Mercurial > repos > tduigou > straindesign_analyzing_model
diff test-data/butanol.xml @ 0:b86c4ac05aab draft
planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
| author | tduigou |
|---|---|
| date | Mon, 15 May 2023 14:05:41 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/butanol.xml Mon May 15 14:05:41 2023 +0000 @@ -0,0 +1,496 @@ +<?xml version="1.0" encoding="UTF-8"?> +<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false"> + <model metaid="meta_butanol" id="butanol" fbc:strict="true"> + <listOfUnitDefinitions> + <unitDefinition id="mmol_per_gDW_per_hr"> + <listOfUnits> + <unit kind="mole" exponent="1" scale="-3" multiplier="1"/> + <unit kind="gram" exponent="-1" scale="0" multiplier="1"/> + <unit kind="second" exponent="-1" scale="0" multiplier="3600"/> + </listOfUnits> + </unitDefinition> + </listOfUnitDefinitions> + <fbc:listOfObjectives fbc:activeObjective="obj"> + <fbc:objective fbc:id="obj" fbc:type="maximize"> + <fbc:listOfFluxObjectives> + <fbc:fluxObjective fbc:reaction="R_EX_1btol_e" fbc:coefficient="0.5"/> + </fbc:listOfFluxObjectives> + </fbc:objective> + </fbc:listOfObjectives> + <listOfCompartments> + <compartment id="c" name="cytosol" constant="true"/> + <compartment id="p" name="periplasm" constant="true"/> + <compartment id="e" name="extracellular space" constant="true"/> + </listOfCompartments> + <listOfSpecies> + <species metaid="meta_M_co2_e" sboTerm="SBO:0000247" id="M_co2_e" name="CO2 CO2" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="CO2"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_co2_e"> + <bqbiol:is> + <rdf:Bag> + 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xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_h_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/h"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:PROTON"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:5584"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13357"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15378"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10744"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59597"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00080"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2000349"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425978"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/74722"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428040"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/427899"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428548"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/156540"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/70106"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425969"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132304"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668577"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1470067"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/163953"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/193465"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113529"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/351626"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425999"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194688"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/374900"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2872447"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/372511"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/39"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00067"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_h_p" sboTerm="SBO:0000247" id="M_h_p" name="H+" compartment="p" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="H"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_h_p"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/bigg.metabolite/h"/> + <rdf:li rdf:resource="https://identifiers.org/biocyc/META:PROTON"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:5584"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:13357"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:15378"/> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:10744"/> + <rdf:li rdf:resource="https://identifiers.org/hmdb/HMDB59597"/> + <rdf:li rdf:resource="https://identifiers.org/inchi_key/GPRLSGONYQIRFK-UHFFFAOYSA-N"/> + <rdf:li rdf:resource="https://identifiers.org/kegg.compound/C00080"/> + <rdf:li rdf:resource="https://identifiers.org/metanetx.chemical/MNXM1"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2000349"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425978"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/74722"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428040"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/427899"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/428548"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/156540"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/70106"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425969"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1132304"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/5668577"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/1470067"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/163953"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/193465"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/113529"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/351626"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/425999"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/194688"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/374900"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/2872447"/> + <rdf:li rdf:resource="https://identifiers.org/reactome.compound/372511"/> + <rdf:li rdf:resource="https://identifiers.org/sabiork/39"/> + <rdf:li rdf:resource="https://identifiers.org/seed.compound/cpd00067"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_c" id="M_1btol_c" name="butan1ol" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_c"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_p" id="M_1btol_p" name="butan1ol" compartment="p" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_p"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + <species metaid="meta_M_1btol_e" id="M_1btol_e" name="butan1ol" compartment="e" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:chemicalFormula="C4H10O"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> + <rdf:Description rdf:about="#meta_M_1btol_e"> + <bqbiol:is> + <rdf:Bag> + <rdf:li rdf:resource="https://identifiers.org/chebi/CHEBI:22936"/> + </rdf:Bag> + </bqbiol:is> + </rdf:Description> + </rdf:RDF> + </annotation> + </species> + </listOfSpecies> + <listOfParameters> + <parameter constant="true" id="cobra_default_lb" name="cobra default - lb" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="-1000"/> + <parameter constant="true" id="cobra_default_ub" name="cobra default - ub" sboTerm="SBO:0000626" units="mmol_per_gDW_per_hr" value="1000"/> + <parameter constant="true" id="cobra_0_bound" name="cobra 0 - bound" sboTerm="SBO:0000625" units="mmol_per_gDW_per_hr" value="0"/> + </listOfParameters> + <listOfReactions> + <reaction metaid="meta_R_EX_1btol_e" sboTerm="SBO:0000627" id="R_EX_1btol_e" name="butan1ol exchange" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/> + </listOfReactants> + </reaction> + <reaction id="R_ButCoaDeh" name="Butyryl-CoA dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_b2coa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButanalDeh" name="Butanal dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btcoa_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButanolDeh" name="Butanol dehydrogenase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_btal_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrP" name="1-Butanol transporter (periplasm)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_c" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_c" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + <speciesReference species="M_h_p" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + <reaction id="R_ButOlTrE" name="1-Butanol transporter (extracellular)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub"> + <listOfReactants> + <speciesReference species="M_1btol_p" stoichiometry="1" constant="true"/> + </listOfReactants> + <listOfProducts> + <speciesReference species="M_1btol_e" stoichiometry="1" constant="true"/> + </listOfProducts> + </reaction> + </listOfReactions> + <groups:listOfGroups> + <groups:group metaid="meta_rp_pathway" groups:id="rp_pathway" groups:kind="collection"> + <annotation> + <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"> + <rdf:BRSynth rdf:about="meta_rp_pathway"> + <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/> + </rdf:BRSynth> + </rdf:RDF> + </annotation> + <groups:listOfMembers> + <groups:member groups:idRef="R_ButCoaDeh"/> + <groups:member groups:idRef="R_ButanalDeh"/> + <groups:member groups:idRef="R_ButanolDeh"/> + <groups:member groups:idRef="R_ButOlTrP"/> + <groups:member groups:idRef="R_ButOlTrE"/> + <groups:member groups:idRef="R_EX_1btol_e"/> + </groups:listOfMembers> + </groups:group> + </groups:listOfGroups> + </model> +</sbml>