263 lines
No EOL
12 KiB
XML
263 lines
No EOL
12 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" fbc:required="false" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
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<model id="DSensor" metaid="iBioSim6">
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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:port comp:id="output__S1" comp:idRef="S1" sboTerm="SBO:0000601"/>
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<comp:port comp:id="Degradation_S1" comp:idRef="Degradation_S1" sboTerm="SBO:0000601"/>
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<comp:port comp:id="input__D" comp:idRef="D" sboTerm="SBO:0000600"/>
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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: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__D" layout:species="D">
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<layout:boundingBox>
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<layout:position layout:x="120" layout:y="127"/>
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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__S1" layout:species="S1">
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<layout:boundingBox>
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<layout:position layout:x="490" layout:y="130"/>
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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__P0" layout:species="P0">
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<layout:boundingBox>
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<layout:position layout:x="303" layout:y="151"/>
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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:listOfReactionGlyphs>
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<layout:reactionGlyph layout:id="Glyph__P0__Production__S1">
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<layout:boundingBox>
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<layout:position layout:x="540" layout:y="145"/>
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<layout:dimensions layout:height="0" layout:width="0"/>
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</layout:boundingBox>
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__P0__Production__S1" layout:role="product" layout:speciesGlyph="Glyph__S1">
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<layout:curve>
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<layout:listOfCurveSegments>
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<layout:curveSegment xsi:type="LineSegment">
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<layout:start layout:x="353" layout:y="166"/>
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<layout:end layout:x="540" layout:y="145"/>
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</layout:curve>
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</layout:speciesReferenceGlyph>
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</layout:listOfSpeciesReferenceGlyphs>
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</layout:reactionGlyph>
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<layout:reactionGlyph layout:id="Glyph__D__activation__P0">
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<layout:boundingBox>
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<layout:position layout:x="353" layout:y="166"/>
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<layout:dimensions layout:height="0" layout:width="0"/>
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</layout:boundingBox>
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__D__activation__P0" layout:role="product" layout:speciesGlyph="Glyph__P0">
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<layout:curve>
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<layout:listOfCurveSegments>
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<layout:curveSegment xsi:type="LineSegment">
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<layout:start layout:x="170" layout:y="142"/>
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<layout:end layout:x="353" layout:y="166"/>
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</layout:curveSegment>
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</layout:listOfCurveSegments>
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</layout:curve>
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</layout:speciesReferenceGlyph>
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</layout:listOfSpeciesReferenceGlyphs>
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</layout:reactionGlyph>
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</layout:listOfReactionGlyphs>
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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__D" layout:id="TextGlyph__D" layout:text="D">
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<layout:boundingBox>
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<layout:position layout:x="120" layout:y="127"/>
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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__S1" layout:id="TextGlyph__S1" layout:text="S1">
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<layout:boundingBox>
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<layout:position layout:x="490" layout:y="130"/>
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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__P0" layout:id="TextGlyph__P0" layout:text="P0">
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<layout:boundingBox>
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<layout:position layout:x="303" layout:y="151"/>
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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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</listOfCompartments>
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<listOfSpecies>
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<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="D" initialAmount="60" metaid="iBioSim1"/>
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<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="0" metaid="iBioSim3"/>
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<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="P0" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590"/>
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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="iBioSim7" name="Reverse repression binding rate" value="1"/>
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<parameter constant="true" id="ka_f" metaid="iBioSim8" name="Forward activation binding rate" value="0.0033"/>
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<parameter constant="true" id="ka_r" metaid="iBioSim9" name="Reverse activation binding rate" value="1"/>
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<parameter constant="true" id="ko_f" metaid="iBioSim10" name="Forward RNAP binding rate" value="0.033"/>
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<parameter constant="true" id="ko_r" metaid="iBioSim11" name="Reverse RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_f" metaid="iBioSim12" name="Forward activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_r" metaid="iBioSim13" name="Reverse activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="nc" metaid="iBioSim14" name="Stoichiometry of binding" value="2"/>
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<parameter constant="true" id="nr" metaid="iBioSim15" name="Initial RNAP count" value="30"/>
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<parameter constant="true" id="ko" metaid="iBioSim16" name="Open complex production rate" value="0.05"/>
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<parameter constant="true" id="kb" metaid="iBioSim17" name="Basal production rate" value="0.0001"/>
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<parameter constant="true" id="ng" metaid="iBioSim18" name="Initial promoter count" value="2"/>
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<parameter constant="true" id="np" metaid="iBioSim19" name="Stoichiometry of production" value="10"/>
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<parameter constant="true" id="ka" metaid="iBioSim20" name="Activated production rate" value="0.25"/>
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<parameter constant="true" id="kd" metaid="iBioSim21" 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="Production_P0" metaid="iBioSim5" reversible="false" sboTerm="SBO:0000589">
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<listOfReactants/>
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<listOfProducts>
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<speciesReference constant="true" species="S1" stoichiometry="10"/>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference sboTerm="SBO:0000598" species="P0"/>
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<modifierSpeciesReference sboTerm="SBO:0000459" species="D"/>
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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> P0 </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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<apply>
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<divide/>
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<apply>
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<times/>
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<ci> kb </ci>
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<ci> ko_f </ci>
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</apply>
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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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<times/>
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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> ka </ci>
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<ci> kao_f </ci>
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</apply>
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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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<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_f </ci>
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<ci> ka_r </ci>
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</apply>
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<ci> D </ci>
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</apply>
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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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</apply>
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<apply>
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<plus/>
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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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<apply>
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<times/>
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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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<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_f </ci>
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<ci> ka_r </ci>
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</apply>
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<ci> D </ci>
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</apply>
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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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</apply>
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</math>
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<listOfLocalParameters/>
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</kineticLaw>
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</reaction>
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<reaction compartment="Cell" id="Degradation_S1" metaid="iBioSim22" reversible="false" sboTerm="SBO:0000179">
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<listOfReactants>
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<speciesReference constant="true" species="S1" 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> S1 </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> |