diff test-data/butanol.xml @ 0:14747c55330c draft

planemo upload for repository https://github.com/brsynth/straindesign commit 38e681e9ebc7bb75ea44f314b48761bf25403420
author tduigou
date Mon, 15 May 2023 14:05:52 +0000
parents
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/butanol.xml	Mon May 15 14:05:52 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>
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+      <species metaid="meta_M_btcoa_c" sboTerm="SBO:0000247" id="M_btcoa_c" name="Gamma-butyrobetainyl-CoA" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="-3" fbc:chemicalFormula="C28H46N8O17P3S">
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+      </species>
+      <species metaid="meta_M_btal_c" sboTerm="SBO:0000247" id="M_btal_c" name="Butanal C4H8O" compartment="c" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="0" fbc:chemicalFormula="C4H8O">
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+                  <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_e" sboTerm="SBO:0000247" id="M_h_e" name="H+" compartment="e" 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_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>