iBioSim/docs/Tutorial/Divide.xml

<?xml version="1.0" encoding="UTF-8"?>
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    <listOfCompartments>
      <compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
    </listOfCompartments>
    <listOfSpecies>
      <species metaid="iBioSim2" id="S0" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
    </listOfSpecies>
    <listOfParameters>
      <parameter metaid="iBioSim3" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
      <parameter metaid="iBioSim4" id="np" name="Stoichiometry of production" value="10" constant="true"/>
      <parameter metaid="iBioSim5" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
      <parameter metaid="iBioSim8" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
      <parameter metaid="iBioSim9" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
      <parameter metaid="iBioSim10" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
      <parameter metaid="iBioSim11" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
    </listOfParameters>
    <listOfReactions>
      <reaction metaid="iBioSim7" sboTerm="SBO:0000396" id="Constitutive_S0" reversible="false" fast="false" compartment="Cell">
        <listOfProducts>
          <speciesReference species="S0" stoichiometry="10" constant="true"/>
        </listOfProducts>
        <kineticLaw>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <ci> ko </ci>
          </math>
        </kineticLaw>
      </reaction>
    </listOfReactions>
    <listOfEvents>
      <event id="event0" useValuesFromTriggerTime="false">
        <annotation>
          <ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="Symmetric Division"/>
        </annotation>
        <trigger initialValue="false" persistent="false">
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <true/>
          </math>
        </trigger>
        <delay>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <cn type="integer"> 200 </cn>
          </math>
        </delay>
      </event>
      <event id="event1" useValuesFromTriggerTime="false">
        <annotation>
          <ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="Death"/>
        </annotation>
        <trigger initialValue="false" persistent="false">
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              <ci> S0 </ci>
              <cn type="integer"> 50 </cn>
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            <cn type="integer"> 100 </cn>
          </math>
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      <layout:layout layout:id="iBioSim">
        <layout:dimensions layout:width="0" layout:height="0"/>
        <layout:listOfCompartmentGlyphs>
          <layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
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          </layout:speciesGlyph>
        </layout:listOfSpeciesGlyphs>
        <layout:listOfTextGlyphs>
          <layout:textGlyph layout:id="TextGlyph__Cell" layout:text="Cell" layout:graphicalObject="Glyph__Cell">
            <layout:boundingBox>
              <layout:position layout:x="0" layout:y="0"/>
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          </layout:textGlyph>
          <layout:textGlyph layout:id="TextGlyph__S0" layout:text="S0" layout:graphicalObject="Glyph__S0">
            <layout:boundingBox>
              <layout:position layout:x="113" layout:y="93"/>
              <layout:dimensions layout:width="100" layout:height="30"/>
            </layout:boundingBox>
          </layout:textGlyph>
          <layout:textGlyph layout:id="TextGlyph__event0" layout:text="event0" layout:graphicalObject="Glyph__event0">
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