644 lines
No EOL
29 KiB
XML
644 lines
No EOL
29 KiB
XML
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
|
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" version="1" layout:required="false">
|
|
<model id="lambda" metaid="iBioSim1" timeUnits="second" extentUnits="nanoMole" substanceUnits="nanoMole" volumeUnits="microLitre">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#"><rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:about="#iBioSim1"><mts:DNAComponents><rdf:Seq><rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_9_31_2013_17_14_57_346_iBioSim"/></rdf:Seq></mts:DNAComponents></rdf:Description></rdf:RDF></ModelToSBOL> </annotation>
|
|
<layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
|
<layout:layout layout:id="iBioSim">
|
|
<layout:dimensions layout:width="0" layout:height="0"/>
|
|
<layout:listOfAdditionalGraphicalObjects>
|
|
<layout:generalGlyph layout:reference="CI_total" layout:id="Glyph__CI_total">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="30" layout:y="120"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:generalGlyph>
|
|
<layout:generalGlyph layout:reference="Total" layout:id="Glyph__Total">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="200"/>
|
|
<layout:dimensions layout:width="50" layout:height="50"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:id="Glyph__Total__substrate__CI" layout:role="substrate" layout:glyph="Glyph__CI"/>
|
|
<layout:referenceGlyph layout:id="Glyph__Total__substrate__CI2" layout:role="substrate" layout:glyph="Glyph__CI2"/>
|
|
<layout:referenceGlyph layout:id="Glyph__Total__product__CI_total" layout:role="product" layout:glyph="Glyph__CI_total"/>
|
|
</layout:listOfReferenceGlyphs>
|
|
</layout:generalGlyph>
|
|
<layout:generalGlyph layout:reference="CI20" layout:id="Glyph__CI20">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="310" layout:y="20"/>
|
|
<layout:dimensions layout:width="50" layout:height="40"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:id="Glyph__CI20__substrate__CI" layout:role="substrate" layout:glyph="Glyph__CI"/>
|
|
</layout:listOfReferenceGlyphs>
|
|
</layout:generalGlyph>
|
|
<layout:generalGlyph layout:reference="CellDivision" layout:id="Glyph__CellDivision">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="350" layout:y="90"/>
|
|
<layout:dimensions layout:width="75" layout:height="25"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CI" layout:role="substrate" layout:glyph="Glyph__CI"/>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI" layout:role="product" layout:glyph="Glyph__CI"/>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CI2" layout:role="substrate" layout:glyph="Glyph__CI2"/>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI2" layout:role="product" layout:glyph="Glyph__CI2"/>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CII" layout:role="substrate" layout:glyph="Glyph__CII"/>
|
|
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CII" layout:role="product" layout:glyph="Glyph__CII"/>
|
|
</layout:listOfReferenceGlyphs>
|
|
</layout:generalGlyph>
|
|
<layout:generalGlyph layout:reference="CII50" layout:id="Glyph__CII50">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="488" layout:y="174"/>
|
|
<layout:dimensions layout:width="50" layout:height="40"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:id="Glyph__CII50__substrate__CII" layout:role="substrate" layout:glyph="Glyph__CII"/>
|
|
</layout:listOfReferenceGlyphs>
|
|
</layout:generalGlyph>
|
|
</layout:listOfAdditionalGraphicalObjects>
|
|
<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__CI" layout:species="CI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="86" layout:y="50"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__CI2" layout:species="CI2">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="103" layout:y="202"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__PR" layout:species="PR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="150" layout:y="340"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__CII" layout:species="CII">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="320" layout:y="200"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
</layout:listOfSpeciesGlyphs>
|
|
<layout:listOfReactionGlyphs>
|
|
<layout:reactionGlyph layout:id="Glyph__CI__complex__CI2">
|
|
<layout:boundingBox>
|
|
<layout:position/>
|
|
<layout:dimensions/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__CI__product__CI2" layout:role="product" layout:speciesGlyph="Glyph__CI2"/>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__PR__Production__CII">
|
|
<layout:boundingBox>
|
|
<layout:position/>
|
|
<layout:dimensions/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__PR__product__CII" layout:role="product" layout:speciesGlyph="Glyph__CII"/>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__CI2__repression__PR">
|
|
<layout:boundingBox>
|
|
<layout:position/>
|
|
<layout:dimensions/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__CI2__product__PR" layout:role="product" layout:speciesGlyph="Glyph__PR"/>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__CII__repression__CI">
|
|
<layout:boundingBox>
|
|
<layout:position/>
|
|
<layout:dimensions/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__CII__product__CI" layout:role="product" layout:speciesGlyph="Glyph__CI"/>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
</layout:listOfReactionGlyphs>
|
|
<layout:listOfTextGlyphs>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="0"/>
|
|
<layout:dimensions layout:width="1070" layout:height="425"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CI" layout:id="TextGlyph__CI" layout:text="CI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="86" layout:y="50"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CI2" layout:id="TextGlyph__CI2" layout:text="CI2">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="103" layout:y="202"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__PR" layout:id="TextGlyph__PR" layout:text="PR">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="150" layout:y="340"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CII" layout:id="TextGlyph__CII" layout:text="CII">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="320" layout:y="200"/>
|
|
<layout:dimensions layout:width="100" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CI_total" layout:id="TextGlyph__CI_total" layout:text="CI_total">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="30" layout:y="120"/>
|
|
<layout:dimensions layout:width="30" layout:height="30"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__Total" layout:id="TextGlyph__Total" layout:text="Total">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="200"/>
|
|
<layout:dimensions layout:width="50" layout:height="50"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CI20" layout:id="TextGlyph__CI20" layout:text="CI20">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="310" layout:y="20"/>
|
|
<layout:dimensions layout:width="50" layout:height="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CellDivision" layout:id="TextGlyph__CellDivision" layout:text="CellDivision">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="350" layout:y="90"/>
|
|
<layout:dimensions layout:width="75" layout:height="25"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__CII50" layout:id="TextGlyph__CII50" layout:text="CII50">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="488" layout:y="174"/>
|
|
<layout:dimensions layout:width="50" layout:height="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
</layout:listOfTextGlyphs>
|
|
</layout:layout>
|
|
</layout:listOfLayouts>
|
|
<listOfFunctionDefinitions>
|
|
<functionDefinition id="total" name="Find total molecules">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<lambda>
|
|
<bvar>
|
|
<ci> x </ci>
|
|
</bvar>
|
|
<bvar>
|
|
<ci> y </ci>
|
|
</bvar>
|
|
<apply>
|
|
<plus/>
|
|
<ci> x </ci>
|
|
<apply>
|
|
<times/>
|
|
<cn type="integer"> 2 </cn>
|
|
<ci> y </ci>
|
|
</apply>
|
|
</apply>
|
|
</lambda>
|
|
</math>
|
|
</functionDefinition>
|
|
<functionDefinition id="uniform" name="Uniform distribution">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<lambda>
|
|
<bvar>
|
|
<ci> a </ci>
|
|
</bvar>
|
|
<bvar>
|
|
<ci> b </ci>
|
|
</bvar>
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<plus/>
|
|
<ci> a </ci>
|
|
<ci> b </ci>
|
|
</apply>
|
|
<cn type="integer"> 2 </cn>
|
|
</apply>
|
|
</lambda>
|
|
</math>
|
|
</functionDefinition>
|
|
</listOfFunctionDefinitions>
|
|
<listOfUnitDefinitions>
|
|
<unitDefinition id="nanoMole">
|
|
<listOfUnits>
|
|
<unit scale="-9" exponent="1" multiplier="1" kind="mole"/>
|
|
</listOfUnits>
|
|
</unitDefinition>
|
|
<unitDefinition id="microLitre">
|
|
<listOfUnits>
|
|
<unit scale="-3" exponent="1" multiplier="1" kind="litre"/>
|
|
</listOfUnits>
|
|
</unitDefinition>
|
|
</listOfUnitDefinitions>
|
|
<listOfCompartments>
|
|
<compartment id="Cell" constant="true" spatialDimensions="3" size="1">
|
|
<annotation>
|
|
</annotation>
|
|
</compartment>
|
|
</listOfCompartments>
|
|
<listOfSpecies>
|
|
<species id="CI" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim2" boundaryCondition="false" compartment="Cell">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
|
<rdf:Description rdf:about="#iBioSim2">
|
|
<mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0034"/>
|
|
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_C0051"/>
|
|
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
|
|
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
|
|
</rdf:Seq>
|
|
</mts:DNAComponents>
|
|
</rdf:Description>
|
|
</rdf:RDF>
|
|
</ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
<species id="CI2" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim3" boundaryCondition="false" compartment="Cell"/>
|
|
<species id="PR" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim4" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
|
|
<species id="CII" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim6" boundaryCondition="false" compartment="Cell"/>
|
|
<species id="PRE" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim7" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
|
|
</listOfSpecies>
|
|
<listOfParameters>
|
|
<parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim10" value="0.0075"/>
|
|
<parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim11" value="0.05"/>
|
|
<parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim12" value="1"/>
|
|
<parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim13" value="2"/>
|
|
<parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim14" value="0.5"/>
|
|
<parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim15" value="1"/>
|
|
<parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim16" value="0.0033"/>
|
|
<parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim17" value="1"/>
|
|
<parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim18" value="0.033"/>
|
|
<parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim19" value="1"/>
|
|
<parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim20" value="1"/>
|
|
<parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim21" value="1"/>
|
|
<parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim22" value="30"/>
|
|
<parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim23" value="0.05"/>
|
|
<parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim24" value="0.0001"/>
|
|
<parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim25" value="2"/>
|
|
<parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim26" value="10"/>
|
|
<parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim27" value="0.25"/>
|
|
<parameter id="CI_total" constant="false" metaid="iBioSim9" value="0" units="nanoMole"/>
|
|
</listOfParameters>
|
|
<listOfRules>
|
|
<assignmentRule metaid="Total" variable="CI_total">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<ci> total </ci>
|
|
<ci> CI </ci>
|
|
<ci> CI2 </ci>
|
|
</apply>
|
|
</math>
|
|
</assignmentRule>
|
|
</listOfRules>
|
|
<listOfConstraints>
|
|
<constraint metaid="CI20">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<leq/>
|
|
<ci> CI </ci>
|
|
<cn type="integer"> 20 </cn>
|
|
</apply>
|
|
</math>
|
|
</constraint>
|
|
<constraint metaid="CII50">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<leq/>
|
|
<ci> CII </ci>
|
|
<cn type="integer"> 50 </cn>
|
|
</apply>
|
|
</math>
|
|
</constraint>
|
|
</listOfConstraints>
|
|
<listOfReactions>
|
|
<reaction id="Degradation_CI" metaid="iBioSim28" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
|
<listOfReactants>
|
|
<speciesReference constant="true" species="CI" stoichiometry="1"/>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> CI </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction id="Complex_CI2" metaid="iBioSim29" reversible="true" sboTerm="SBO:0000177" fast="false" compartment="Cell">
|
|
<listOfReactants>
|
|
<speciesReference constant="true" species="CI" stoichiometry="2"/>
|
|
</listOfReactants>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" species="CI2" stoichiometry="1"/>
|
|
</listOfProducts>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<minus/>
|
|
<apply>
|
|
<times/>
|
|
<ci> kc_f </ci>
|
|
<apply>
|
|
<power/>
|
|
<ci> CI </ci>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<ci> kc_r </ci>
|
|
<ci> CI2 </ci>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
<listOfLocalParameters>
|
|
<localParameter id="kc_f" value="0.1"/>
|
|
<localParameter id="kc_r" value="1"/>
|
|
</listOfLocalParameters>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction id="Degradation_CI2" metaid="iBioSim30" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
|
<listOfReactants>
|
|
<speciesReference constant="true" species="CI2" stoichiometry="1"/>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> CI2 </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction id="Production_PR" metaid="iBioSim5" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
|
<rdf:Description rdf:about="#iBioSim5">
|
|
<mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_R0051"/>
|
|
</rdf:Seq>
|
|
</mts:DNAComponents>
|
|
</rdf:Description>
|
|
</rdf:RDF>
|
|
</ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" species="CII" stoichiometry="10"/>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference species="PR" sboTerm="SBO:0000598"/>
|
|
<modifierSpeciesReference species="CI2" sboTerm="SBO:0000020"/>
|
|
</listOfModifiers>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> PR </ci>
|
|
<ci> ko </ci>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kr_CI2_f </ci>
|
|
<ci> kr_CI2_r </ci>
|
|
</apply>
|
|
<ci> CI2 </ci>
|
|
</apply>
|
|
<ci> nc_CI2_r </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
<listOfLocalParameters>
|
|
<localParameter id="nc_CI2_r" value="1"/>
|
|
<localParameter id="kr_CI2_f" value="0.2165"/>
|
|
<localParameter id="kr_CI2_r" value="1"/>
|
|
<localParameter id="ko" value="0.014"/>
|
|
<localParameter id="ko_f" value="0.69422"/>
|
|
<localParameter id="ko_r" value="1"/>
|
|
</listOfLocalParameters>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction id="Degradation_CII" metaid="iBioSim31" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
|
<listOfReactants>
|
|
<speciesReference constant="true" species="CII" stoichiometry="1"/>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> CII </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction id="Production_PRE" metaid="iBioSim8" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
|
|
<listOfProducts>
|
|
<speciesReference constant="true" species="CI" stoichiometry="10"/>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference species="PRE" sboTerm="SBO:0000598"/>
|
|
<modifierSpeciesReference species="CII" sboTerm="SBO:0000459"/>
|
|
</listOfModifiers>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> PRE </ci>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<times/>
|
|
<ci> kb </ci>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<ci> ka </ci>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kao_f </ci>
|
|
<ci> kao_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ka_CII_f </ci>
|
|
<ci> ka_CII_r </ci>
|
|
</apply>
|
|
<ci> CII </ci>
|
|
</apply>
|
|
<ci> nc_CII_a </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kao_f </ci>
|
|
<ci> kao_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ka_CII_f </ci>
|
|
<ci> ka_CII_r </ci>
|
|
</apply>
|
|
<ci> CII </ci>
|
|
</apply>
|
|
<ci> nc_CII_a </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
<listOfLocalParameters>
|
|
<localParameter id="kb" value="4E-5"/>
|
|
<localParameter id="ka" value="0.015"/>
|
|
<localParameter id="ko_f" value="0.01"/>
|
|
<localParameter id="ko_r" value="1"/>
|
|
<localParameter id="nc_CII_a" value="1"/>
|
|
<localParameter id="ka_CII_f" value="0.00161"/>
|
|
<localParameter id="ka_CII_r" value="1"/>
|
|
</listOfLocalParameters>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
<listOfEvents>
|
|
<event id="CellDivision" useValuesFromTriggerTime="false">
|
|
<annotation>
|
|
<ibiosim:ibiosim ibiosim:type="Symmetric Division" xmlns:ibiosim="http://www.fakeuri.com"/>
|
|
</annotation>
|
|
<trigger persistent="false" initialValue="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"> 2100 </cn>
|
|
</math>
|
|
</delay>
|
|
<listOfEventAssignments>
|
|
<eventAssignment variable="CI">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<ci> CI </ci>
|
|
<apply>
|
|
<ci> uniform </ci>
|
|
<cn type="integer"> 1 </cn>
|
|
<cn type="integer"> 2 </cn>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</eventAssignment>
|
|
<eventAssignment variable="CI2">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<ci> CI2 </ci>
|
|
<apply>
|
|
<ci> uniform </ci>
|
|
<cn type="integer"> 1 </cn>
|
|
<cn type="integer"> 2 </cn>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</eventAssignment>
|
|
<eventAssignment variable="CII">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<ci> CII </ci>
|
|
<apply>
|
|
<ci> uniform </ci>
|
|
<cn type="integer"> 1 </cn>
|
|
<cn type="integer"> 2 </cn>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</eventAssignment>
|
|
</listOfEventAssignments>
|
|
</event>
|
|
</listOfEvents>
|
|
</model>
|
|
</sbml> |