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iBioSim/prismtest/SimpleChem.xml
LukasBuecherl 2674494894 Working
2023-03-06 12:20:29 +00:00

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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" comp:required="true" fbc:required="false" layout:required="false" level="3" version="2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
<model id="SimpleChem" metaid="iBioSim6">
<comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
<comp:port comp:id="compartment__Cell" comp:idRef="Cell" sboTerm="SBO:0000601"/>
</comp:listOfPorts>
<layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<layout:layout layout:id="iBioSim">
<layout:dimensions layout:depth="0" layout:height="425" layout:width="1070"/>
<layout:listOfAdditionalGraphicalObjects>
<layout:generalGlyph layout:id="Glyph__c0" layout:metaidRef="c0">
<layout:boundingBox>
<layout:position layout:x="657" layout:y="179"/>
<layout:dimensions layout:height="40" layout:width="50"/>
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph layout:glyph="Glyph__S2" layout:id="Glyph__c0__substrate__S2" layout:role="substrate">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="480" layout:y="175"/>
<layout:end layout:x="682" layout:y="199"/>
</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__S0" layout:species="S0">
<layout:boundingBox>
<layout:position layout:x="104" layout:y="93"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__S1" layout:species="S1">
<layout:boundingBox>
<layout:position layout:x="128" layout:y="248"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__S2" layout:species="S2">
<layout:boundingBox>
<layout:position layout:x="430" layout:y="160"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:speciesGlyph>
</layout:listOfSpeciesGlyphs>
<layout:listOfReactionGlyphs>
<layout:reactionGlyph layout:id="Glyph__R0" layout:reaction="R0">
<layout:boundingBox>
<layout:position layout:x="306" layout:y="178"/>
<layout:dimensions layout:height="20" layout:width="20"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__S0" layout:role="substrate" layout:speciesGlyph="Glyph__S0">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="154" layout:y="108"/>
<layout:end layout:x="316" layout:y="188"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__S1" layout:role="substrate" layout:speciesGlyph="Glyph__S1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="178" layout:y="263"/>
<layout:end layout:x="316" layout:y="188"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__product__S2" layout:role="product" layout:speciesGlyph="Glyph__S2">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="316" layout:y="188"/>
<layout:end layout:x="480" layout:y="175"/>
</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__S0" layout:id="TextGlyph__S0" layout:text="S0">
<layout:boundingBox>
<layout:position layout:x="104" layout:y="93"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__S1" layout:id="TextGlyph__S1" layout:text="S1">
<layout:boundingBox>
<layout:position layout:x="128" layout:y="248"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__R0" layout:id="TextGlyph__R0" layout:text="R0">
<layout:boundingBox>
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</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__S2" layout:id="TextGlyph__S2" layout:text="S2">
<layout:boundingBox>
<layout:position layout:x="430" layout:y="160"/>
<layout:dimensions layout:height="30" layout:width="100"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__c0" layout:id="TextGlyph__c0" layout:text="c0">
<layout:boundingBox>
<layout:position layout:x="657" layout:y="179"/>
<layout:dimensions layout:height="40" layout:width="50"/>
</layout:boundingBox>
</layout:textGlyph>
</layout:listOfTextGlyphs>
</layout:layout>
</layout:listOfLayouts>
<listOfFunctionDefinitions>
<functionDefinition id="F" name="Eventually Property">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> t </ci>
</bvar>
<bvar>
<ci> x </ci>
</bvar>
<apply>
<or/>
<apply>
<not/>
<ci> t </ci>
</apply>
<apply>
<not/>
<ci> x </ci>
</apply>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfCompartments>
<compartment constant="true" id="Cell" size="1" spatialDimensions="3"/>
</listOfCompartments>
<listOfSpecies>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S0" initialAmount="10" metaid="iBioSim1"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S1" initialAmount="10" metaid="iBioSim3"/>
<species boundaryCondition="false" compartment="Cell" constant="false" hasOnlySubstanceUnits="true" id="S2" initialAmount="0" metaid="iBioSim5"/>
</listOfSpecies>
<listOfParameters>
<parameter constant="true" id="kd" metaid="iBioSim2" name="Degradation rate" value="0.0075"/>
</listOfParameters>
<listOfConstraints>
<constraint metaid="c0">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> F </ci>
<apply>
<leq/>
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
<cn type="integer"> 100 </cn>
</apply>
<apply>
<gt/>
<ci> S2 </ci>
<cn type="integer"> 8 </cn>
</apply>
</apply>
</math>
</constraint>
</listOfConstraints>
<listOfReactions>
<reaction compartment="Cell" id="R0" metaid="iBioSim4" reversible="false">
<listOfReactants>
<speciesReference constant="true" species="S0" stoichiometry="1"/>
<speciesReference constant="true" species="S1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="S2" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<times/>
<ci> kf </ci>
<ci> S0 </ci>
</apply>
<ci> S1 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kf" value="0.1"/>
<localParameter id="kr" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
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