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TBModelPh3.xml
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</bvar>
<bvar>
<ci> T </ci>
</bvar>
<bvar>
<ci> k </ci>
</bvar>
<bvar>
<ci> Mf </ci>
</bvar>
<bvar>
<ci> FB6 </ci>
</bvar>
<bvar>
<ci> PTf </ci>
</bvar>
<bvar>
<ci> M </ci>
</bvar>
<bvar>
<ci> Fd </ci>
</bvar>
<bvar>
<ci> s </ci>
</bvar>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> a2 </ci>
<ci> T </ci>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> T </ci>
<ci> k </ci>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> Mf </ci>
<ci> FB6 </ci>
<ci> PTf </ci>
</apply>
</apply>
<apply>
<times/>
<ci> M </ci>
<apply>
<divide/>
<ci> T </ci>
<ci> PTf </ci>
</apply>
<ci> Fd </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> Mf </ci>
<ci> FB6 </ci>
<ci> s </ci>
</apply>
</apply>
</apply>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition metaid="Phagocytosed_Tuberculosis" id="Phagocytosed_Tuberculosis" name="Phagocytosed_Tuberculosis">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> a3 </ci>
</bvar>
<bvar>
<ci> Tf </ci>
</bvar>
<bvar>
<ci> ka </ci>
</bvar>
<bvar>
<ci> Mf </ci>
</bvar>
<bvar>
<ci> M </ci>
</bvar>
<bvar>
<ci> PTf </ci>
</bvar>
<bvar>
<ci> T </ci>
</bvar>
<bvar>
<ci> Fd </ci>
</bvar>
<bvar>
<ci> FB6 </ci>
</bvar>
<bvar>
<ci> s </ci>
</bvar>
<bvar>
<ci> Fg </ci>
</bvar>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> a3 </ci>
<ci> Tf </ci>
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<apply>
<divide/>
<ci> Tf </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> ka </ci>
<ci> Mf </ci>
</apply>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> M </ci>
<apply>
<divide/>
<cn type="integer"> 1 </cn>
<ci> PTf </ci>
</apply>
<ci> T </ci>
<ci> Fd </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> Mf </ci>
<ci> FB6 </ci>
<ci> s </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> Mf </ci>
<ci> Tf </ci>
<ci> Fg </ci>
</apply>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition metaid="substance" id="substance" name="substance">
<listOfUnits>
<unit metaid="CDMT00057" kind="mole"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="volume" id="volume" name="volume">
<listOfUnits>
<unit metaid="CDMT00058" kind="litre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="area" id="area" name="area">
<listOfUnits>
<unit metaid="CDMT00059" kind="metre" exponent="2"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="length" id="length" name="length">
<listOfUnits>
<unit metaid="CDMT00060" kind="metre"/>
</listOfUnits>
</unitDefinition>
<unitDefinition metaid="time" id="time" name="time">
<listOfUnits>
<unit metaid="CDMT00061" kind="second"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="M" name="M" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
<celldesigner:name>M</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re17"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s2" id="Mf" name="Mf" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
<celldesigner:name>Mf</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re2"/>
<celldesigner:catalyzed reaction="re6"/>
<celldesigner:catalyzed reaction="re8"/>
<celldesigner:catalyzed reaction="re9"/>
<celldesigner:catalyzed reaction="re17"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s3" id="T" name="T" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
<celldesigner:name>T</celldesigner:name>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re1"/>
<celldesigner:catalyzed reaction="re3"/>
<celldesigner:catalyzed reaction="re5"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s4" id="Tf" name="Tf" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
<celldesigner:name>Tf</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s5</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s6</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s7</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s8</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s10" id="s10" name="s10" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s10</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s11" id="s11" name="s11" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" charge="0" constant="true">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>DEGRADED</celldesigner:class>
<celldesigner:name>s11</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false" fast="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="M" alias="sa1">
<celldesigner:linkAnchor position="ESE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="Mf" alias="sa2">
<celldesigner:linkAnchor position="WSW"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="T" aliases="sa3" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="T" alias="sa3">
<celldesigner:linkAnchor position="N"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="M">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00002" species="Mf">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00038" species="T">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
<kineticLaw metaid="CDMT00004">
<annotation>
<celldesigner:extension>
<celldesigner:selectedFunction>NonPredefinedFunction</celldesigner:selectedFunction>
</celldesigner:extension>
</annotation>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> M </ci>
<apply>
<divide/>
<ci> T </ci>
<ci> PTf </ci>
</apply>
<ci> Fd </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> Mf </ci>
<ci> FB6 </ci>
<ci> s </ci>
</apply>
</apply>
</apply>
</math>
<listOfParameters>
<parameter metaid="PTf" id="PTf" name="PTf" value="7" units="substance"/>
<parameter metaid="Fd" id="Fd" name="Fd" value="2.176e-10" units="substance"/>
<parameter metaid="FB6" id="FB6" name="FB6" value="4" units="substance"/>
<parameter metaid="s" id="s" name="s" value="5.6957" units="substance"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="re2" id="re2" reversible="false" fast="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s5" alias="sa5">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="M" alias="sa1">
<celldesigner:linkAnchor position="N"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="Mf" aliases="sa2" targetLineIndex="-1,2">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="Mf" alias="sa2">
<celldesigner:linkAnchor position="WNW"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00005" species="s5">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa5</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00006" species="M">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00039" species="Mf">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
<kineticLaw metaid="CDMT00009">
<annotation>
<celldesigner:extension>
<celldesigner:selectedFunction>NonPredefinedFunction</celldesigner:selectedFunction>
</celldesigner:extension>
</annotation>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> Mf </ci>
<ci> Fa1 </ci>
</apply>
</math>
<listOfParameters>
<parameter metaid="Fa1" id="Fa1" name="Fa1" value="1000" units="substance"/>
<parameter metaid="CDMT00040" id="PTf" name="PTf" value="7" units="substance"/>
<parameter metaid="CDMT00041" id="Fd" name="Fd" value="2.176e-10" units="substance"/>
<parameter metaid="CDMT00042" id="FB6" name="FB6" value="4" units="substance"/>
<parameter metaid="CDMT00043" id="s" name="s" value="5.6957" units="substance"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="re3" id="re3" reversible="false" fast="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="M" alias="sa1">
<celldesigner:linkAnchor position="S"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s6" alias="sa6">
<celldesigner:linkAnchor position="N"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="T" aliases="sa3" targetLineIndex="-1,5">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="T" alias="sa3">
<celldesigner:linkAnchor position="WNW"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00010" species="M">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00011" species="s6">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa6</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00044" species="T">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa3</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
<kineticLaw metaid="CDMT00013">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<ci> M </ci>
<ci> B1 </ci>
</apply>
<apply>
<times/>
<ci> M </ci>
<ci> T </ci>
<ci> FB4 </ci>
</apply>
</apply>
</math>
<listOfParameters>
<parameter metaid="B1" id="B1" name="B1" value="0.0019" units="substance"/>
<parameter metaid="FB4" id="FB4" name="FB4" value="6.7929e-11" units="substance"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction metaid="re5" id="re5" reversible="false" fast="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="Mf" alias="sa2">
<celldesigner:linkAnchor position="SSE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s8" alias="sa8">
<celldesigner:linkAnchor position="NNE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="T" aliases="sa3" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="T" alias="sa3">