<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
  <model id="base">
    <listOfCompartments>
      <compartment id="cell" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="octopine" compartment="cell" initialConcentration="0"/>
      <species id="OOHL" compartment="cell" initialConcentration="200"/>
      <species id="traAPromoter" compartment="cell" initialConcentration="1"/>
      <species id="traAmRNA" compartment="cell" initialConcentration="10"/>
      <species id="TraA" compartment="cell" initialConcentration="10"/>
      <species id="traRPromoter" compartment="cell" initialConcentration="1"/>
      <species id="traRmRNA" compartment="cell" initialConcentration="10"/>
      <species id="FreeTraR" compartment="cell" initialConcentration="1"/>
      <species id="BoundTraR" compartment="cell" initialConcentration="0"/>
      <species id="TraRDimer" compartment="cell" initialConcentration="0"/>
      <species id="traIPromoter" compartment="cell" initialConcentration="1"/>
      <species id="traImRNA" compartment="cell" initialConcentration="10"/>
      <species id="TraI" compartment="cell" initialConcentration="10"/>
      <species id="Plac" compartment="cell" initialConcentration="0"/>
      <species id="hotFreeTraR" compartment="cell" initialConcentration="0"/>
      <species id="hotBoundTraR" compartment="cell" initialConcentration="0"/>
      <species id="hotTraRDimer" compartment="cell" initialConcentration="0"/>
      <species id="radiolabel" compartment="cell" initialConcentration="0"/>
      <species id="unradiolabel" compartment="cell" initialConcentration="1"/>
      <species id="hotTotalTraR" compartment="cell"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter id="k_traRbasal" name="k_{traRbasal}" value="0.000525152"/>
      <parameter id="k_tmR" value="1.16279e-06"/>
      <parameter id="Km_tmR" value="50"/>
      <parameter id="k_dmR" value="0.000332932"/>
      <parameter id="k_tpR" value="0.0529688"/>
      <parameter id="k_dpR" value="0.369439"/>
      <parameter id="k_ROOHL" value="1.9799e-06"/>
      <parameter id="k_dimR" value="6.95149e-06"/>
      <parameter id="k_traIbasal" value="0.00175608"/>
      <parameter id="k_tmI" value="17.6984"/>
      <parameter id="Km_tmI" value="50"/>
      <parameter id="k_dmI" value="7.90914e-05"/>
      <parameter id="k_tpI" value="0.263034"/>
      <parameter id="k_dpI" value="0.0834003"/>
      <parameter id="k_OOHL" value="0.096461"/>
      <parameter id="k_traAbasal" value="0.00194671"/>
      <parameter id="k_tmA" value="1687.79"/>
      <parameter id="Km_tmA" value="50"/>
      <parameter id="k_dmA" value="1.08953e-05"/>
      <parameter id="k_tpA" value="1.35524e-05"/>
      <parameter id="k_dpA" value="1.21211e-05"/>
      <parameter id="k_dOOHL" value="2.36129e-11"/>
      <parameter id="k_Plac" value="0.01"/>
      <parameter id="k_doublingtime" value="0.003"/>
    </listOfParameters>
    <listOfRules>
      <assignmentRule variable="hotTotalTraR">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <plus/>
            <ci> hotFreeTraR </ci>
            <ci> hotBoundTraR </ci>
            <apply>
              <times/>
              <cn> 2 </cn>
              <ci> hotTraRDimer </ci>
            </apply>
          </apply>
        </math>
      </assignmentRule>
    </listOfRules>
    <listOfReactions>
      <reaction id="TraRBasalTranscription">
        <listOfProducts>
          <speciesReference species="traRmRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traRPromoter"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_traRbasal </ci>
              <ci> traRPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="OctopineInducedTraRTranscription">
        <listOfProducts>
          <speciesReference species="traRmRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traRPromoter"/>
          <modifierSpeciesReference species="octopine"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> k_tmR </ci>
                <ci> traRPromoter </ci>
                <ci> octopine </ci>
              </apply>
              <apply>
                <plus/>
                <ci> octopine </ci>
                <ci> Km_tmR </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRmRNADegradation">
        <listOfReactants>
          <speciesReference species="traRmRNA"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dmR </ci>
              <ci> traRmRNA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRTranslation">
        <listOfProducts>
          <speciesReference species="FreeTraR"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="unradiolabel"/>
          <modifierSpeciesReference species="traRmRNA"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_tpR </ci>
              <ci> traRmRNA </ci>
              <ci> unradiolabel </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRDegradation">
        <listOfReactants>
          <speciesReference species="FreeTraR"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dpR </ci>
              <ci> FreeTraR </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraROOHLBinding">
        <listOfReactants>
          <speciesReference species="OOHL"/>
          <speciesReference species="FreeTraR"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="BoundTraR"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_ROOHL </ci>
              <ci> FreeTraR </ci>
              <ci> OOHL </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRDimerization">
        <listOfReactants>
          <speciesReference species="BoundTraR" stoichiometry="2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="TraRDimer"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dimR </ci>
              <apply>
                <power/>
                <ci> BoundTraR </ci>
                <cn type="integer"> 2 </cn>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraIBasalTranscription">
        <listOfProducts>
          <speciesReference species="traImRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traIPromoter"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_traIbasal </ci>
              <ci> traIPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRInducedTraITranscription">
        <listOfProducts>
          <speciesReference species="traImRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="TraRDimer"/>
          <modifierSpeciesReference species="traIPromoter"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> k_tmI </ci>
                <ci> traIPromoter </ci>
                <ci> TraRDimer </ci>
              </apply>
              <apply>
                <plus/>
                <ci> TraRDimer </ci>
                <ci> Km_tmI </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraImRNADegradation">
        <listOfReactants>
          <speciesReference species="traImRNA"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dmI </ci>
              <ci> traImRNA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraITranslation">
        <listOfProducts>
          <speciesReference species="TraI"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traImRNA"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_tpI </ci>
              <ci> traImRNA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraIDegradation">
        <listOfReactants>
          <speciesReference species="TraI"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dpI </ci>
              <ci> TraI </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="OOHLSynthesis">
        <listOfProducts>
          <speciesReference species="OOHL"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="TraI"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_OOHL </ci>
              <ci> TraI </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraABasalTranscription">
        <listOfProducts>
          <speciesReference species="traAmRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traAPromoter"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_traAbasal </ci>
              <ci> traAPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRInducedTraATranscription">
        <listOfProducts>
          <speciesReference species="traAmRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="TraRDimer"/>
          <modifierSpeciesReference species="traAPromoter"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> k_tmA </ci>
                <ci> traAPromoter </ci>
                <ci> TraRDimer </ci>
              </apply>
              <apply>
                <plus/>
                <ci> TraRDimer </ci>
                <ci> Km_tmA </ci>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraAmRNADegradation">
        <listOfReactants>
          <speciesReference species="traAmRNA"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dmA </ci>
              <ci> traAmRNA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraATranslation">
        <listOfProducts>
          <speciesReference species="TraA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traAmRNA"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_tpA </ci>
              <ci> traAmRNA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraADegradation">
        <listOfReactants>
          <speciesReference species="TraA"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dpA </ci>
              <ci> TraA </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="OOHLLoss">
        <listOfReactants>
          <speciesReference species="OOHL"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dOOHL </ci>
              <ci> OOHL </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="traAGeneReplication">
        <listOfProducts>
          <speciesReference species="traAPromoter"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_doublingtime </ci>
              <ci> traAPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="traRGeneReplication">
        <listOfProducts>
          <speciesReference species="traRPromoter"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_doublingtime </ci>
              <ci> traRPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="traIGeneReplication">
        <listOfProducts>
          <speciesReference species="traIPromoter"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_doublingtime </ci>
              <ci> traIPromoter </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="TraRTranscriptionFromPlac">
        <listOfProducts>
          <speciesReference species="traRmRNA"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="Plac"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_Plac </ci>
              <ci> Plac </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="hotTraRTranslation">
        <listOfProducts>
          <speciesReference species="hotFreeTraR"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="traRmRNA"/>
          <modifierSpeciesReference species="radiolabel"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_tpR </ci>
              <ci> traRmRNA </ci>
              <ci> radiolabel </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="hotTraRDegradation">
        <listOfReactants>
          <speciesReference species="hotFreeTraR"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dpR </ci>
              <ci> hotFreeTraR </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="hotTraROOHLBinding">
        <listOfReactants>
          <speciesReference species="OOHL"/>
          <speciesReference species="hotFreeTraR"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="hotBoundTraR"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_ROOHL </ci>
              <ci> hotFreeTraR </ci>
              <ci> OOHL </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
      <reaction id="hotTraRDimerization">
        <listOfReactants>
          <speciesReference species="hotBoundTraR" stoichiometry="2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="hotTraRDimer"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k_dimR </ci>
              <apply>
                <power/>
                <ci> hotBoundTraR </ci>
                <cn type="integer"> 2 </cn>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
