464 lines
No EOL
27 KiB
XML
464 lines
No EOL
27 KiB
XML
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
|
<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">
|
|
<model id="YFPpart_module" metaid="iBioSim13">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim1">
|
|
<mts:ModuleDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
|
|
<comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
|
|
<comp:port comp:id="output__YFP_protein" comp:idRef="YFP_protein" sboTerm="SBO:0000601"/>
|
|
<comp:port comp:id="input__BetI_protein" comp:idRef="BetI_protein" sboTerm="SBO:0000600"/>
|
|
<comp:port comp:id="input__PhlF_protein" comp:idRef="PhlF_protein" sboTerm="SBO:0000600"/>
|
|
</comp:listOfPorts>
|
|
<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:depth="0" layout:height="425" layout:width="1070"/>
|
|
<layout:listOfCompartmentGlyphs>
|
|
<layout:compartmentGlyph layout:compartment="Cell" layout:id="Glyph__Cell">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="0"/>
|
|
<layout:dimensions layout:height="425" layout:width="1070"/>
|
|
</layout:boundingBox>
|
|
</layout:compartmentGlyph>
|
|
</layout:listOfCompartmentGlyphs>
|
|
<layout:listOfSpeciesGlyphs>
|
|
<layout:speciesGlyph layout:id="Glyph__pPhlF" layout:species="pPhlF">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="130" layout:y="90"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__pBetI" layout:species="pBetI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="90"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="95" layout:y="194.4775390625"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__BetI_protein" layout:species="BetI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="30" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__PhlF_protein" layout:species="PhlF_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="160" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
</layout:listOfSpeciesGlyphs>
|
|
<layout:listOfReactionGlyphs>
|
|
<layout:reactionGlyph layout:id="Glyph__pPhlF__Production__YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="115" layout:y="214.4775390625"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pPhlF__Production__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="180" layout:y="105"/>
|
|
<layout:end layout:x="115" layout:y="214.4775390625"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__pPhlF">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="180" layout:y="105"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__pPhlF" layout:role="product" layout:speciesGlyph="Glyph__pPhlF">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="180" layout:y="20"/>
|
|
<layout:end layout:x="180" layout:y="105"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__pBetI__Production__YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="115" layout:y="214.4775390625"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pBetI__Production__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="50" layout:y="105"/>
|
|
<layout:end layout:x="115" layout:y="214.4775390625"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__pBetI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="50" layout:y="105"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__BetI_protein__repression__pBetI" layout:role="product" layout:speciesGlyph="Glyph__pBetI">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="50" layout:y="20"/>
|
|
<layout:end layout:x="50" layout:y="105"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
</layout:listOfReactionGlyphs>
|
|
<layout:listOfTextGlyphs>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__pPhlF" layout:id="TextGlyph__pPhlF" layout:text="pPhlF">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="130" layout:y="90"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__pBetI" layout:id="TextGlyph__pBetI" layout:text="pBetI">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="0" layout:y="90"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<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:height="425" layout:width="1070"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__YFP_protein" layout:id="TextGlyph__YFP_protein" layout:text="YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="95" layout:y="194.4775390625"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__BetI_protein" layout:id="TextGlyph__BetI_protein" layout:text="BetI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="30" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__PhlF_protein" layout:id="TextGlyph__PhlF_protein" layout:text="PhlF_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="160" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
</layout:listOfTextGlyphs>
|
|
</layout:layout>
|
|
</layout:listOfLayouts>
|
|
<listOfFunctionDefinitions/>
|
|
<listOfUnitDefinitions/>
|
|
<listOfCompartments>
|
|
<compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
|
|
</listOfCompartments>
|
|
<listOfSpecies>
|
|
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="YFP_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim2">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="BetI_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim3">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pPhlF" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim4">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pBetI" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim5">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="PhlF_protein" initialAmount="0" metaid="iBioSim6" sboTerm="SBO:0000252">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim6">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
</listOfSpecies>
|
|
<listOfParameters>
|
|
<parameter constant="true" id="kr_f" metaid="iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
|
|
</listOfParameters>
|
|
<listOfConstraints/>
|
|
<listOfReactions>
|
|
<reaction compartment="Cell" id="YFP_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim7">
|
|
<mts:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="iBioSim9" species="YFP_protein" stoichiometry="10">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim9">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="pPhlF">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000020" species="PhlF_protein">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim8">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
</listOfModifiers>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> pPhlF </ci>
|
|
<ci> ko </ci>
|
|
</apply>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<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>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kr_f </ci>
|
|
<ci> kr_r </ci>
|
|
</apply>
|
|
<ci> PhlF_protein </ci>
|
|
</apply>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="YFP_protein_interaction_1" metaid="iBioSim10" reversible="false" sboTerm="SBO:0000589">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim10">
|
|
<mts:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="iBioSim12" species="YFP_protein" stoichiometry="10">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim12">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="pBetI">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/PhlF_protein_pPhlF_repression/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/YFP_protein_interaction/YFPpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein_pBetI_repression/YFPpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="BetI_protein">
|
|
<annotation>
|
|
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#">
|
|
<rdf:Description rdf:about="#iBioSim11">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/YFPpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
</listOfModifiers>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> pBetI </ci>
|
|
<ci> ko </ci>
|
|
</apply>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<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>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kr_f </ci>
|
|
<ci> kr_r </ci>
|
|
</apply>
|
|
<ci> BetI_protein </ci>
|
|
</apply>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
<listOfEvents/>
|
|
</model>
|
|
</sbml> |