<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
  <model id="Model_1" name="Rab5-Rab7 anti-phase Cut-Out switch">
    <notes>
      <body xmlns="http://www.w3.org/1999/xhtml"></body>
    </notes>
    <listOfFunctionDefinitions>
      <functionDefinition id="function_5" name="3 hydrolysis">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> kh </ci>
            </bvar>
            <bvar>
              <ci> R </ci>
            </bvar>
            <apply>
              <times/>
              <ci> kh </ci>
              <ci> R </ci>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
      <functionDefinition id="function_4" name="2 Sigmoid Activation ">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> ke </ci>
            </bvar>
            <bvar>
              <ci> r </ci>
            </bvar>
            <bvar>
              <ci> kg </ci>
            </bvar>
            <bvar>
              <ci> R </ci>
            </bvar>
            <bvar>
              <ci> kf </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> ke </ci>
                <ci> r </ci>
              </apply>
              <apply>
                <plus/>
                <cn> 1 </cn>
                <apply>
                  <exp/>
                  <apply>
                    <times/>
                    <apply>
                      <minus/>
                      <ci> kg </ci>
                      <ci> R </ci>
                    </apply>
                    <ci> kf </ci>
                  </apply>
                </apply>
              </apply>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
      <functionDefinition id="function_3" name="2 Hills activation">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> r </ci>
            </bvar>
            <bvar>
              <ci> ke </ci>
            </bvar>
            <bvar>
              <ci> R </ci>
            </bvar>
            <bvar>
              <ci> h </ci>
            </bvar>
            <bvar>
              <ci> kg </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> r </ci>
                <ci> ke </ci>
                <apply>
                  <power/>
                  <ci> R </ci>
                  <ci> h </ci>
                </apply>
              </apply>
              <apply>
                <plus/>
                <ci> kg </ci>
                <apply>
                  <power/>
                  <ci> R </ci>
                  <ci> h </ci>
                </apply>
              </apply>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
      <functionDefinition id="function_2" name="4 extraction">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> kminus1 </ci>
            </bvar>
            <bvar>
              <ci> r </ci>
            </bvar>
            <apply>
              <times/>
              <ci> kminus1 </ci>
              <ci> r </ci>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
      <functionDefinition id="function_1" name="2 Sigmoid Activation 3 (t)">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> r </ci>
            </bvar>
            <bvar>
              <ci> ke </ci>
            </bvar>
            <bvar>
              <ci> t </ci>
            </bvar>
            <bvar>
              <ci> kg </ci>
            </bvar>
            <bvar>
              <ci> R </ci>
            </bvar>
            <bvar>
              <ci> kf </ci>
            </bvar>
            <apply>
              <divide/>
              <apply>
                <times/>
                <ci> r </ci>
                <apply>
                  <divide/>
                  <apply>
                    <times/>
                    <ci> ke </ci>
                    <ci> t </ci>
                  </apply>
                  <apply>
                    <plus/>
                    <cn> 100 </cn>
                    <ci> t </ci>
                  </apply>
                </apply>
              </apply>
              <apply>
                <plus/>
                <cn> 1 </cn>
                <apply>
                  <exp/>
                  <apply>
                    <times/>
                    <apply>
                      <minus/>
                      <ci> kg </ci>
                      <ci> R </ci>
                    </apply>
                    <ci> kf </ci>
                  </apply>
                </apply>
              </apply>
            </apply>
          </lambda>
        </math>
      </functionDefinition>
      <functionDefinition id="function_0" name="1 recruitment">
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <lambda>
            <bvar>
              <ci> K1 </ci>
            </bvar>
            <ci> K1 </ci>
          </lambda>
        </math>
      </functionDefinition>
    </listOfFunctionDefinitions>
    <listOfUnitDefinitions>
      <unitDefinition id="volume">
        <listOfUnits>
          <unit kind="litre" scale="-3" multiplier="1" offset="0"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="time">
        <listOfUnits>
          <unit kind="second" multiplier="60" offset="0"/>
        </listOfUnits>
      </unitDefinition>
      <unitDefinition id="substance">
        <listOfUnits>
          <unit kind="mole" scale="-3" multiplier="1" offset="0"/>
        </listOfUnits>
      </unitDefinition>
    </listOfUnitDefinitions>
    <listOfCompartments>
      <compartment id="compartment_0" name="compartment" size="1"/>
    </listOfCompartments>
    <listOfSpecies>
      <species id="species_0" name="r5" compartment="compartment_0" initialConcentration="1"/>
      <species id="species_1" name="R5" compartment="compartment_0" initialConcentration="0.001"/>
      <species id="species_2" name="r7" compartment="compartment_0" initialConcentration="1"/>
      <species id="species_3" name="R7" compartment="compartment_0" initialConcentration="0.001"/>
    </listOfSpecies>
    <listOfReactions>
      <reaction id="reaction_0" name="51 recruitment of Rab5" reversible="false">
        <listOfProducts>
          <speciesReference species="species_0"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_0 </ci>
                <ci> K1 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="K1" value="1"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_1" name="525 activation of Rab5 (time)" reversible="false">
        <listOfReactants>
          <speciesReference species="species_0"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_1"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="species_1"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_1 </ci>
                <ci> species_0 </ci>
                <ci> ke </ci>
                <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
                <ci> kg </ci>
                <ci> species_1 </ci>
                <ci> kf </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="ke" value="0.3"/>
            <parameter id="kg" value="0.1"/>
            <parameter id="kf" value="2.5"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_2" name="54 extraction of Rab5" reversible="false">
        <listOfReactants>
          <speciesReference species="species_0"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_2 </ci>
                <ci> kminus1 </ci>
                <ci> species_0 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="kminus1" value="1"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_3" name="71 recruitment of Rab7" reversible="false">
        <listOfProducts>
          <speciesReference species="species_2"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_0 </ci>
                <ci> K1 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="K1" value="0.483"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_4" name="727 activation of Rab7 by GEF7" reversible="false">
        <listOfReactants>
          <speciesReference species="species_2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_3"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="species_3"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_3 </ci>
                <ci> species_2 </ci>
                <ci> ke </ci>
                <ci> species_3 </ci>
                <ci> h </ci>
                <ci> kg </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="ke" value="0.21"/>
            <parameter id="h" value="3"/>
            <parameter id="kg" value="0.1"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_5" name="725 activation of Rab7 by GEF5" reversible="false">
        <listOfReactants>
          <speciesReference species="species_2"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_3"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="species_1"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_4 </ci>
                <ci> ke </ci>
                <ci> species_2 </ci>
                <ci> kg </ci>
                <ci> species_1 </ci>
                <ci> kf </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="ke" value="0.021"/>
            <parameter id="kg" value="1"/>
            <parameter id="kf" value="3"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_6" name="537 hydrolysis of Rab5 by Rab7" reversible="false">
        <listOfReactants>
          <speciesReference species="species_1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_0"/>
        </listOfProducts>
        <listOfModifiers>
          <modifierSpeciesReference species="species_3"/>
        </listOfModifiers>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_4 </ci>
                <ci> ke </ci>
                <ci> species_1 </ci>
                <ci> kg </ci>
                <ci> species_3 </ci>
                <ci> kf </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="ke" value="0.31"/>
            <parameter id="kg" value="0.3"/>
            <parameter id="kf" value="3"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_7" name="74 extraction of rab7" reversible="false">
        <listOfReactants>
          <speciesReference species="species_2"/>
        </listOfReactants>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_2 </ci>
                <ci> kminus1 </ci>
                <ci> species_2 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="kminus1" value="0.483"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_8" name="53 hydrolysis of Rab5 (intr.)" reversible="false">
        <listOfReactants>
          <speciesReference species="species_1"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_0"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_5 </ci>
                <ci> kh </ci>
                <ci> species_1 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="kh" value="0.06"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
      <reaction id="reaction_9" name="73 hydrolysis of Rab7 (intr.)" reversible="false">
        <listOfReactants>
          <speciesReference species="species_3"/>
        </listOfReactants>
        <listOfProducts>
          <speciesReference species="species_2"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> compartment_0 </ci>
              <apply>
                <ci> function_5 </ci>
                <ci> kh </ci>
                <ci> species_3 </ci>
              </apply>
            </apply>
          </math>
          <listOfParameters>
            <parameter id="kh" value="0.15"/>
          </listOfParameters>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>
