Mercurial > repos > metexplore > met4j
diff tools/attributes/SbmlSetChargesFromFile/test-data/toy_model.xml @ 0:dcd16521b969 draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 5dab0a2d83a1fdd7a1878a50ba0f24e752505393
| author | metexplore |
|---|---|
| date | Fri, 10 Jun 2022 10:31:34 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/attributes/SbmlSetChargesFromFile/test-data/toy_model.xml Fri Jun 10 10:31:34 2022 +0000 @@ -0,0 +1,119 @@ +<?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> \ No newline at end of file