<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
  <model id="Elowitz_Nature2000" name="model_Elowitz_Nature2000">
    <notes>
      <body xmlns="http://www.w3.org/1999/xhtml">
        <pre>PEtab implementation of the model from Elowitz et al. (2000), Nature. 2000 Jan 20;403(6767):335-8</pre>
      </body>
    </notes>
    <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="#arFramework3">
          <dc:creator>
            <rdf:Bag>
              <rdf:li rdf:parseType="Resource">
                <vCard:N rdf:parseType="Resource">
                  <vCard:Family>Elowitz</vCard:Family>
                  <vCard:Given>Micheal</vCard:Given>
                </vCard:N>
              </rdf:li>
            </rdf:Bag>
          </dc:creator>
          <dcterms:created rdf:parseType="Resource">
            <dcterms:W3CDTF>2019-11-29T09:41:48Z</dcterms:W3CDTF>
          </dcterms:created>
          <dcterms:modified rdf:parseType="Resource">
            <dcterms:W3CDTF>2019-11-29T09:41:48Z</dcterms:W3CDTF>
          </dcterms:modified>
          <bqbiol:isDescribedBy>
            <rdf:Bag>
              <rdf:li rdf:resource="http://identifiers.org/doi/10.1038/35002125"/>
            </rdf:Bag>
          </bqbiol:isDescribedBy>
        </rdf:Description>
      </rdf:RDF>
    </annotation>
    <listOfUnitDefinitions>
      <unitDefinition id="time" name="time">
        <listOfUnits>
          <unit kind="second" exponent="1" scale="0" multiplier="60"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="cell" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="X_protein" name="LacI protein" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="Y_protein" name="TetR protein" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="Z_protein" name="cI protein" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="GFP" name="GFP" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="X_mRNA" name="LacI mRNA" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="Y_mRNA" name="TetR mRNA" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="Z_mRNA" name="cI mRNA" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
      <species id="GFP_mRNA" name="GFP mRNA" compartment="cell" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="KM" value="1.00013184764194e-05" constant="true"/>
      <parameter id="eff" value="0.0301592803622868" constant="true"/>
      <parameter id="eff_GFP" value="0.00195212197096568" constant="true"/>
      <parameter id="init_GFP" value="3.38716998236181e-05" constant="true"/>
      <parameter id="init_GFP_mRNA" value="131.435737789559" constant="true"/>
      <parameter id="init_X_mRNA" value="2.55665758135759" constant="true"/>
      <parameter id="init_X_protein" value="30.8087735629587" constant="true"/>
      <parameter id="init_Y_mRNA" value="999.999945990876" constant="true"/>
      <parameter id="init_Y_protein" value="0.000818268062900602" constant="true"/>
      <parameter id="init_Z_mRNA" value="19.3670294497271" constant="true"/>
      <parameter id="init_Z_protein" value="994.381959318238" constant="true"/>
      <parameter id="n_Hill" value="1.52254567553984" constant="true"/>
      <parameter id="tau_mRNA" value="12.624824570772" constant="true"/>
      <parameter id="tau_mRNA_GFP" value="0.000404064377463447" constant="true"/>
      <parameter id="tau_prot" value="5.35926527470063" constant="true"/>
      <parameter id="tau_prot_GFP" value="71.9312640934983" constant="true"/>
      <parameter id="tps_active" value="0.612278991244992" constant="true"/>
      <parameter id="tps_repr" value="1.00000000000883e-05" constant="true"/>
    </listOfParameters>
    <listOfInitialAssignments>
      <initialAssignment symbol="X_protein">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_X_protein </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="Y_protein">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_Y_protein </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="Z_protein">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_Z_protein </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="GFP">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_GFP </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="X_mRNA">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_X_mRNA </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="Y_mRNA">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_Y_mRNA </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="Z_mRNA">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_Z_mRNA </ci>
        </math>
      </initialAssignment>
      <initialAssignment symbol="GFP_mRNA">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <ci> init_GFP_mRNA </ci>
        </math>
      </initialAssignment>
    </listOfInitialAssignments>
    <listOfReactions>
      <reaction id="v1_v_0" name="v_0" reversible="false">
        <listOfReactants>
          <speciesReference species="X_mRNA" stoichiometry="1"/>
        </listOfReactants>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> X_mRNA </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_mRNA </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
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      <reaction id="v2_v_1" name="v_1" reversible="false">
        <listOfReactants>
          <speciesReference species="Y_mRNA" stoichiometry="1"/>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Y_mRNA </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_mRNA </ci>
              </apply>
            </apply>
          </math>
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      </reaction>
      <reaction id="v3_v_2" name="v_2" reversible="false">
        <listOfReactants>
          <speciesReference species="Z_mRNA" stoichiometry="1"/>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Z_mRNA </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
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                <ci> tau_mRNA </ci>
              </apply>
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      <reaction id="v4_v_3" name="v_3" reversible="false">
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          <speciesReference species="GFP_mRNA" stoichiometry="1"/>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> GFP_mRNA </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_mRNA_GFP </ci>
              </apply>
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          </math>
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      </reaction>
      <reaction id="v5_v_4" name="v_4" reversible="false">
        <listOfProducts>
          <speciesReference species="X_protein" stoichiometry="1"/>
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        </listOfModifiers>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> X_mRNA </ci>
                  <ci> eff </ci>
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                <ci> tau_mRNA </ci>
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      <reaction id="v6_v_5" name="v_5" reversible="false">
        <listOfProducts>
          <speciesReference species="Y_protein" stoichiometry="1"/>
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          <modifierSpeciesReference species="Y_mRNA"/>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Y_mRNA </ci>
                  <ci> eff </ci>
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                <ci> tau_mRNA </ci>
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      <reaction id="v7_v_6" name="v_6" reversible="false">
        <listOfProducts>
          <speciesReference species="Z_protein" stoichiometry="1"/>
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        <listOfModifiers>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Z_mRNA </ci>
                  <ci> eff </ci>
                </apply>
                <ci> tau_mRNA </ci>
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      </reaction>
      <reaction id="v8_v_7" name="v_7" reversible="false">
        <listOfProducts>
          <speciesReference species="GFP" stoichiometry="1"/>
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        <listOfModifiers>
          <modifierSpeciesReference species="GFP_mRNA"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> GFP_mRNA </ci>
                  <ci> eff_GFP </ci>
                </apply>
                <ci> tau_mRNA_GFP </ci>
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        <listOfReactants>
          <speciesReference species="X_protein" stoichiometry="1"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> X_protein </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_prot </ci>
              </apply>
            </apply>
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      <reaction id="v10_v_9" name="v_9" reversible="false">
        <listOfReactants>
          <speciesReference species="Y_protein" stoichiometry="1"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Y_protein </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_prot </ci>
              </apply>
            </apply>
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      <reaction id="v11_v_10" name="v_10" reversible="false">
        <listOfReactants>
          <speciesReference species="Z_protein" stoichiometry="1"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> Z_protein </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_prot </ci>
              </apply>
            </apply>
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      <reaction id="v12_v_11" name="v_11" reversible="false">
        <listOfReactants>
          <speciesReference species="GFP" stoichiometry="1"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <divide/>
                <apply>
                  <times/>
                  <ci> GFP </ci>
                  <apply>
                    <ln/>
                    <cn type="integer"> 2 </cn>
                  </apply>
                </apply>
                <ci> tau_prot_GFP </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="v13_v_12" name="v_12" reversible="false">
        <listOfProducts>
          <speciesReference species="X_mRNA" stoichiometry="1"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="Z_protein"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
              <apply>
                <minus/>
                <apply>
                  <times/>
                  <cn type="integer"> 60 </cn>
                  <ci> tps_repr </ci>
                </apply>
                <apply>
                  <divide/>
                  <apply>
                    <times/>
                    <apply>
                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                    <apply>
                      <minus/>
                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_repr </ci>
                      </apply>
                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_active </ci>
                      </apply>
                    </apply>
                  </apply>
                  <apply>
                    <plus/>
                    <apply>
                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                    <apply>
                      <power/>
                      <ci> Z_protein </ci>
                      <ci> n_Hill </ci>
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      <reaction id="v14_v_13" name="v_13" reversible="false">
        <listOfProducts>
          <speciesReference species="Y_mRNA" stoichiometry="1"/>
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          <modifierSpeciesReference species="X_protein"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
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                  <times/>
                  <cn type="integer"> 60 </cn>
                  <ci> tps_repr </ci>
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                <apply>
                  <divide/>
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                    <times/>
                    <apply>
                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                    <apply>
                      <minus/>
                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_repr </ci>
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                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_active </ci>
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                  <apply>
                    <plus/>
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                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                    <apply>
                      <power/>
                      <ci> X_protein </ci>
                      <ci> n_Hill </ci>
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      <reaction id="v15_v_14" name="v_14" reversible="false">
        <listOfProducts>
          <speciesReference species="Z_mRNA" stoichiometry="1"/>
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        <listOfModifiers>
          <modifierSpeciesReference species="Y_protein"/>
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        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
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                  <times/>
                  <cn type="integer"> 60 </cn>
                  <ci> tps_repr </ci>
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                <apply>
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                    <times/>
                    <apply>
                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                      <minus/>
                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_repr </ci>
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                      <apply>
                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_active </ci>
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                    <plus/>
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                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                    <apply>
                      <power/>
                      <ci> Y_protein </ci>
                      <ci> n_Hill </ci>
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      </reaction>
      <reaction id="v16_v_15" name="v_15" reversible="false">
        <listOfProducts>
          <speciesReference species="GFP" stoichiometry="1"/>
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        <listOfModifiers>
          <modifierSpeciesReference species="X_protein"/>
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          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> cell </ci>
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                  <times/>
                  <cn type="integer"> 60 </cn>
                  <ci> tps_repr </ci>
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                  <divide/>
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                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_repr </ci>
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                        <times/>
                        <cn type="integer"> 60 </cn>
                        <ci> tps_active </ci>
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                    <plus/>
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                      <power/>
                      <ci> KM </ci>
                      <ci> n_Hill </ci>
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                      <power/>
                      <ci> X_protein </ci>
                      <ci> n_Hill </ci>
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  </model>
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