00net.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.InvokegetSpeciesNamessbml0species00names11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity
system
libsbmlj.jar
java.lang.String
true
sbml
0
text/plain
0
species
0
1
names
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.InvokeselectworkerinputList1outputList11net.sf.taverna.t2.activitiesbeanshell-activity1.0net.sf.taverna.t2.activities.beanshell.BeanshellActivity
workflow
java.lang.String
true
inputList
1
text/plain
1
outputList
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.InvokeparseSbrmlsbrmlrunTimeCourseSimsbrmlparseSbrmlspeciesgetSpeciesNamesspeciesparseSbrmlselectedSpeciesNamesselectworkeroutputListvisualiseResultscsvparseSbrmloutputrunTimeCourseSimdurationdurationvaluerunTimeCourseSimstepNumberstepnumbervaluerunTimeCourseSimsbmlsbmlgetSpeciesNamessbmlsbmlselectworkerinputListgetSpeciesNamesnamessbrmlrunTimeCourseSimsbrmlplotvisualiseResultsgraph_image
Copasi time simulation of SBML model
2010-02-26 16:13:21.34 GMT
Peter Li
2010-02-26 16:10:38.703 GMT
Time course simulation of SBML model using CopasiWS
2010-03-25 13:45:16.664 GMT
Perform time simulation of SBML model using Copasi web service
2010-02-26 16:11:06.656 GMT
Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.
2010-02-26 16:12:48.956 GMT
Copasi_time_simulation_of_SBML_modelduration00stepNumber00sbml00sbrml
The results of the time course simulation in SBRML format
2010-02-26 16:15:08.243 GMT
runCopasiTimeCourseSimRunDeterministicSimulatorRequest0RunDeterministicSimulatorResponse00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.WSDLActivity
http://www.comp-sys-bio.org/CopasiWS/services/TimeCourseService?wsdl
runDeterministicSimulator
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
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net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokerequestparameters0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="RunDeterministicSimulator" name="RunDeterministicSimulatorRequest" qname="{http://timecoursews.services.copasiws.copasi.org/types}RunDeterministicSimulator"><s:elements><s:complextype optional="false" unbounded="false" typename="DeterministicParameters" name="parameters" qname=">RunDeterministicSimulator>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="copasiml" qname="DeterministicParameters>copasiml" /><s:basetype optional="true" unbounded="false" typename="string" name="sbml" qname="DeterministicParameters>sbml" /><s:basetype optional="false" unbounded="false" typename="boolean" name="IntegrateReducedModel" qname="DeterministicParameters>IntegrateReducedModel" /><s:basetype optional="false" unbounded="false" typename="float" name="RelativeTolerance" qname="DeterministicParameters>RelativeTolerance" /><s:basetype optional="false" unbounded="false" typename="float" name="AbsoluteTolerance" qname="DeterministicParameters>AbsoluteTolerance" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="AdamsMaxOrder" qname="DeterministicParameters>AdamsMaxOrder" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="BDFMaxOrder" qname="DeterministicParameters>BDFMaxOrder" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="MaxInternalSteps" qname="DeterministicParameters>MaxInternalSteps" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="StepNumber" qname="DeterministicParameters>StepNumber" /><s:basetype optional="false" unbounded="false" typename="float" name="StepSize" qname="DeterministicParameters>StepSize" /><s:basetype optional="false" unbounded="false" typename="float" name="Duration" qname="DeterministicParameters>Duration" /><s:basetype optional="false" unbounded="false" typename="float" name="OutputStartTime" qname="DeterministicParameters>OutputStartTime" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
false
parameters
0
'text/xml'
0
output
0
'text/xml'
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
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeinputDuration0StepSize0sbml0output00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="DeterministicParameters" name="parameters" qname=">RunDeterministicSimulator>parameters"><s:elements><s:basetype optional="true" unbounded="false" typename="string" name="copasiml" qname="DeterministicParameters>copasiml" /><s:basetype optional="true" unbounded="false" typename="string" name="sbml" qname="DeterministicParameters>sbml" /><s:basetype optional="false" unbounded="false" typename="boolean" name="IntegrateReducedModel" qname="DeterministicParameters>IntegrateReducedModel" /><s:basetype optional="false" unbounded="false" typename="float" name="RelativeTolerance" qname="DeterministicParameters>RelativeTolerance" /><s:basetype optional="false" unbounded="false" typename="float" name="AbsoluteTolerance" qname="DeterministicParameters>AbsoluteTolerance" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="AdamsMaxOrder" qname="DeterministicParameters>AdamsMaxOrder" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="BDFMaxOrder" qname="DeterministicParameters>BDFMaxOrder" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="MaxInternalSteps" qname="DeterministicParameters>MaxInternalSteps" /><s:basetype optional="false" unbounded="false" typename="nonNegativeInteger" name="StepNumber" qname="DeterministicParameters>StepNumber" /><s:basetype optional="false" unbounded="false" typename="float" name="StepSize" qname="DeterministicParameters>StepSize" /><s:basetype optional="false" unbounded="false" typename="float" name="Duration" qname="DeterministicParameters>Duration" /><s:basetype optional="false" unbounded="false" typename="float" name="OutputStartTime" qname="DeterministicParameters>OutputStartTime" /></s:elements></s:complextype></s:extensions>
false
copasiml
0
'text/plain'
false
sbml
0
'text/plain'
false
IntegrateReducedModel
0
'text/plain'
false
RelativeTolerance
0
'text/plain'
false
AbsoluteTolerance
0
'text/plain'
false
AdamsMaxOrder
0
'text/plain'
false
BDFMaxOrder
0
'text/plain'
false
MaxInternalSteps
0
'text/plain'
false
StepNumber
0
'text/plain'
false
StepSize
0
'text/plain'
false
Duration
0
'text/plain'
false
OutputStartTime
0
'text/plain'
0
output
0
'text/xml'
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
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0
net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeresponseinput0outputResult00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="RunDeterministicSimulatorResponse" name="RunDeterministicSimulatorResponse" qname="{http://timecoursews.services.copasiws.copasi.org/types}RunDeterministicSimulatorResponse"><s:elements><s:complextype optional="false" unbounded="false" typename="OutputResult" name="outputResult" qname=">RunDeterministicSimulatorResponse>outputResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="result" qname="{http://copasi.org/copasiws/schemas}OutputResult>result" /></s:elements></s:complextype></s:elements></s:complextype></s:extensions>
java.lang.String
false
input
0
'text/xml'
0
outputResult
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net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeoutputResultinput0result00net.sf.taverna.t2.activitieswsdl-activity1.0.1net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity
<s:extensions xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha"><s:complextype optional="false" unbounded="false" typename="OutputResult" name="outputResult" qname=">RunDeterministicSimulatorResponse>outputResult"><s:elements><s:basetype optional="false" unbounded="false" typename="string" name="result" qname="{http://copasi.org/copasiws/schemas}OutputResult>result" /></s:elements></s:complextype></s:extensions>
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net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize
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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
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net.sf.taverna.t2.coreworkflowmodel-impl1.0net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokerunCopasiTimeCourseSimRunDeterministicSimulatorRequestrequestoutputrequestparametersinputoutputinputDurationdurationinputStepSizestepNumberinputsbmlsbmlresponseinputrunCopasiTimeCourseSimRunDeterministicSimulatorResponseoutputResultinputresponseoutputResultsbrmloutputResultresult
Uses the synchronous Copasi time simulation web service to predict the concentrations of species over a time period. The results from Copasi are provided in SBRML format which is visualised as a graph using an R script.
2010-02-26 16:12:48.956 GMT
Copasi time simulation of SBML model
2010-02-26 16:13:21.34 GMT
Perform time simulation of SBML model using Copasi web service
2010-02-26 16:11:06.656 GMT
Peter Li
2010-02-26 16:10:38.703 GMT