There there are five different reactions. In Reaction1 an A molecule makes a B molecule in CompartmentThree. In Reaction2 D molecules are degraded. In Reaction3 B molecules are degraded in CompartmentOne. In Reaction4 B molecule dimerize to D molecules CompartmentTwo. In Reaction5 an D molecule fall apart into B molecules.

<listOfReactions>

  <reaction id="Reaction1" reversible="false">
    <listOfReactants>
      <speciesReference species="A3"/>
      </listOfReactants>
    <listOfProducts>
      <speciesReference species="A3"/>
      <speciesReference species="B3"/>
    </listOfProducts>
    <kineticLaw>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci>k</ci>
          <ci>A3</ci>
        </apply>
      </math>
    </kineticLaw>
  </reaction>

  <reaction id="Reaction2" reversible="false">
    <listOfReactants>
      <speciesReference species="D2"/>
    </listOfReactants>		
    <kineticLaw>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci>mu2</ci>
          <ci>D2</ci>
        </apply>
      </math>
    </kineticLaw>
  </reaction>

  <reaction id="Reaction3" reversible="false">
    <listOfReactants>
      <speciesReference species="B1"/>
    </listOfReactants>		
    <kineticLaw>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci>mu</ci>
          <ci>B1</ci>
        </apply>
      </math>
    </kineticLaw>
  </reaction>

  <reaction id="Reaction4" reversible="false">
    <listOfReactants>
      <speciesReference species="B2" stoichiometry="2" />
    </listOfReactants>
    <listOfProducts>
      <speciesReference species="D2"/>
    </listOfProducts>
    <kineticLaw>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci>ka</ci>
          <ci>B2</ci>
          <apply>
            <minus/>
            <ci>B2</ci>
            <ci>one_molecule_molar_spec</ci>	            
          </apply>
        </apply>
      </math>
    </kineticLaw>
  </reaction>

  <reaction id="Reaction5" reversible="false">
    <listOfReactants>
      <speciesReference species="D2"/>
    </listOfReactants>
    <listOfProducts>
      <speciesReference species="B2" stoichiometry="2" />
    </listOfProducts>
    <kineticLaw>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <apply>
          <times/>
          <ci>kd</ci>
          <ci>D2</ci>
        </apply>
      </math>
    </kineticLaw>
  </reaction>
</listOfReactions>
    

Note that we use the id of the species in the definition of the kineticLaw. This will define the compartment of the reaction. Note the parameter one_molecule_molar_spc in Reaction 4. This parameter takes it value at runtime and it is very special. It takes different values in the deterministic and the stochastic modes! In the stochastic mode it takes the value of the concentration of one molecule in a subvolume. In the deterministic mode it is zero, since this is the minimal change in concentration. The parameter was implemented to model the reaction X+X-> with a rate proportional to #X*(#X-1) in the stochastic mode and a rate proportional to #X*#X in the deterministic, using the same SBML code.

Finally, we need to close the model and sbml definitions we started in the section called “ Units ”.

</model>
</sbml>