787 lines
36 KiB
XML
787 lines
36 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" layout:required="false" comp:required="true">
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<model metaid="iBioSim1" id="lambda" substanceUnits="nanoMole" timeUnits="second" volumeUnits="microLitre" extentUnits="nanoMole">
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<annotation>
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<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:Description rdf:about="#iBioSim1">
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<mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_5_17_2013_9_52_52_892_iBioSim"/>
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</rdf:Seq>
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</mts:DNAComponents>
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</rdf:Description>
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</rdf:RDF>
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</ModelToSBOL>
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</annotation>
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<listOfFunctionDefinitions>
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<functionDefinition id="total" name="Find total molecules">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<lambda>
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<bvar>
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<ci> x </ci>
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</bvar>
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<bvar>
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<ci> y </ci>
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</bvar>
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<apply>
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<plus/>
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<ci> x </ci>
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<apply>
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<times/>
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<cn type="integer"> 2 </cn>
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<ci> y </ci>
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</apply>
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</apply>
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</lambda>
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</math>
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</functionDefinition>
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<functionDefinition id="uniform" name="Uniform distribution">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<lambda>
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<bvar>
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<ci> a </ci>
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</bvar>
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<bvar>
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<ci> b </ci>
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</bvar>
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<apply>
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<divide/>
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<apply>
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<plus/>
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<ci> a </ci>
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<ci> b </ci>
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</apply>
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<cn type="integer"> 2 </cn>
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</apply>
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</lambda>
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</math>
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</functionDefinition>
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</listOfFunctionDefinitions>
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<listOfUnitDefinitions>
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<unitDefinition id="nanoMole">
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<listOfUnits>
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<unit kind="mole" exponent="1" scale="-9" multiplier="1"/>
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</listOfUnits>
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</unitDefinition>
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<unitDefinition id="microLitre">
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<listOfUnits>
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<unit kind="litre" exponent="1" scale="-3" 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="iBioSim2" id="CI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
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<annotation>
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<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:Description rdf:about="#iBioSim2">
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<mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0034"/>
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<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_C0051"/>
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<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
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<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
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</rdf:Seq>
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</mts:DNAComponents>
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</rdf:Description>
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</rdf:RDF>
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</ModelToSBOL>
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</annotation>
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</species>
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<species metaid="iBioSim3" id="CI2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim4" sboTerm="SBO:0000590" id="PR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim6" id="CII" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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<species metaid="iBioSim7" sboTerm="SBO:0000590" id="PRE" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
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</listOfSpecies>
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<listOfParameters>
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<parameter metaid="iBioSim10" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
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<parameter metaid="iBioSim11" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim12" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
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<parameter metaid="iBioSim13" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
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<parameter metaid="iBioSim14" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
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<parameter metaid="iBioSim15" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim16" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
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<parameter metaid="iBioSim17" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim18" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
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<parameter metaid="iBioSim19" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim20" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim21" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
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<parameter metaid="iBioSim22" id="nr" name="Initial RNAP count" value="30" constant="true"/>
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<parameter metaid="iBioSim23" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim24" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
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<parameter metaid="iBioSim25" id="ng" name="Initial promoter count" value="2" constant="true"/>
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<parameter metaid="iBioSim26" id="np" name="Stoichiometry of production" value="10" constant="true"/>
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<parameter metaid="iBioSim27" id="ka" name="Activated production rate" value="0.25" constant="true"/>
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<parameter metaid="iBioSim9" id="CI_total" value="0" units="nanoMole" constant="false"/>
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</listOfParameters>
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<listOfRules>
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<assignmentRule metaid="Total" variable="CI_total">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<ci> total </ci>
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<ci> CI </ci>
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<ci> CI2 </ci>
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</apply>
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</math>
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</assignmentRule>
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</listOfRules>
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<listOfConstraints>
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<constraint metaid="CI20">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<leq/>
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<ci> CI </ci>
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<cn type="integer"> 20 </cn>
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</apply>
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</math>
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</constraint>
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<constraint metaid="CII50">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<leq/>
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<ci> CII </ci>
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<cn type="integer"> 50 </cn>
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</apply>
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</math>
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</constraint>
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</listOfConstraints>
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<listOfReactions>
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<reaction metaid="iBioSim28" sboTerm="SBO:0000179" id="Degradation_CI" reversible="false" fast="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="CI" 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> CI </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim29" sboTerm="SBO:0000177" id="Complex_CI2" reversible="true" fast="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="CI" stoichiometry="2" constant="true"/>
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</listOfReactants>
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<listOfProducts>
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<speciesReference species="CI2" 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> kc_f </ci>
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<apply>
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<power/>
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<ci> CI </ci>
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<ci> nc </ci>
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</apply>
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</apply>
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<apply>
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<times/>
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<ci> kc_r </ci>
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<ci> CI2 </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="kc_f" value="0.1"/>
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<localParameter id="kc_r" value="1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim30" sboTerm="SBO:0000179" id="Degradation_CI2" reversible="false" fast="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="CI2" 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> CI2 </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim5" sboTerm="SBO:0000589" id="Production_PR" reversible="false" fast="false" compartment="Cell">
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<annotation>
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<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
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<rdf:Description rdf:about="#iBioSim5">
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<mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_R0051"/>
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</rdf:Seq>
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</mts:DNAComponents>
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</rdf:Description>
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</rdf:RDF>
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</ModelToSBOL>
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</annotation>
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<listOfProducts>
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<speciesReference species="CII" stoichiometry="10" constant="true"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference sboTerm="SBO:0000598" species="PR"/>
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<modifierSpeciesReference sboTerm="SBO:0000020" species="CI2"/>
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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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<divide/>
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<apply>
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<times/>
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<ci> PR </ci>
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<ci> ko </ci>
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<apply>
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<divide/>
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<ci> ko_f </ci>
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<ci> ko_r </ci>
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</apply>
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<ci> nr </ci>
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</apply>
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<apply>
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<plus/>
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<cn type="integer"> 1 </cn>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> ko_f </ci>
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<ci> ko_r </ci>
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</apply>
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<ci> nr </ci>
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</apply>
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<apply>
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<power/>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> kr_CI2_f </ci>
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<ci> kr_CI2_r </ci>
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</apply>
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<ci> CI2 </ci>
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</apply>
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<ci> nc_CI2_r </ci>
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</apply>
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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="nc_CI2_r" value="1"/>
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<localParameter id="kr_CI2_f" value="0.2165"/>
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<localParameter id="kr_CI2_r" value="1"/>
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<localParameter id="ko" value="0.014"/>
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<localParameter id="ko_f" value="0.69422"/>
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<localParameter id="ko_r" value="1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim31" sboTerm="SBO:0000179" id="Degradation_CII" reversible="false" fast="false" compartment="Cell">
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<listOfReactants>
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<speciesReference species="CII" 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> CII </ci>
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</apply>
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</math>
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</kineticLaw>
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</reaction>
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<reaction metaid="iBioSim8" sboTerm="SBO:0000589" id="Production_PRE" reversible="false" fast="false" compartment="Cell">
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<listOfProducts>
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<speciesReference species="CI" stoichiometry="10" constant="true"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference sboTerm="SBO:0000598" species="PRE"/>
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<modifierSpeciesReference sboTerm="SBO:0000459" species="CII"/>
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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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<divide/>
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<apply>
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<times/>
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<ci> PRE </ci>
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<apply>
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<plus/>
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<apply>
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<times/>
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<ci> kb </ci>
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<apply>
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<divide/>
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<ci> ko_f </ci>
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<ci> ko_r </ci>
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</apply>
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<ci> nr </ci>
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</apply>
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<apply>
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<times/>
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<ci> ka </ci>
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<apply>
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<divide/>
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<ci> kao_f </ci>
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<ci> kao_r </ci>
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</apply>
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<ci> nr </ci>
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<apply>
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<power/>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> ka_CII_f </ci>
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<ci> ka_CII_r </ci>
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</apply>
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<ci> CII </ci>
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</apply>
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<ci> nc_CII_a </ci>
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</apply>
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</apply>
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</apply>
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</apply>
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<apply>
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<plus/>
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<cn type="integer"> 1 </cn>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> ko_f </ci>
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<ci> ko_r </ci>
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</apply>
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<ci> nr </ci>
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</apply>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> kao_f </ci>
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<ci> kao_r </ci>
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</apply>
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<ci> nr </ci>
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<apply>
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<power/>
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<apply>
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<times/>
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<apply>
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<divide/>
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<ci> ka_CII_f </ci>
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<ci> ka_CII_r </ci>
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</apply>
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<ci> CII </ci>
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</apply>
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<ci> nc_CII_a </ci>
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</apply>
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</apply>
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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="kb" value="4e-05"/>
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<localParameter id="ka" value="0.015"/>
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<localParameter id="ko_f" value="0.01"/>
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<localParameter id="ko_r" value="1"/>
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<localParameter id="nc_CII_a" value="1"/>
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<localParameter id="ka_CII_f" value="0.00161"/>
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<localParameter id="ka_CII_r" value="1"/>
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</listOfLocalParameters>
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</kineticLaw>
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</reaction>
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</listOfReactions>
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|
<listOfEvents>
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|
<event id="CellDivision" useValuesFromTriggerTime="false">
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|
<annotation>
|
|
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="Symmetric Division"/>
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</annotation>
|
|
<trigger initialValue="false" persistent="false">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<true/>
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</math>
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|
</trigger>
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|
<delay>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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|
<cn type="integer"> 2100 </cn>
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|
</math>
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|
</delay>
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|
<listOfEventAssignments>
|
|
<eventAssignment variable="CI">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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|
<divide/>
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<ci> CI </ci>
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<apply>
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<ci> uniform </ci>
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<cn type="integer"> 1 </cn>
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<cn type="integer"> 2 </cn>
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</apply>
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</apply>
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</math>
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</eventAssignment>
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<eventAssignment variable="CI2">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
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<divide/>
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<ci> CI2 </ci>
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<apply>
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|
<ci> uniform </ci>
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<cn type="integer"> 1 </cn>
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<cn type="integer"> 2 </cn>
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</apply>
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</apply>
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</math>
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</eventAssignment>
|
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<eventAssignment variable="CII">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<apply>
|
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<divide/>
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<ci> CII </ci>
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<apply>
|
|
<ci> uniform </ci>
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<cn type="integer"> 1 </cn>
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<cn type="integer"> 2 </cn>
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</apply>
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</apply>
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</math>
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</eventAssignment>
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</listOfEventAssignments>
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</event>
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</listOfEvents>
|
|
<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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<layout:layout layout:id="iBioSim">
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</layout:compartmentGlyph>
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<layout:listOfSpeciesGlyphs>
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</layout:boundingBox>
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</layout:speciesGlyph>
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<layout:dimensions layout:width="100" layout:height="30"/>
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</layout:boundingBox>
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<layout:dimensions layout:width="100" layout:height="30"/>
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</layout:boundingBox>
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</layout:speciesGlyph>
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<layout:speciesGlyph layout:id="Glyph__CII" layout:species="CII">
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<layout:dimensions layout:width="100" layout:height="30"/>
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</layout:boundingBox>
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</layout:speciesGlyph>
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</layout:listOfSpeciesGlyphs>
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="Glyph__CI__product__CI2" layout:speciesGlyph="Glyph__CI2" layout:role="product">
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="Glyph__PR__product__CII" layout:speciesGlyph="Glyph__CII" layout:role="product">
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<layout:curve>
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<layout:reactionGlyph layout:id="Glyph__CI2__repression__PR">
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<layout:textGlyph layout:id="TextGlyph__CI2" layout:text="CI2" layout:graphicalObject="Glyph__CI2">
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<layout:textGlyph layout:id="TextGlyph__CII" layout:text="CII" layout:graphicalObject="Glyph__CII">
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<layout:textGlyph layout:id="TextGlyph__CI_total" layout:text="CI_total" layout:graphicalObject="Glyph__CI_total">
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