2009 lines
124 KiB
XML
2009 lines
124 KiB
XML
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
|
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" fbc:required="false" layout:required="false" level="2" version="2" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
|
|
<model id="topModel" metaid="iBioSim3" name="Created by iBioSim flatten routine">
|
|
<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/topModel"/></rdf:Bag></mts:ModuleDefinitions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2"/>
|
|
<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:listOfAdditionalGraphicalObjects>
|
|
<layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="120" layout:y="300"/>
|
|
<layout:dimensions layout:height="40" layout:width="50"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:glyph="Glyph__YFP_protein" layout:id="Glyph__c0__substrate__YFP_protein" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="159" layout:y="380"/>
|
|
<layout:end layout:x="145" layout:y="320"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:referenceGlyph>
|
|
</layout:listOfReferenceGlyphs>
|
|
</layout:generalGlyph>
|
|
</layout:listOfAdditionalGraphicalObjects>
|
|
<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__AmtR_protein" layout:species="AmtR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="180"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__Ara_AraC_protein" layout:species="Ara_AraC_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="38" layout:y="5"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__TetR_protein" layout:species="TetR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="187" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__LacI_protein" layout:species="LacI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="126" layout:y="180"/>
|
|
<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="227" layout:y="180"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__HlyIIR_protein" layout:species="HlyIIR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="121" layout:y="90"/>
|
|
<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="95" layout:y="270"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
<layout:speciesGlyph layout:id="Glyph__YFP_protein" layout:species="YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="139" layout:y="360"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
</layout:listOfSpeciesGlyphs>
|
|
<layout:listOfReactionGlyphs>
|
|
<layout:reactionGlyph layout:id="Glyph__PhlF_degradation_interaction" layout:reaction="PhlF_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="30"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__PhlF_degradation_interaction__substrate__PhlF_protein" layout:role="substrate" layout:speciesGlyph="Glyph__PhlF_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="115" layout:y="290"/>
|
|
<layout:end layout:x="30" layout:y="40"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__YFP_degradation_interaction" layout:reaction="YFP_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="40" layout:y="60"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__YFP_degradation_interaction__substrate__YFP_protein" layout:role="substrate" layout:speciesGlyph="Glyph__YFP_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="159" layout:y="380"/>
|
|
<layout:end layout:x="50" layout:y="70"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__HlyIIR_degradation_interaction" layout:reaction="HlyIIR_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="60" layout:y="90"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__HlyIIR_degradation_interaction__substrate__HlyIIR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__HlyIIR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="141" layout:y="110"/>
|
|
<layout:end layout:x="70" layout:y="100"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__BetI_degradation_interaction" layout:reaction="BetI_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="80" layout:y="120"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__BetI_degradation_interaction__substrate__BetI_protein" layout:role="substrate" layout:speciesGlyph="Glyph__BetI_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="247" layout:y="200"/>
|
|
<layout:end layout:x="90" layout:y="130"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__AmtR_degradation_interaction" layout:reaction="AmtR_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="100" layout:y="150"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="Glyph__AmtR_degradation_interaction__substrate__AmtR_protein" layout:role="substrate" layout:speciesGlyph="Glyph__AmtR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="40" layout:y="200"/>
|
|
<layout:end layout:x="110" layout:y="160"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__AmtR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="40" layout:y="200"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="88" layout:y="20"/>
|
|
<layout:end layout:x="40" layout:y="200"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__AmtR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="40" layout:y="200"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__AmtR_protein" layout:role="product" layout:speciesGlyph="Glyph__AmtR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="141" layout:y="110"/>
|
|
<layout:end layout:x="40" layout:y="200"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__PhlF_protein__repression__YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="159" layout:y="380"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__PhlF_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="115" layout:y="290"/>
|
|
<layout:end layout:x="159" layout:y="380"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__BetI_protein__repression__YFP_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="159" layout:y="380"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__BetI_protein__repression__YFP_protein" layout:role="product" layout:speciesGlyph="Glyph__YFP_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="247" layout:y="200"/>
|
|
<layout:end layout:x="159" layout:y="380"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__HlyIIR_protein__repression__BetI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="247" layout:y="200"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__HlyIIR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="141" layout:y="110"/>
|
|
<layout:end layout:x="247" layout:y="200"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__BetI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="247" layout:y="200"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__BetI_protein" layout:role="product" layout:speciesGlyph="Glyph__BetI_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="207" layout:y="20"/>
|
|
<layout:end layout:x="247" layout:y="200"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__LacI_protein__repression__PhlF_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="115" layout:y="290"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI_protein__repression__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="146" layout:y="200"/>
|
|
<layout:end layout:x="115" layout:y="290"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__AmtR_protein__repression__PhlF_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="115" layout:y="290"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__AmtR_protein__repression__PhlF_protein" layout:role="product" layout:speciesGlyph="Glyph__PhlF_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="40" layout:y="200"/>
|
|
<layout:end layout:x="115" layout:y="290"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__Ara_AraC_protein__repression__HlyIIR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="141" layout:y="110"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__Ara_AraC_protein__repression__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="88" layout:y="20"/>
|
|
<layout:end layout:x="141" layout:y="110"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</layout:listOfSpeciesReferenceGlyphs>
|
|
</layout:reactionGlyph>
|
|
<layout:reactionGlyph layout:id="Glyph__TetR_protein__repression__HlyIIR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="141" layout:y="110"/>
|
|
<layout:dimensions layout:height="0" layout:width="0"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfSpeciesReferenceGlyphs>
|
|
<layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR_protein__repression__HlyIIR_protein" layout:role="product" layout:speciesGlyph="Glyph__HlyIIR_protein">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="207" layout:y="20"/>
|
|
<layout:end layout:x="141" layout:y="110"/>
|
|
</layout:curveSegment>
|
|
</layout:listOfCurveSegments>
|
|
</layout:curve>
|
|
</layout:speciesReferenceGlyph>
|
|
</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:height="425" layout:width="1070"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__AmtR_protein" layout:id="TextGlyph__AmtR_protein" layout:text="AmtR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="180"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__Ara_AraC_protein" layout:id="TextGlyph__Ara_AraC_protein" layout:text="Ara_AraC_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="38" layout:y="5"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__TetR_protein" layout:id="TextGlyph__TetR_protein" layout:text="TetR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="187" layout:y="0"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__LacI_protein" layout:id="TextGlyph__LacI_protein" layout:text="LacI_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="126" layout:y="180"/>
|
|
<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="227" layout:y="180"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__HlyIIR_protein" layout:id="TextGlyph__HlyIIR_protein" layout:text="HlyIIR_protein">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="121" layout:y="90"/>
|
|
<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="95" layout:y="270"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</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="139" layout:y="360"/>
|
|
<layout:dimensions layout:height="40" layout:width="40"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__PhlF_degradation_interaction" layout:id="TextGlyph__PhlF_degradation_interaction" layout:text="PhlF_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="20" layout:y="30"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__YFP_degradation_interaction" layout:id="TextGlyph__YFP_degradation_interaction" layout:text="YFP_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="40" layout:y="60"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__HlyIIR_degradation_interaction" layout:id="TextGlyph__HlyIIR_degradation_interaction" layout:text="HlyIIR_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="60" layout:y="90"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__BetI_degradation_interaction" layout:id="TextGlyph__BetI_degradation_interaction" layout:text="BetI_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="80" layout:y="120"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__AmtR_degradation_interaction" layout:id="TextGlyph__AmtR_degradation_interaction" layout:text="AmtR_degradation_interaction">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="100" layout:y="150"/>
|
|
<layout:dimensions layout:height="20" layout:width="20"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
<layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
|
|
<layout:boundingBox>
|
|
<layout:position layout:x="120" layout:y="300"/>
|
|
<layout:dimensions layout:height="40" layout:width="50"/>
|
|
</layout:boundingBox>
|
|
</layout:textGlyph>
|
|
</layout:listOfTextGlyphs>
|
|
</layout:layout>
|
|
</layout:listOfLayouts>
|
|
<listOfCompartments>
|
|
<compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
|
|
</listOfCompartments>
|
|
<listOfSpecies>
|
|
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="AmtR_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/AmtR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/AmtR_protein/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="Ara_AraC_protein" initialAmount="0" metaid="iBioSim4" sboTerm="SBO:0000253">
|
|
<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="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Ara_AraC_protein/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="TetR_protein" initialAmount="60" metaid="iBioSim5" 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="#iBioSim5">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/TetR_protein/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="LacI_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/LacI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/LacI_protein/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="BetI_protein" initialAmount="70" metaid="iBioSim11" 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="#iBioSim11">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/BetI_protein/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="HlyIIR_protein" initialAmount="70" metaid="iBioSim12" 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="#iBioSim12">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/HlyIIR_protein/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="PhlF_protein" initialAmount="70" metaid="iBioSim13" 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="#iBioSim13">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/PhlF_protein/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="YFP_protein" initialAmount="0" metaid="iBioSim14" 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="#iBioSim14">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/1"/></rdf:Bag></mts:ComponentDefinitions><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/YFP_protein/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="topModel_AmtRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_AmtRpart_module_sub__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/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/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="topModel_AmtRpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_AmtRpart_module_sub__iBioSim6" 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="#iBioSim6">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart/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="topModel_YFPpart_module_sub__pPhlF" initialAmount="2" metaid="topModel_YFPpart_module_sub__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="topModel_YFPpart_module_sub__pBetI" initialAmount="2" metaid="topModel_YFPpart_module_sub__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="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="topModel_BetIpart_module_sub__pHlyIIR" initialAmount="2" metaid="topModel_BetIpart_module_sub__iBioSim3" 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="#iBioSim3">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/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="topModel_BetIpart_module_sub__pTet" initialAmount="2" metaid="topModel_BetIpart_module_sub__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/BetIpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/BetIpart/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="topModel_PhlFpart_module_sub__pTac" initialAmount="2" metaid="topModel_PhlFpart_module_sub__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/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/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="topModel_PhlFpart_module_sub__pAmtR" initialAmount="2" metaid="topModel_PhlFpart_module_sub__iBioSim6" 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="#iBioSim6">
|
|
<mts:ComponentDefinitions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart/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="topModel_HlyIIRpart_module_sub__pTet" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__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/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/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="topModel_HlyIIRpart_module_sub__pBAD" initialAmount="2" metaid="topModel_HlyIIRpart_module_sub__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/HlyIIRpart/1"/></rdf:Bag></mts:ComponentDefinitions><mts:FunctionalComponents>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Bag></mts:FunctionalComponents><mts:DNAComponents>
|
|
<rdf:Seq>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/HlyIIRpart/1"/></rdf:Seq></mts:DNAComponents><mts:Strand>+</mts:Strand></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</species>
|
|
</listOfSpecies>
|
|
<listOfParameters>
|
|
<parameter constant="true" id="kd" metaid="iBioSim1" name="Degradation rate" value="0.00075"/>
|
|
<parameter constant="true" id="kc_f" metaid="iBioSim66" name="Forward complex formation rate" value="0.05"/>
|
|
<parameter constant="true" id="kc_r" metaid="iBioSim67" name="Reverse complex formation rate" value="1"/>
|
|
<parameter constant="true" id="nc" metaid="iBioSim68" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__kr_f" metaid="topModel_AmtRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__kr_r" metaid="topModel_AmtRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ka_f" metaid="topModel_AmtRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ka_r" metaid="topModel_AmtRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ko_f" metaid="topModel_AmtRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ko_r" metaid="topModel_AmtRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__kao_f" metaid="topModel_AmtRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__kao_r" metaid="topModel_AmtRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__nc" metaid="topModel_AmtRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__nr" metaid="topModel_AmtRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ko" metaid="topModel_AmtRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__kb" metaid="topModel_AmtRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ng" metaid="topModel_AmtRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__np" metaid="topModel_AmtRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="topModel_AmtRpart_module_sub__ka" metaid="topModel_AmtRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__kr_f" metaid="topModel_YFPpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__kr_r" metaid="topModel_YFPpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ka_f" metaid="topModel_YFPpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ka_r" metaid="topModel_YFPpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ko_f" metaid="topModel_YFPpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ko_r" metaid="topModel_YFPpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__kao_f" metaid="topModel_YFPpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__kao_r" metaid="topModel_YFPpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__nc" metaid="topModel_YFPpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__nr" metaid="topModel_YFPpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ko" metaid="topModel_YFPpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__kb" metaid="topModel_YFPpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ng" metaid="topModel_YFPpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__np" metaid="topModel_YFPpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="topModel_YFPpart_module_sub__ka" metaid="topModel_YFPpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__kr_f" metaid="topModel_BetIpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__kr_r" metaid="topModel_BetIpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ka_f" metaid="topModel_BetIpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ka_r" metaid="topModel_BetIpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ko_f" metaid="topModel_BetIpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ko_r" metaid="topModel_BetIpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__kao_f" metaid="topModel_BetIpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__kao_r" metaid="topModel_BetIpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__nc" metaid="topModel_BetIpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__nr" metaid="topModel_BetIpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ko" metaid="topModel_BetIpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__kb" metaid="topModel_BetIpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ng" metaid="topModel_BetIpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__np" metaid="topModel_BetIpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="topModel_BetIpart_module_sub__ka" metaid="topModel_BetIpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__kr_f" metaid="topModel_PhlFpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__kr_r" metaid="topModel_PhlFpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ka_f" metaid="topModel_PhlFpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ka_r" metaid="topModel_PhlFpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ko_f" metaid="topModel_PhlFpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ko_r" metaid="topModel_PhlFpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__kao_f" metaid="topModel_PhlFpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__kao_r" metaid="topModel_PhlFpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__nc" metaid="topModel_PhlFpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__nr" metaid="topModel_PhlFpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ko" metaid="topModel_PhlFpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__kb" metaid="topModel_PhlFpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ng" metaid="topModel_PhlFpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__np" metaid="topModel_PhlFpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="topModel_PhlFpart_module_sub__ka" metaid="topModel_PhlFpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim1" name="Forward repression binding rate" value="0.5"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__kr_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim14" name="Reverse repression binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim15" name="Forward activation binding rate" value="0.0033"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim16" name="Reverse activation binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim17" name="Forward RNAP binding rate" value="0.033"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim18" name="Reverse RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_f" metaid="topModel_HlyIIRpart_module_sub__iBioSim19" name="Forward activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__kao_r" metaid="topModel_HlyIIRpart_module_sub__iBioSim20" name="Reverse activated RNAP binding rate" value="1"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__nc" metaid="topModel_HlyIIRpart_module_sub__iBioSim21" name="Stoichiometry of binding" value="2"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__nr" metaid="topModel_HlyIIRpart_module_sub__iBioSim22" name="Initial RNAP count" value="30"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ko" metaid="topModel_HlyIIRpart_module_sub__iBioSim23" name="Open complex production rate" value="0.05"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__kb" metaid="topModel_HlyIIRpart_module_sub__iBioSim24" name="Basal production rate" value="0.0001"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ng" metaid="topModel_HlyIIRpart_module_sub__iBioSim25" name="Initial promoter count" value="2"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__np" metaid="topModel_HlyIIRpart_module_sub__iBioSim26" name="Stoichiometry of production" value="10"/>
|
|
<parameter constant="true" id="topModel_HlyIIRpart_module_sub__ka" metaid="topModel_HlyIIRpart_module_sub__iBioSim27" name="Activated production rate" value="0.25"/>
|
|
</listOfParameters>
|
|
<listOfConstraints>
|
|
<constraint metaid="c0">
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<lt/>
|
|
<ci> YFP_protein </ci>
|
|
<cn type="integer"> 30 </cn>
|
|
</apply>
|
|
</math>
|
|
</constraint>
|
|
</listOfConstraints>
|
|
<listOfReactions>
|
|
<reaction compartment="Cell" id="PhlF_degradation_interaction" metaid="iBioSim73" reversible="false">
|
|
<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:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfReactants>
|
|
<speciesReference constant="true" metaid="iBioSim24" species="PhlF_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="#iBioSim24">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/PhlF_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> PhlF_protein </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="YFP_degradation_interaction" metaid="iBioSim75" reversible="false">
|
|
<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:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfReactants>
|
|
<speciesReference constant="true" metaid="iBioSim30" 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="#iBioSim30">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/YFP_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> YFP_protein </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="HlyIIR_degradation_interaction" metaid="iBioSim77" reversible="false">
|
|
<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:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfReactants>
|
|
<speciesReference constant="true" metaid="iBioSim36" 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="#iBioSim36">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/HlyIIR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> HlyIIR_protein </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="BetI_degradation_interaction" metaid="iBioSim78" reversible="false">
|
|
<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:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfReactants>
|
|
<speciesReference constant="true" metaid="iBioSim37" species="BetI_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="#iBioSim37">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/BetI_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> BetI_protein </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="AmtR_degradation_interaction" metaid="iBioSim79" reversible="false">
|
|
<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:Interactions>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_degradation_interaction"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfReactants>
|
|
<speciesReference constant="true" metaid="iBioSim38" species="AmtR_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="#iBioSim38">
|
|
<mts:Participations>
|
|
<rdf:Bag>
|
|
<rdf:li rdf:resource="http://www.async.utah.edu/topModel/AmtR_protein"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> AmtR_protein </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_0" metaid="topModel_AmtRpart_module_sub__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/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim9" species="AmtR_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/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__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/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___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/AmtRpart_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> topModel_AmtRpart_module_sub__pBAD </ci>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_AmtRpart_module_sub__kb </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_AmtRpart_module_sub__ka </ci>
|
|
<ci> topModel_AmtRpart_module_sub__kao_f </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__kao_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__ka_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__ko_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__kao_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__kao_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__ka_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_AmtRpart_module_sub__AmtR_protein_interaction_1" metaid="topModel_AmtRpart_module_sub__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/AmtRpart_module/AmtR_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/Ara_AraC_protein_pBAD_activation/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_AmtRpart_module_sub___iBioSim12" species="AmtR_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/AmtRpart_module/AmtR_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_AmtRpart_module_sub__pHlyIIR">
|
|
<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/AmtRpart_module/Ara_AraC_protein_pBAD_activation/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/AmtR_protein_interaction/AmtRpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/AmtRpart_module/HlyIIR_protein_pHlyIIR_repression/AmtRpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_AmtRpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="HlyIIR_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/AmtRpart_module/HlyIIR_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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_AmtRpart_module_sub__pHlyIIR </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__ko_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_AmtRpart_module_sub__kr_f </ci>
|
|
<ci> topModel_AmtRpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> HlyIIR_protein </ci>
|
|
</apply>
|
|
<ci> topModel_AmtRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_0" metaid="topModel_YFPpart_module_sub__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="topModel_YFPpart_module_sub___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="topModel_YFPpart_module_sub__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="topModel_YFPpart_module_sub___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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_YFPpart_module_sub__pPhlF </ci>
|
|
<ci> topModel_YFPpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_YFPpart_module_sub__ko_f </ci>
|
|
<ci> topModel_YFPpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_YFPpart_module_sub__kr_f </ci>
|
|
<ci> topModel_YFPpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> PhlF_protein </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_YFPpart_module_sub__YFP_protein_interaction_1" metaid="topModel_YFPpart_module_sub__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="topModel_YFPpart_module_sub___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="topModel_YFPpart_module_sub__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="topModel_YFPpart_module_sub___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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_YFPpart_module_sub__pBetI </ci>
|
|
<ci> topModel_YFPpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_YFPpart_module_sub__ko_f </ci>
|
|
<ci> topModel_YFPpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_YFPpart_module_sub__kr_f </ci>
|
|
<ci> topModel_YFPpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> BetI_protein </ci>
|
|
</apply>
|
|
<ci> topModel_YFPpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_0" metaid="topModel_BetIpart_module_sub__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/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim9" species="BetI_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/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pHlyIIR">
|
|
<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/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_BetIpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="HlyIIR_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/BetIpart_module/HlyIIR_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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_BetIpart_module_sub__pHlyIIR </ci>
|
|
<ci> topModel_BetIpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_BetIpart_module_sub__ko_f </ci>
|
|
<ci> topModel_BetIpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_BetIpart_module_sub__kr_f </ci>
|
|
<ci> topModel_BetIpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> HlyIIR_protein </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_BetIpart_module_sub__BetI_protein_interaction_1" metaid="topModel_BetIpart_module_sub__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/BetIpart_module/BetI_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_BetIpart_module_sub___iBioSim12" species="BetI_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/BetIpart_module/BetI_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_BetIpart_module_sub__pTet">
|
|
<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/BetIpart_module/HlyIIR_protein_pHlyIIR_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/TetR_protein_pTet_repression/BetIpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/BetIpart_module/BetI_protein_interaction/BetIpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_BetIpart_module_sub___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/BetIpart_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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_BetIpart_module_sub__pTet </ci>
|
|
<ci> topModel_BetIpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_BetIpart_module_sub__ko_f </ci>
|
|
<ci> topModel_BetIpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_BetIpart_module_sub__kr_f </ci>
|
|
<ci> topModel_BetIpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> TetR_protein </ci>
|
|
</apply>
|
|
<ci> topModel_BetIpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_0" metaid="topModel_PhlFpart_module_sub__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/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim9" species="PhlF_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/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pTac">
|
|
<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/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim8" sboTerm="SBO:0000020" species="LacI_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/PhlFpart_module/LacI_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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_PhlFpart_module_sub__pTac </ci>
|
|
<ci> topModel_PhlFpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_PhlFpart_module_sub__ko_f </ci>
|
|
<ci> topModel_PhlFpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_PhlFpart_module_sub__kr_f </ci>
|
|
<ci> topModel_PhlFpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> LacI_protein </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_PhlFpart_module_sub__PhlF_protein_interaction_1" metaid="topModel_PhlFpart_module_sub__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/PhlFpart_module/PhlF_protein_interaction/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/1"/></rdf:Bag></mts:Interactions></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
<listOfProducts>
|
|
<speciesReference constant="true" metaid="topModel_PhlFpart_module_sub___iBioSim12" species="PhlF_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/PhlFpart_module/PhlF_protein/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</speciesReference>
|
|
</listOfProducts>
|
|
<listOfModifiers>
|
|
<modifierSpeciesReference sboTerm="SBO:0000598" species="topModel_PhlFpart_module_sub__pAmtR">
|
|
<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/PhlFpart_module/PhlF_protein_interaction/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/LacI_protein_pTac_repression/PhlFpart_fc/1"/><rdf:li rdf:resource="http://www.async.utah.edu/PhlFpart_module/AmtR_protein_pAmtR_repression/PhlFpart_fc/1"/></rdf:Bag></mts:Participations></rdf:Description></rdf:RDF></ModelToSBOL>
|
|
</annotation>
|
|
</modifierSpeciesReference>
|
|
<modifierSpeciesReference metaid="topModel_PhlFpart_module_sub___iBioSim11" sboTerm="SBO:0000020" species="AmtR_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/PhlFpart_module/AmtR_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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_PhlFpart_module_sub__pAmtR </ci>
|
|
<ci> topModel_PhlFpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_PhlFpart_module_sub__ko_f </ci>
|
|
<ci> topModel_PhlFpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_PhlFpart_module_sub__kr_f </ci>
|
|
<ci> topModel_PhlFpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> AmtR_protein </ci>
|
|
</apply>
|
|
<ci> topModel_PhlFpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0" metaid="topModel_HlyIIRpart_module_sub__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/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="topModel_HlyIIRpart_module_sub___iBioSim9" 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="#iBioSim9">
|
|
<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="topModel_HlyIIRpart_module_sub__pTet">
|
|
<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="topModel_HlyIIRpart_module_sub___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> topModel_HlyIIRpart_module_sub__pTet </ci>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_HlyIIRpart_module_sub__kb </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_HlyIIRpart_module_sub__ka </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__ka_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__kao_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__kao_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__ka_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ka_r </ci>
|
|
</apply>
|
|
<ci> Ara_AraC_protein </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
<reaction compartment="Cell" id="topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1" metaid="topModel_HlyIIRpart_module_sub__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="topModel_HlyIIRpart_module_sub___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="topModel_HlyIIRpart_module_sub__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="topModel_HlyIIRpart_module_sub___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>
|
|
<divide/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<times/>
|
|
<ci> topModel_HlyIIRpart_module_sub__pBAD </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
<apply>
|
|
<plus/>
|
|
<apply>
|
|
<plus/>
|
|
<cn type="integer"> 1 </cn>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__ko_r </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nr </ci>
|
|
</apply>
|
|
</apply>
|
|
<apply>
|
|
<power/>
|
|
<apply>
|
|
<times/>
|
|
<apply>
|
|
<divide/>
|
|
<ci> topModel_HlyIIRpart_module_sub__kr_f </ci>
|
|
<ci> topModel_HlyIIRpart_module_sub__kr_r </ci>
|
|
</apply>
|
|
<ci> TetR_protein </ci>
|
|
</apply>
|
|
<ci> topModel_HlyIIRpart_module_sub__nc </ci>
|
|
</apply>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
</model>
|
|
</sbml>
|