508 lines
No EOL
28 KiB
XML
508 lines
No EOL
28 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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<model id="HlyIIRpart_module" metaid="iBioSim13">
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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:ModuleDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/1"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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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__HlyIIR_protein" comp:idRef="HlyIIR_protein" sboTerm="SBO:0000601"/>
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<comp:port comp:id="input__TetR_protein" comp:idRef="TetR_protein" sboTerm="SBO:0000600"/>
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<comp:port comp:id="input__Ara_AraC_protein" comp:idRef="Ara_AraC_protein" 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: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__pTet" layout:species="pTet">
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<layout:boundingBox>
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<layout:position layout:x="130" layout:y="90"/>
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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__pBAD" layout:species="pBAD">
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<layout:boundingBox>
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<layout:position layout:x="0" layout:y="90"/>
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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__HlyIIR_protein" layout:species="HlyIIR_protein">
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<layout:boundingBox>
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</layout:boundingBox>
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</layout:speciesGlyph>
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<layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
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<layout:boundingBox>
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<layout:position layout:x="28" layout:y="0"/>
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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__pTet__Production__HlyIIR_protein">
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</layout:boundingBox>
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__pTet__Production__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
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<layout:listOfCurveSegments>
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<layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__activation__pTet">
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:listOfSpeciesReferenceGlyphs>
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</layout:reactionGlyph>
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<layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__pBAD">
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<layout:boundingBox>
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<layout:listOfSpeciesReferenceGlyphs>
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<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__pBAD" layout:role="product" layout:speciesGlyph="Glyph__pBAD">
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<layout:curveSegment xsi:type="LineSegment">
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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__pTet" layout:id="TextGlyph__pTet" layout:text="pTet">
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<layout:boundingBox>
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<layout:position layout:x="130" layout:y="90"/>
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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__pBAD" layout:id="TextGlyph__pBAD" layout:text="pBAD">
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<layout:boundingBox>
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<layout:position layout:x="0" layout:y="90"/>
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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__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
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<layout:boundingBox>
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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__HlyIIR_protein" layout:id="TextGlyph__HlyIIR_protein" layout:text="HlyIIR_protein">
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<layout:boundingBox>
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<layout:position layout:x="95" layout:y="194.4775390625"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:graphicalObject="Glyph__TetR_protein" layout:id="TextGlyph__TetR_protein" layout:text="TetR_protein">
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<layout:boundingBox>
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<layout:position layout:x="28" layout:y="0"/>
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<layout:dimensions layout:height="40" layout:width="40"/>
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</layout:boundingBox>
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</layout:textGlyph>
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<layout:textGlyph layout:graphicalObject="Glyph__Ara_AraC_protein" layout:id="TextGlyph__Ara_AraC_protein" layout:text="Ara_AraC_protein">
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<layout:boundingBox>
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<layout:position layout:x="130" layout:y="5"/>
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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="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="HlyIIR_protein" initialAmount="0" metaid="iBioSim2" sboTerm="SBO:0000252">
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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:ComponentDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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</species>
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<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="TetR_protein" initialAmount="0" metaid="iBioSim3" sboTerm="SBO:0000252">
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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="#iBioSim3">
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<mts:ComponentDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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</species>
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<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pTet" initialAmount="2" metaid="iBioSim4" sboTerm="SBO:0000590">
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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="#iBioSim4">
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<mts:ComponentDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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</species>
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<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="pBAD" initialAmount="2" metaid="iBioSim5" sboTerm="SBO:0000590">
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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:ComponentDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
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<rdf:Seq>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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</species>
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<species boundaryCondition="true" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="Ara_AraC_protein" initialAmount="0" metaid="iBioSim6" sboTerm="SBO:0000253">
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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="#iBioSim6">
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<mts:ComponentDefinitions>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
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<rdf:Bag>
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<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:FunctionalComponents></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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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="iBioSim1" name="Forward repression binding rate" value="0.5"/>
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<parameter constant="true" id="kr_r" metaid="iBioSim14" name="Reverse repression binding rate" value="1"/>
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<parameter constant="true" id="ka_f" metaid="iBioSim15" name="Forward activation binding rate" value="0.0033"/>
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<parameter constant="true" id="ka_r" metaid="iBioSim16" name="Reverse activation binding rate" value="1"/>
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<parameter constant="true" id="ko_f" metaid="iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
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<parameter constant="true" id="ko_r" metaid="iBioSim18" name="Reverse RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_f" metaid="iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="kao_r" metaid="iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
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<parameter constant="true" id="nc" metaid="iBioSim21" name="Stoichiometry of binding" value="2"/>
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<parameter constant="true" id="nr" metaid="iBioSim22" name="Initial RNAP count" value="30"/>
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<parameter constant="true" id="ko" metaid="iBioSim23" name="Open complex production rate" value="0.05"/>
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<parameter constant="true" id="kb" metaid="iBioSim24" name="Basal production rate" value="0.0001"/>
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<parameter constant="true" id="ng" metaid="iBioSim25" name="Initial promoter count" value="2"/>
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<parameter constant="true" id="np" metaid="iBioSim26" name="Stoichiometry of production" value="10"/>
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<parameter constant="true" id="ka" metaid="iBioSim27" name="Activated production rate" value="0.25"/>
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</listOfParameters>
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<listOfConstraints/>
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<listOfReactions>
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<reaction compartment="Cell" id="HlyIIR_protein_interaction_0" metaid="iBioSim7" reversible="false" sboTerm="SBO:0000589">
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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="#iBioSim7">
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<mts:Interactions>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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<listOfProducts>
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<speciesReference constant="true" metaid="iBioSim9" species="HlyIIR_protein" stoichiometry="10">
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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="#iBioSim9">
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<mts:Participations>
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<rdf:Bag>
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<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
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</annotation>
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</speciesReference>
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</listOfProducts>
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<listOfModifiers>
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<modifierSpeciesReference sboTerm="SBO:0000598" species="pTet">
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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="#">
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|
<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="iBioSim8" sboTerm="SBO:0000459" species="Ara_AraC_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/HlyIIRpart_module/Ara_AraC_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/>
|
|
<ci> pTet </ci>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> kb </ci>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ko_f </ci>
|
|
<ci> ko_r </ci>
|
|
</apply>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> ka </ci>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kao_f </ci>
|
|
<ci> kao_r </ci>
|
|
</apply>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ka_f </ci>
|
|
<ci> ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</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>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> kao_f </ci>
|
|
<ci> kao_r </ci>
|
|
</apply>
|
|
<ci> nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> ka_f </ci>
|
|
<ci> ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="HlyIIR_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/HlyIIRpart_module/HlyIIR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="iBioSim12" species="HlyIIR_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/HlyIIRpart_module/HlyIIR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="pBAD">
|
|
<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/HlyIIRpart_module/TetR_protein_pTet_repression/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/HlyIIR_protein_interaction/HlyIIRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart_module/Ara_AraC_protein_pBAD_activation/HlyIIRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="iBioSim11" sboTerm="SBO:0000020" species="TetR_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/HlyIIRpart_module/TetR_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> pBAD </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> TetR_protein </ci>
|
|
</apply>
|
|
<ci> nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
<listOfEvents/>
|
|
</model>
|
|
</sbml> |