Benchmark-Models-PEtab/Benchmark-Models/Bertozzi_PNAS2020/model.xml at master · Benchmarking-Initiative/Benchmark-Models-PEtab · GitHub

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<?xml version='1.0' encoding='UTF-8'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
  <model id="Bertozzi_PNAS2020" name="Bertozzi_PNAS2020">
    <annotation>
      <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
        <rdf:Description rdf:about="#benchmark_models_petab">
          <bqbiol:isDescribedBy>
            <rdf:Bag>
              <rdf:li rdf:resource="http://identifiers.org/doi/10.1073/pnas.2006520117"/>
            </rdf:Bag>
          </bqbiol:isDescribedBy>
        </rdf:Description>
      </rdf:RDF>
    </annotation>
    <listOfCompartments>
	<compartment id="compartment" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="I_" compartment="compartment" initialConcentration="0.1" boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
      <species id="R_" compartment="compartment" initialConcentration="0"   boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
      <species id="S_" compartment="compartment" initialConcentration="0.9" boundaryCondition="false" constant="false" hasOnlySubstanceUnits="true"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="N_"     value="1"   constant="true"/>
      <parameter id="beta_N" value="0"   constant="true"/>
      <parameter id="gamma_" value="0.1" constant="true"/>
      <parameter id="I0_"    value="0.1" constant="true"/>
      <parameter id="R0_"    value="0.1" constant="true"/>
    </listOfParameters>
    <listOfInitialAssignments>
      <initialAssignment symbol="I_">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
	  <apply>
            <times/>
            <ci> I0_ </ci>
	  </apply>
        </math>
      </initialAssignment>
      <initialAssignment symbol="S_">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <minus/>
            <ci> N_ </ci>
            <ci> I0_ </ci>
          </apply>
        </math>
      </initialAssignment>
      <initialAssignment symbol="beta_N">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <divide/>
            <apply>
              <times/>
              <ci> R0_ </ci>
              <ci> gamma_ </ci>
            </apply>
            <ci> N_ </ci>
          </apply>
        </math>
      </initialAssignment>
    </listOfInitialAssignments>
    <listOfReactions>
      <reaction id="infection" reversible="false">
        <listOfReactants>
          <speciesReference species="S_" stoichiometry="1" constant="true"/>
          <speciesReference species="I_" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="I_" stoichiometry="2" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> beta_N </ci>
              <ci> I_ </ci>
              <ci> S_ </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="recovery" reversible="false">
        <listOfReactants>
          <speciesReference species="I_" stoichiometry="1" constant="true"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="R_" stoichiometry="1" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> gamma_ </ci>
              <ci> I_ </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>