1022 lines
53 KiB
XML
1022 lines
53 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns="http://www.sbml.org/sbml/level3/version2/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="2" comp:required="true" fbc:required="false" arrays:required="true" layout:required="false">
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<model metaid="iBioSim1" id="GeneticToggle" name="Created by iBioSim flatten routine" substanceUnits="mole" volumeUnits="litre" fbc:strict="false">
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<listOfUnitDefinitions>
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<unitDefinition id="u_1_second_n1">
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<listOfUnits>
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<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u_1_mole_n1_1_second_n1">
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<listOfUnits>
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<unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
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<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="u_1_mole_n1">
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<listOfUnits>
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<unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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</listOfUnitDefinitions>
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<listOfCompartments>
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<compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
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</listOfCompartments>
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<listOfSpecies>
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<species metaid="iBioSim48" id="GFP" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim49" id="LacI" compartment="Cell" initialAmount="60" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim50" id="TetR" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim51" id="IPTG" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
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<species metaid="iBioSim52" id="aTc" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
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<species metaid="iBioSim53" id="IPTG_LacI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim54" id="aTc_TetR" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim55" id="C1__pLac" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim56" id="C2__P0" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim57" id="C1__pLac_RNAP" name="C1__pLac_RNAP" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim58" id="C1__pLac_LacI" name="C1__pLac_LacI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim59" id="C2__P0_RNAP" name="C2__P0_RNAP" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim60" id="C2__P0_TetR" name="C2__P0_TetR" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim61" id="RNAP" name="RNAP" compartment="Cell" initialAmount="30" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim62" id="Cell__RNAP" name="Cell__RNAP" compartment="Cell" initialAmount="30" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter metaid="iBioSim3" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
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<parameter metaid="iBioSim4" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim5" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
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<parameter metaid="iBioSim6" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
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<parameter metaid="iBioSim7" id="C1__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
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<parameter metaid="iBioSim8" id="C1__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim9" id="C1__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
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<parameter metaid="iBioSim10" id="C1__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim11" id="C1__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
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<parameter metaid="iBioSim12" id="C1__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim13" id="C1__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim14" id="C1__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim15" id="C1__nc" name="Stoichiometry of binding" value="2" constant="true"/>
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<parameter metaid="iBioSim16" id="C1__nr" name="Initial RNAP count" value="30" constant="true"/>
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<parameter metaid="iBioSim17" id="C1__ko" name="Open complex production rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim18" id="C1__kb" name="Basal production rate" value="0.0001" constant="true"/>
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<parameter metaid="iBioSim19" id="C1__ng" name="Initial promoter count" value="2" constant="true"/>
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<parameter metaid="iBioSim20" id="C1__np" name="Stoichiometry of production" value="10" constant="true"/>
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<parameter metaid="iBioSim21" id="C1__ka" name="Activated production rate" value="0.25" constant="true"/>
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<parameter metaid="iBioSim22" id="C2__kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
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<parameter metaid="iBioSim23" id="C2__kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim24" id="C2__ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
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<parameter metaid="iBioSim25" id="C2__ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim26" id="C2__ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
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<parameter metaid="iBioSim27" id="C2__ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim28" id="C2__kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim29" id="C2__kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim37" id="C2__nc" name="Stoichiometry of binding" value="2" constant="true"/>
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<parameter metaid="iBioSim38" id="C2__nr" name="Initial RNAP count" value="30" constant="true"/>
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<parameter metaid="iBioSim39" id="C2__ko" name="Open complex production rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim40" id="C2__kb" name="Basal production rate" value="0.0001" constant="true"/>
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<parameter metaid="iBioSim41" id="C2__ng" name="Initial promoter count" value="2" constant="true"/>
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<parameter metaid="iBioSim42" id="C2__np" name="Stoichiometry of production" value="10" constant="true"/>
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<parameter metaid="iBioSim43" id="C2__ka" name="Activated production rate" value="0.25" constant="true"/>
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</listOfParameters>
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<listOfReactions>
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<reaction metaid="iBioSim63" id="Degradation_GFP" reversible="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="GFP" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kd </ci>
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<ci> GFP </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim64" id="Degradation_IPTG_LacI" reversible="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="IPTG_LacI" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kd </ci>
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<ci> IPTG_LacI </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim65" id="Degradation_LacI" reversible="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="LacI" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kd </ci>
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<ci> LacI </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim66" id="Degradation_aTc_TetR" reversible="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="aTc_TetR" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kd </ci>
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<ci> aTc_TetR </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim67" id="Degradation_TetR" reversible="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="TetR" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> kd </ci>
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<ci> TetR </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim68" id="R_constitutive_production_C1__pLac" reversible="false" compartment="Cell">
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<listOfProducts>
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<speciesReference species="GFP" stoichiometry="10" constant="true"/>
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<speciesReference species="TetR" stoichiometry="10" constant="true"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference species="C1__pLac_RNAP"/>
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</listOfModifiers>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> ko </ci>
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<ci> C1__pLac_RNAP </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="ko" value="0.05" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim69" id="R_constitutive_production_C2__P0" reversible="false" compartment="Cell">
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<listOfProducts>
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<speciesReference species="LacI" stoichiometry="10" constant="true"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference species="C2__P0_RNAP"/>
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</listOfModifiers>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<times/>
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<ci> ko </ci>
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<ci> C2__P0_RNAP </ci>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="ko" value="0.05" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim70" id="R_C1__pLac_RNAP" reversible="true" compartment="Cell">
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<listOfReactants>
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<speciesReference species="RNAP" stoichiometry="1" constant="true"/>
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<speciesReference species="C1__pLac" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="C1__pLac_RNAP" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> ko_f </ci>
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<ci> RNAP </ci>
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<ci> C1__pLac </ci>
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</apply>
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<apply>
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<times/>
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<ci> ko_r </ci>
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<ci> C1__pLac_RNAP </ci>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="ko_f" value="0.033" units="u_1_mole_n1_1_second_n1"/>
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<localParameter id="ko_r" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim71" id="R_repression_binding_C1__pLac_LacI" reversible="true" compartment="Cell">
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<listOfReactants>
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<speciesReference species="C1__pLac" stoichiometry="1" constant="true"/>
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<speciesReference species="LacI" stoichiometry="2" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="C1__pLac_LacI" stoichiometry="1" constant="true"/>
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</listOfProducts>
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<kineticLaw>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<minus/>
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<apply>
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<times/>
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<ci> kr_f </ci>
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<apply>
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<power/>
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<ci> Kr </ci>
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<apply>
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<minus/>
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<ci> nc </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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</apply>
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<apply>
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<power/>
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<ci> LacI </ci>
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<ci> nc </ci>
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</apply>
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<ci> C1__pLac </ci>
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</apply>
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<apply>
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<times/>
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<ci> kr_r </ci>
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<ci> C1__pLac_LacI </ci>
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</apply>
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</apply>
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</math>
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<listOfLocalParameters>
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<localParameter id="kr_f" value="0.5" units="u_1_mole_n1_1_second_n1"/>
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<localParameter id="kr_r" value="1" units="u_1_second_n1"/>
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<localParameter id="Kr" value="0.5" units="u_1_mole_n1"/>
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<localParameter id="nc" value="2" units="dimensionless"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim72" id="R_C2__P0_RNAP" reversible="true" compartment="Cell">
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<listOfReactants>
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<speciesReference species="RNAP" stoichiometry="1" constant="true"/>
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<speciesReference species="C2__P0" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="C2__P0_RNAP" stoichiometry="1" constant="true"/>
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</listOfProducts>
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|
<kineticLaw>
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|
<math xmlns="http://www.w3.org/1998/Math/MathML">
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|
<apply>
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<minus/>
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<apply>
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<times/>
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<ci> ko_f </ci>
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<ci> RNAP </ci>
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<ci> C2__P0 </ci>
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</apply>
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<apply>
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<times/>
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<ci> ko_r </ci>
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<ci> C2__P0_RNAP </ci>
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</apply>
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</apply>
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|
</math>
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|
<listOfLocalParameters>
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|
<localParameter id="ko_f" value="0.033" units="u_1_mole_n1_1_second_n1"/>
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<localParameter id="ko_r" value="1" units="u_1_second_n1"/>
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</listOfLocalParameters>
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|
</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim73" id="R_repression_binding_C2__P0_TetR" reversible="true" compartment="Cell">
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<listOfReactants>
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|
<speciesReference species="C2__P0" stoichiometry="1" constant="true"/>
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<speciesReference species="TetR" stoichiometry="2" constant="true"/>
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</listOfReactants>
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|
<listOfProducts>
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|
<speciesReference species="C2__P0_TetR" stoichiometry="1" constant="true"/>
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|
</listOfProducts>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
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|
<minus/>
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|
<apply>
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|
<times/>
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|
<ci> kr_f </ci>
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<apply>
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|
<power/>
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<ci> Kr </ci>
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|
<apply>
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|
<minus/>
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<ci> nc </ci>
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<cn type="integer"> 1 </cn>
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</apply>
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</apply>
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<apply>
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<power/>
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<ci> TetR </ci>
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<ci> nc </ci>
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</apply>
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<ci> C2__P0 </ci>
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</apply>
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<apply>
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<times/>
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<ci> kr_r </ci>
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<ci> C2__P0_TetR </ci>
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</apply>
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</apply>
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|
</math>
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<listOfLocalParameters>
|
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<localParameter id="kr_f" value="0.5" units="u_1_mole_n1_1_second_n1"/>
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<localParameter id="kr_r" value="1" units="u_1_second_n1"/>
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|
<localParameter id="Kr" value="0.5" units="u_1_mole_n1"/>
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<localParameter id="nc" value="2" units="dimensionless"/>
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</listOfLocalParameters>
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|
</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim74" id="Complex_IPTG_LacI" reversible="true" compartment="Cell">
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<listOfReactants>
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<speciesReference species="IPTG" stoichiometry="1" constant="true"/>
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<speciesReference species="LacI" stoichiometry="1" constant="true"/>
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</listOfReactants>
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<listOfProducts>
|
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<speciesReference species="IPTG_LacI" stoichiometry="1" constant="true"/>
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</listOfProducts>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
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<apply>
|
|
<minus/>
|
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<apply>
|
|
<times/>
|
|
<ci> kf_c </ci>
|
|
<apply>
|
|
<power/>
|
|
<ci> IPTG </ci>
|
|
<ci> nc__IPTG_IPTG_LacI </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<ci> LacI </ci>
|
|
<ci> nc__LacI_IPTG_LacI </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<ci> kr_c </ci>
|
|
<ci> IPTG_LacI </ci>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
<listOfLocalParameters>
|
|
<localParameter id="nc__IPTG_IPTG_LacI" value="1" units="dimensionless"/>
|
|
<localParameter id="nc__LacI_IPTG_LacI" value="1" units="dimensionless"/>
|
|
<localParameter id="kf_c" value="0.05" units="u_1_mole_n1_1_second_n1"/>
|
|
<localParameter id="kr_c" value="1" units="u_1_second_n1"/>
|
|
</listOfLocalParameters>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction metaid="iBioSim75" id="Complex_aTc_TetR" reversible="true" compartment="Cell">
|
|
<listOfReactants>
|
|
<speciesReference species="TetR" stoichiometry="1" constant="true"/>
|
|
<speciesReference species="aTc" stoichiometry="1" constant="true"/>
|
|
</listOfReactants>
|
|
<listOfProducts>
|
|
<speciesReference species="aTc_TetR" stoichiometry="1" constant="true"/>
|
|
</listOfProducts>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<minus/>
|
|
<apply>
|
|
<times/>
|
|
<ci> kf_c </ci>
|
|
<apply>
|
|
<power/>
|
|
<ci> TetR </ci>
|
|
<ci> nc__TetR_aTc_TetR </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<ci> aTc </ci>
|
|
<ci> nc__aTc_aTc_TetR </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<ci> kr_c </ci>
|
|
<ci> aTc_TetR </ci>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
<listOfLocalParameters>
|
|
<localParameter id="nc__TetR_aTc_TetR" value="1" units="dimensionless"/>
|
|
<localParameter id="nc__aTc_aTc_TetR" value="1" units="dimensionless"/>
|
|
<localParameter id="kf_c" value="0.05" units="u_1_mole_n1_1_second_n1"/>
|
|
<localParameter id="kr_c" value="1" units="u_1_second_n1"/>
|
|
</listOfLocalParameters>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
<listOfEvents>
|
|
<event metaid="iBioSim76" id="IPTG_High" useValuesFromTriggerTime="false">
|
|
<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"> 2000 </cn>
|
|
</math>
|
|
</delay>
|
|
<listOfEventAssignments>
|
|
<eventAssignment variable="IPTG">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<cn type="integer"> 60 </cn>
|
|
</math>
|
|
</eventAssignment>
|
|
</listOfEventAssignments>
|
|
</event>
|
|
<event metaid="iBioSim77" id="IPTG_Low" useValuesFromTriggerTime="false">
|
|
<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"> 4000 </cn>
|
|
</math>
|
|
</delay>
|
|
<listOfEventAssignments>
|
|
<eventAssignment variable="IPTG">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<cn type="integer"> 0 </cn>
|
|
</math>
|
|
</eventAssignment>
|
|
</listOfEventAssignments>
|
|
</event>
|
|
<event metaid="iBioSim78" id="aTc_High" useValuesFromTriggerTime="false">
|
|
<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"> 6000 </cn>
|
|
</math>
|
|
</delay>
|
|
<listOfEventAssignments>
|
|
<eventAssignment variable="aTc">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<cn type="integer"> 60 </cn>
|
|
</math>
|
|
</eventAssignment>
|
|
</listOfEventAssignments>
|
|
</event>
|
|
<event metaid="iBioSim79" id="aTc_Low" useValuesFromTriggerTime="false">
|
|
<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"> 8000 </cn>
|
|
</math>
|
|
</delay>
|
|
<listOfEventAssignments>
|
|
<eventAssignment variable="aTc">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<cn type="integer"> 0 </cn>
|
|
</math>
|
|
</eventAssignment>
|
|
</listOfEventAssignments>
|
|
</event>
|
|
</listOfEvents>
|
|
<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
|
|
<layout:layout layout:id="iBioSim">
|
|
<layout:dimensions layout:width="1070" layout:height="425" layout:depth="0"/>
|
|
<layout:listOfCompartmentGlyphs>
|
|
<layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="0"/>
|
|
<layout:dimensions layout:width="1070" layout:height="425"/>
|
|
</layout:boundingBox>
|
|
</layout:compartmentGlyph>
|
|
</layout:listOfCompartmentGlyphs>
|
|
<layout:listOfSpeciesGlyphs>
|
|
<layout:speciesGlyph layout:id="Glyph__GFP" layout:species="GFP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="707" layout:y="373"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__LacI" layout:species="LacI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="556" layout:y="173"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__TetR" layout:species="TetR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="556" layout:y="296"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__IPTG" layout:species="IPTG">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="556" layout:y="27"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__aTc" layout:species="aTc">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="556" layout:y="110"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__IPTG_LacI" layout:species="IPTG_LacI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="707" layout:y="1"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__aTc_TetR" layout:species="aTc_TetR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="707" layout:y="124"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C1__pLac" layout:species="C1__pLac">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="250"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C2__P0" layout:species="C2__P0">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="124"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C1__pLac_RNAP" layout:species="C1__pLac_RNAP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="150" layout:y="264"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C1__pLac_LacI" layout:species="C1__pLac_LacI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="707" layout:y="187"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C2__P0_RNAP" layout:species="C2__P0_RNAP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="150" layout:y="155"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__C2__P0_TetR" layout:species="C2__P0_TetR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="707" layout:y="250"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__RNAP" layout:species="RNAP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="187"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__Cell__RNAP" layout:species="Cell__RNAP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="300" layout:y="200"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
</layout:listOfSpeciesGlyphs>
|
|
<layout:listOfReactionGlyphs>
|
|
<layout:reactionGlyph layout:id="Glyph__Degradation_GFP" layout:reaction="Degradation_GFP">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="907.5" layout:y="373"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__Degradation_GFP__substrate__GFP" layout:speciesGlyph="Glyph__GFP" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="757" layout:y="388"/>
|
|
<layout:end layout:x="922.5" layout:y="388"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Degradation_IPTG_LacI" layout:reaction="Degradation_IPTG_LacI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="907.5" layout:y="1"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__Degradation_IPTG_LacI__substrate__IPTG_LacI" layout:speciesGlyph="Glyph__IPTG_LacI" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="757" layout:y="16"/>
|
|
<layout:end layout:x="922.5" layout:y="16"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Degradation_LacI" layout:reaction="Degradation_LacI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="742" layout:y="62"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__Degradation_LacI__substrate__LacI" layout:speciesGlyph="Glyph__LacI" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="606" layout:y="188"/>
|
|
<layout:end layout:x="757" layout:y="77"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Degradation_aTc_TetR" layout:reaction="Degradation_aTc_TetR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="907.5" layout:y="124"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__Degradation_aTc_TetR__substrate__aTc_TetR" layout:speciesGlyph="Glyph__aTc_TetR" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="757" layout:y="139"/>
|
|
<layout:end layout:x="922.5" layout:y="139"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Degradation_TetR" layout:reaction="Degradation_TetR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="742" layout:y="311"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__Degradation_TetR__substrate__TetR" layout:speciesGlyph="Glyph__TetR" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="606" layout:y="311"/>
|
|
<layout:end layout:x="757" layout:y="326"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__R_constitutive_production_C1__pLac" layout:reaction="R_constitutive_production_C1__pLac">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="388" layout:y="357"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__R_constitutive_production_C1__pLac__modifier__C1__pLac_RNAP" layout:speciesGlyph="Glyph__C1__pLac_RNAP" layout:role="modifier">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="200" layout:y="279"/>
|
|
<layout:end layout:x="403" layout:y="372"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__R_constitutive_production_C1__pLac__product__GFP" layout:speciesGlyph="Glyph__GFP" layout:role="product">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="403" layout:y="372"/>
|
|
<layout:end layout:x="757" layout:y="388"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__R_constitutive_production_C1__pLac__product__TetR" layout:speciesGlyph="Glyph__TetR" layout:role="product">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
<layout:start layout:x="403" layout:y="372"/>
|
|
<layout:end layout:x="606" layout:y="311"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__R_constitutive_production_C2__P0" layout:reaction="R_constitutive_production_C2__P0">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="388" layout:y="267"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__R_constitutive_production_C2__P0__modifier__C2__P0_RNAP" layout:speciesGlyph="Glyph__C2__P0_RNAP" layout:role="modifier">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
|
|
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<layout:referenceGlyph layout:id="Glyph__aTc_Low__product__aTc" layout:glyph="Glyph__aTc" layout:role="product">
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