132 lines
No EOL
7.9 KiB
XML
132 lines
No EOL
7.9 KiB
XML
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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<comp:listOfExternalModelDefinitions xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
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<comp:externalModelDefinition comp:id="DSensor" comp:md5="2b2abc20e4c21f932e52e1ff6c71104c" comp:source="DSensor.xml"/>
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</comp:listOfExternalModelDefinitions>
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<model id="topModel" metaid="iBioSim1">
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<comp:listOfSubmodels xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
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<comp:submodel comp:id="C1" comp:modelRef="DSensor" metaid="iBioSim17"/>
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</comp:listOfSubmodels>
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<comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
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<comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
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</comp:listOfPorts>
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<layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<layout:layout layout:id="iBioSim">
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<layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
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<layout:listOfAdditionalGraphicalObjects>
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<layout:generalGlyph layout:id="Glyph__C1" layout:reference="C1">
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<layout:boundingBox>
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<layout:position layout:x="350" layout:y="160"/>
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<layout:dimensions layout:height="40" layout:width="80"/>
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</layout:boundingBox>
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</layout:generalGlyph>
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</layout:listOfAdditionalGraphicalObjects>
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<layout:listOfCompartmentGlyphs>
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<layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
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<layout:boundingBox>
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<layout:position layout:x="0" layout:y="0"/>
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<layout:dimensions layout:height="425" layout:width="1070"/>
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</layout:boundingBox>
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</layout:compartmentGlyph>
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</layout:listOfCompartmentGlyphs>
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<layout:listOfSpeciesGlyphs>
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<layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
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<layout:boundingBox>
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<layout:position layout:x="160" layout:y="140"/>
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<layout:dimensions layout:height="30" layout:width="100"/>
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</layout:boundingBox>
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</layout:speciesGlyph>
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<layout:speciesGlyph layout:id="Glyph__S3" layout:species="S3">
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<layout:boundingBox>
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<layout:position layout:x="553" layout:y="143"/>
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<layout:dimensions layout:height="30" layout:width="100"/>
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</layout:boundingBox>
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</layout:speciesGlyph>
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</layout:listOfSpeciesGlyphs>
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<layout:listOfTextGlyphs>
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<layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
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<layout:boundingBox>
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<layout:position layout:x="0" layout:y="0"/>
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<layout:dimensions layout:height="425" layout:width="1070"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:graphicalObject="Glyph__C1" layout:id="TextGlyph__C1" layout:text="C1">
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<layout:boundingBox>
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<layout:position layout:x="350" layout:y="160"/>
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<layout:dimensions layout:height="40" layout:width="80"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:graphicalObject="Glyph__S2" layout:id="TextGlyph__S2" layout:text="S2">
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<layout:boundingBox>
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<layout:position layout:x="160" layout:y="140"/>
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<layout:dimensions layout:height="30" layout:width="100"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:graphicalObject="Glyph__S3" layout:id="TextGlyph__S3" layout:text="S3">
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<layout:boundingBox>
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<layout:position layout:x="553" layout:y="143"/>
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<layout:dimensions layout:height="30" layout:width="100"/>
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</layout:boundingBox>
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</layout:textGlyph>
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</layout:listOfTextGlyphs>
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</layout:layout>
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</layout:listOfLayouts>
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<listOfFunctionDefinitions/>
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<listOfUnitDefinitions/>
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<listOfCompartments>
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<compartment constant="true" id="Cell" size="1" spatialDimensions="3">
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<comp:listOfReplacedElements xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
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<comp:replacedElement comp:portRef="compartment__Cell" comp:submodelRef="C1"/>
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</comp:listOfReplacedElements>
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</compartment>
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</listOfCompartments>
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<listOfSpecies>
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<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="60" metaid="iBioSim18">
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<comp:listOfReplacedElements xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
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<comp:replacedElement comp:portRef="input__D" comp:submodelRef="C1"/>
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</comp:listOfReplacedElements>
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</species>
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<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S3" initialAmount="0" metaid="iBioSim19">
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<comp:replacedBy xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:portRef="output__S1" comp:submodelRef="C1"/>
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</species>
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</listOfSpecies>
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<listOfParameters>
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<parameter constant="true" id="kr_f" metaid="iBioSim2" name="Forward repression binding rate" value="0.5"/>
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<parameter constant="true" id="kr_r" metaid="iBioSim3" name="Reverse repression binding rate" value="1"/>
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<parameter constant="true" id="ka_f" metaid="iBioSim4" name="Forward activation binding rate" value="0.0033"/>
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<parameter constant="true" id="ka_r" metaid="iBioSim5" name="Reverse activation binding rate" value="1"/>
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<parameter constant="true" id="ko_f" metaid="iBioSim6" name="Forward RNAP binding rate" value="0.033"/>
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<parameter constant="true" id="ko_r" metaid="iBioSim7" name="Reverse RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_f" metaid="iBioSim8" name="Forward activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_r" metaid="iBioSim9" name="Reverse activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="nc" metaid="iBioSim10" name="Stoichiometry of binding" value="2"/>
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<parameter constant="true" id="nr" metaid="iBioSim11" name="Initial RNAP count" value="30"/>
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<parameter constant="true" id="ko" metaid="iBioSim12" name="Open complex production rate" value="0.05"/>
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<parameter constant="true" id="kb" metaid="iBioSim13" name="Basal production rate" value="0.0001"/>
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<parameter constant="true" id="ng" metaid="iBioSim14" name="Initial promoter count" value="2"/>
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<parameter constant="true" id="np" metaid="iBioSim15" name="Stoichiometry of production" value="10"/>
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<parameter constant="true" id="ka" metaid="iBioSim16" name="Activated production rate" value="0.25"/>
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<parameter constant="true" id="kd" name="Degradation rate" value="0.0075"/>
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</listOfParameters>
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<listOfInitialAssignments/>
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<listOfConstraints/>
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<listOfReactions>
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<reaction compartment="Cell" id="Degradation_S3" reversible="false" sboTerm="SBO:0000179">
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<comp:replacedBy xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:portRef="Degradation_S1" comp:submodelRef="C1"/>
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<listOfReactants>
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<speciesReference constant="true" species="S3" stoichiometry="1"/>
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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> S3 </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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</listOfReactions>
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<listOfEvents/>
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</model>
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</sbml> |