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view build/tools/SbmlSetPathwaysFromFile/test-data/toy_model.xml @ 6:7a6f2380fc1d draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
author metexplore
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>