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view test-data/scored_pathway.xml @ 2:caf2b5731a5e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 2333b7b56422febf439cd9f4cd3e6eda858b2690
author tduigou
date Tue, 28 Mar 2023 12:11:14 +0000
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children d9287c69a7f4
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<?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="df484cacc87fa9b4c456e5cff8b987518115bb998c2f7ce8d76e46ebc4ce7a50" id="rp_001_0001" name="rp_001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">
    <listOfCompartments>
      <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">
        <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="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
      </compartment>
    </listOfCompartments>
    <listOfSpecies>
      <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
                <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
                <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="_7d22781170c09f66099e3d92f82fe456ce2c3f02d9162656e7ca49a0cc9c7b16" id="CMPD_0000000002" name="CMPD_0000000002" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <annotation>
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              <bqbiol:is>
                <rdf:Bag/>
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              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
                <brsynth:inchi value="InChI=1S/C9H8O2/c10-9(11)7-6-8-4-2-1-3-5-8/h1-7H,(H,10,11)"/>
                <brsynth:inchikey value="WBYWAXJHAXSJNI-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="O=C=O"/>
                <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
                <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25" id="MNXM1" name="MNXM1" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <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="#ada4d198af79d26a0eb691008fc79b883e3ee4d3ef8ce39c18214444cc981f25">
              <bqbiol:is>
                <rdf:Bag/>
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            </rdf:Description>
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              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H+]"/>
                <brsynth:inchi value="InChI=1S/p+1"/>
                <brsynth:inchikey value="GPRLSGONYQIRFK-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <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="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
                <brsynth:inchi value="InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"/>
                <brsynth:inchikey value="PPBRXRYQALVLMV-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
      <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
        <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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
              <bqbiol:is>
                <rdf:Bag/>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="N"/>
                <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
                <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </species>
    </listOfSpecies>
    <listOfParameters>
      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0_0" value="0" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
        <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="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
            <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]&gt;&gt;[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].N"/>
                <brsynth:rp2_transfo_id value="TRS_0_1_1"/>
                <brsynth:rule_ids/>
                <brsynth:tmpl_rxn_ids>
                  <brsynth:MNXR106649/>
                  <brsynth:MNXR131345/>
                </brsynth:tmpl_rxn_ids>
                <brsynth:rule_score value="0.5869134225065102"/>
                <brsynth:idx_in_path value="1"/>
                <brsynth:fba_biomass>
                  <brsynth:value value="0.0"/>
                  <brsynth:units value="gDW / gDW / hour"/>
                </brsynth:fba_biomass>
                <brsynth:fba_fraction>
                  <brsynth:value value="1.3666677776240859"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-3.619165315209898"/>
                  <brsynth:error value="0.5540714922475698"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-20.73400284993093"/>
                  <brsynth:error value="0.5540714922475698"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-3.619165315209898"/>
                  <brsynth:error value="0.5540714922475698"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-2.0435274124526472"/>
                  <brsynth:error value="0.5540714922475698"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="MNXM97" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM15" stoichiometry="1" constant="true"/>
        </listOfProducts>
      </reaction>
      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0_0" fbc:upperFluxBound="BRS_FBC_10000_0">
        <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="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/>
                </rdf:Bag>
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                <brsynth:smiles value="[H]OC(=O)C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H].[H+]&gt;&gt;O=C=O.[H]C([H])=C([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
                <brsynth:rp2_transfo_id value="TRS_0_0_0"/>
                <brsynth:rule_ids/>
                <brsynth:tmpl_rxn_ids>
                  <brsynth:MNXR114372/>
                </brsynth:tmpl_rxn_ids>
                <brsynth:rule_score value="1.0"/>
                <brsynth:idx_in_path value="2"/>
                <brsynth:fba_biomass>
                  <brsynth:value value="0.0"/>
                  <brsynth:units value="gDW / gDW / hour"/>
                </brsynth:fba_biomass>
                <brsynth:fba_fraction>
                  <brsynth:value value="1.3666677776240859"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-5.570411694686811"/>
                  <brsynth:error value="5.365139708628456"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG0_prime>
                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-22.685249229407844"/>
                  <brsynth:error value="5.365139708628456"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dGm_prime>
                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-5.570411694686811"/>
                  <brsynth:error value="5.365139708628456"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG_prime>
                <brsynth:thermo_dG>
                  <brsynth:value value="-49.87811933289868"/>
                  <brsynth:error value="5.365139708628456"/>
                  <brsynth:units value="kilojoule / mole"/>
                </brsynth:thermo_dG>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="CMPD_0000000002" stoichiometry="1" constant="true"/>
          <speciesReference species="MNXM1" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="MNXM13" stoichiometry="1" constant="true"/>
          <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
        </listOfProducts>
      </reaction>
    </listOfReactions>
    <groups:listOfGroups>
      <groups:group metaid="_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299" groups:id="rp_pathway" groups:kind="collection">
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          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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                <brsynth:fba_biomass>
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                <brsynth:fba_fraction>
                  <brsynth:value value="1.3666677776240859"/>
                  <brsynth:units value="milimole / gDW / hour"/>
                </brsynth:fba_fraction>
                <brsynth:thermo_dG0_prime>
                  <brsynth:value value="-9.189577009896766"/>
                  <brsynth:error value="5.336452836371218"/>
                  <brsynth:units value="kilojoule / mole"/>
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                <brsynth:thermo_dGm_prime>
                  <brsynth:value value="-43.41925207933883"/>
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                  <brsynth:units value="kilojoule / mole"/>
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                <brsynth:thermo_dG_prime>
                  <brsynth:value value="-9.189577009896766"/>
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                  <brsynth:units value="kilojoule / mole"/>
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                <brsynth:thermo_dG>
                  <brsynth:value value="-51.92164674535138"/>
                  <brsynth:error value="5.336452836371218"/>
                  <brsynth:units value="kilojoule / mole"/>
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                <brsynth:global_score value="0.9923127055168152"/>
              </brsynth:brsynth>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="rxn_1"/>
          <groups:member groups:idRef="rxn_2"/>
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        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="CMPD_0000000002"/>
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        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="TARGET_0000000001"/>
          <groups:member groups:idRef="MNXM97"/>
          <groups:member groups:idRef="CMPD_0000000002"/>
        </groups:listOfMembers>
      </groups:group>
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          <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="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM13"/>
          <groups:member groups:idRef="MNXM1"/>
          <groups:member groups:idRef="MNXM15"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" 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="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
        <groups:listOfMembers>
          <groups:member groups:idRef="MNXM13"/>
          <groups:member groups:idRef="MNXM1"/>
          <groups:member groups:idRef="MNXM15"/>
          <groups:member groups:idRef="MNXM97"/>
        </groups:listOfMembers>
      </groups:group>
      <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" 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="#a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </groups:group>
      <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" 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="#fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8">
              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>
            </rdf:BRSynth>
          </rdf:RDF>
        </annotation>
      </groups:group>
    </groups:listOfGroups>
  </model>
</sbml>