139 lines
No EOL
6.2 KiB
XML
139 lines
No EOL
6.2 KiB
XML
<?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="SimplerChem" metaid="iBioSim3">
|
|
<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>
|
|
<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="659" layout:y="175"/>
|
|
<layout:dimensions layout:height="40" layout:width="50"/>
|
|
</layout:boundingBox>
|
|
<layout:listOfReferenceGlyphs>
|
|
<layout:referenceGlyph layout:glyph="Glyph__S0" layout:id="Glyph__c0__substrate__S0" layout:role="substrate">
|
|
<layout:curve>
|
|
<layout:listOfCurveSegments>
|
|
<layout:curveSegment xsi:type="LineSegment">
|
|
<layout:start layout:x="421" layout:y="226"/>
|
|
<layout:end layout:x="684" layout:y="195"/>
|
|
</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="371" layout:y="211"/>
|
|
<layout:dimensions layout:height="30" layout:width="100"/>
|
|
</layout:boundingBox>
|
|
</layout:speciesGlyph>
|
|
</layout:listOfSpeciesGlyphs>
|
|
<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="371" layout:y="211"/>
|
|
<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="659" layout:y="175"/>
|
|
<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="50" metaid="iBioSim1"/>
|
|
</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>
|
|
<lt/>
|
|
<ci> S0 </ci>
|
|
<cn type="integer"> 1 </cn>
|
|
</apply>
|
|
</apply>
|
|
</math>
|
|
</constraint>
|
|
</listOfConstraints>
|
|
<listOfReactions>
|
|
<reaction compartment="Cell" id="Degradation_S0" metaid="iBioSim4" reversible="false" sboTerm="SBO:0000179">
|
|
<listOfReactants>
|
|
<speciesReference constant="true" species="S0" stoichiometry="1"/>
|
|
</listOfReactants>
|
|
<kineticLaw>
|
|
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
|
<apply>
|
|
<times/>
|
|
<ci> kd </ci>
|
|
<ci> S0 </ci>
|
|
</apply>
|
|
</math>
|
|
</kineticLaw>
|
|
</reaction>
|
|
</listOfReactions>
|
|
</model>
|
|
</sbml> |