<?xml version="1.0" encoding="utf-8"?>
<!--
 | @file    me.xml
 | @author  Emmet Caulfield
 | @brief   Validated SBML model for a metabolite-enzyme 
 |          reaction.
 | @version 0.3
 |
 | This is an initial attempt at describing the reaction in 
 | Section 5.1, "Metabolites controled (sic.) by enzymes",
 | on p.15 of Hellander & Lotstedt, "Hybrid Method for the
 | Chemical Master Equation", 2006.
 |
 | $Id: me.xml 14 2008-12-23 08:32:48Z emmet $
-->
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" version="3">

  <annotation>
    <svn:subversion xmlns:svn="http://svnbook.red-bean.com/en/1.4/svn.advanced.props.special.keywords.html">
      <svn:Rev>$Rev: 33 $</svn:Rev>
      <svn:Id>$Id: me.xml 14 2008-12-23 08:32:48Z emmet $</svn:Id>
    </svn:subversion>

    <kit:provenance xmlns:kit="http://polacksbacken.net/wiki/SSACBE" />

  </annotation>

  <model name="MetaboliteEnzyme">
    <listOfCompartments>
      <compartment id="cell" size="1"/>

      </listOfCompartments>

    <listOfSpecies>
      <species id="A"  name="Species A" initialAmount="35" compartment="cell"/>
      <species id="B"  name="Species B" initialAmount="30" compartment="cell"/>
      <species id="Ea" name="Enzyme A"  initialAmount="6"  compartment="cell"/>
      <species id="Eb" name="Enzyme B"  initialAmount="5"  compartment="cell"/>
    </listOfSpecies>

    <listOfParameters>
      <parameter id="kA"  value= "0.3"   />
      <parameter id="kB"  value= "0.3"   />
      <parameter id="k2"  value= "0.001" />
      <parameter id="Ki"  value="60.0"   />
      <parameter id="mu"  value= "0.002" />
      <parameter id="kEa" value= "0.02"  />
      <parameter id="kEb" value= "0.02"  />
      <parameter id="Kr"  value="30.0"   />
    </listOfParameters>

    <listOfReactions>
      <reaction id="SynthA" reversible="false">
        <listOfProducts>
          <speciesReference species="A"/>
        </listOfProducts>
	<listOfModifiers>
	  <modifierSpeciesReference species="Ea"/>
        </listOfModifiers>
        <!-- rate[SynA] = kA*popn[Ea]/(1.0+(double)popn[A]/Ki); -->
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
	      <apply>
                <times/>
                <ci> kA </ci>
                <ci> Ea </ci>
              </apply>
	      <apply>
                <plus/>
                <cn type="integer"> 1 </cn>
		<apply>
                  <divide/>
                  <ci> A </ci>
                  <ci> Ki </ci>
                </apply>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>

      <reaction id="SynthB" reversible="false">
        <listOfProducts>
          <speciesReference species="B"/>
        </listOfProducts>
	<listOfModifiers>
	  <modifierSpeciesReference species="Eb"/>
        </listOfModifiers>
        <!-- rate[SynB] = kB*popn[Eb]/(1.0+(double)popn[B]/Ki); -->
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
	      <apply>
                <times/>
                <ci> kB </ci>
                <ci> Eb </ci>
              </apply>
	      <apply>
                <plus/>
                <cn type="integer"> 1 </cn>
		<apply>
                  <divide/>
                  <ci> B </ci>
                  <ci> Ki </ci>
                </apply>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>

      <reaction id="SynthEa" reversible="false">
        <listOfProducts>
          <speciesReference species="Ea"/>
        </listOfProducts>
	<listOfModifiers>
	  <modifierSpeciesReference species="A"/>
        </listOfModifiers>

        <!-- rate[SynEa] = keA/(1.0+(double)popn[A]/Kr); -->
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <ci> kEa </ci>
	      <apply>
                <plus/>
                <cn type="integer"> 1 </cn>
		<apply>
                  <divide/>
                  <ci> A </ci>
                  <ci> Kr </ci>
                </apply>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>

      <reaction id="SynthEb" reversible="false">
        <listOfProducts>
          <speciesReference species="Eb"/>
        </listOfProducts>
	<listOfModifiers>
	  <modifierSpeciesReference species="B"/>
        </listOfModifiers>
        <!-- rate[SynEb] = keB/(1.0+(double)popn[B]/Kr); -->
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <divide/>
              <ci> kEb </ci>
	      <apply>
                <plus/>
                <cn type="integer"> 1 </cn>
		<apply>
                  <divide/>
                  <ci> B </ci>
                  <ci> Kr </ci>
                </apply>
              </apply>
            </apply>
          </math>
        </kineticLaw>
      </reaction>

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

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

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

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

      <reaction id="AnnhiAB" reversible="false">
        <listOfReactants>
          <speciesReference species="A"/>
          <speciesReference species="B"/>
        </listOfReactants>
        <!-- rate[AnnAB] = k2*(double)(popn[A]*popn[B]); -->
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci> k2 </ci>
              <ci> A </ci>
              <ci> B </ci>
            </apply>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
  </model>
</sbml>

