Mercurial > repos > metexplore > met4j
view build/tools/ExtractSubBipNetwork/test-data/toy_model.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author | metexplore |
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date | Wed, 17 May 2023 13:26:37 +0000 |
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<?xml version="1.0" encoding='UTF-8' ?> <sbml fbc:required="false" groups:required="false" level="3" version="1" xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1"> <model fbc:strict="true" name="toy model"> <listOfUnitDefinitions> <unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr"> <listOfUnits> <unit exponent="-1" kind="gram" multiplier="1" scale="0"/> <unit exponent="1" kind="mole" multiplier="1" scale="-3"/> <unit exponent="-1" kind="second" multiplier="0.00027777" scale="0"/> </listOfUnits> </unitDefinition> </listOfUnitDefinitions> <listOfCompartments> <compartment constant="false" id="c" name="Cytosol"/> <compartment constant="false" id="e" name="Extracellular"/> </listOfCompartments> <listOfSpecies> <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A_ext" name="A_ext"> <notes> <body xmlns="http://www.w3.org/1999/xhtml"> <p>SMILES: C[C@@H](C(=O)O)NC</p> </body> </notes> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> <rdf:Description rdf:about="#A_ext"> <bqbiol:is> <in:inchi xmlns:in="https://biomodels.net/inchi">InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</in:inchi> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species> <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="A" name="A"/> <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="B" name="B"/> <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="C" name="C"/> <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D" name="D"/> <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="D_ext" name="D_ext"/> <species boundaryCondition="false" compartment="e" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E_ext" name="E_ext"/> <species boundaryCondition="false" compartment="c" constant="false" fbc:charge="0" hasOnlySubstanceUnits="false" id="E" name="E"/> </listOfSpecies> <listOfParameters> <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-100000.0"/> <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="100000.0"/> <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0.0"/> <parameter constant="true" id="reac1_upper_bound" name="reac1 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="10.0"/> <parameter constant="true" id="reac6_upper_bound" name="reac6 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="3.0"/> <parameter constant="true" id="reac2_upper_bound" name="reac2 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> <parameter constant="true" id="reac3_upper_bound" name="reac3 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> <parameter constant="true" id="reac4_upper_bound" name="reac4 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> <parameter constant="true" id="reac5_upper_bound" name="reac5 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> <parameter constant="true" id="reac7_upper_bound" name="reac7 upper bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="100000.0"/> </listOfParameters> <listOfReactions> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac1_upper_bound" id="reac1" name="reac1" reversible="false"> <listOfReactants> <speciesReference constant="true" species="A_ext" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="A" stoichiometry="1.0"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="reac2_upper_bound" id="reac2" name="reac2" reversible="true"> <listOfReactants> <speciesReference constant="true" species="A" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="B" stoichiometry="1.0"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac3_upper_bound" id="reac3" name="reac3" reversible="false"> <listOfReactants> <speciesReference constant="true" species="A" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="C" stoichiometry="1.0"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac4_upper_bound" id="reac4" name="reac4" reversible="false"> <listOfReactants> <speciesReference constant="true" species="B" stoichiometry="1.0"/> <speciesReference constant="true" species="C" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="D" stoichiometry="1.5"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac5_upper_bound" id="reac5" name="reac5" reversible="false"> <listOfReactants> <speciesReference constant="true" species="D" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="D_ext" stoichiometry="1.0"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac6_upper_bound" id="reac6" name="reac6" reversible="false"> <listOfReactants> <speciesReference constant="true" species="E_ext" stoichiometry="1.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="E" stoichiometry="1.0"/> </listOfProducts> </reaction> <reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="reac7_upper_bound" id="reac7" name="reac7" reversible="false"> <listOfReactants> <speciesReference constant="true" species="E" stoichiometry="2.0"/> </listOfReactants> <listOfProducts> <speciesReference constant="true" species="D" stoichiometry="1.0"/> </listOfProducts> </reaction> </listOfReactions> </model> </sbml>