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iBioSim/docs/SysBioTutorial/CII_Degradation.xml
cjmyers 34cb8350fd Updated documentation.
2015-01-28 14:58:11 +00:00

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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" arrays:required="true" fbc:required="false" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" comp:required="true" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" version="1" layout:required="false">
<model id="CII_Degradation" metaid="iBioSim2">
<comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
<comp:port comp:idRef="Cell" sboTerm="SBO:0000601" comp:id="compartment__Cell"/>
<comp:port comp:idRef="CII" sboTerm="SBO:0000600" comp:id="input__CII"/>
</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:width="1070" layout:height="425" layout:depth="0"/>
<layout:listOfCompartmentGlyphs>
<layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
<layout:boundingBox>
<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="1070" layout:height="425"/>
</layout:boundingBox>
</layout:compartmentGlyph>
</layout:listOfCompartmentGlyphs>
<layout:listOfSpeciesGlyphs>
<layout:speciesGlyph layout:id="Glyph__CII" layout:species="CII">
<layout:boundingBox>
<layout:position layout:x="67" layout:y="70"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__CII_P1" layout:species="CII_P1">
<layout:boundingBox>
<layout:position layout:x="144" layout:y="205"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__P1" layout:species="P1">
<layout:boundingBox>
<layout:position layout:x="277" layout:y="78"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
</layout:listOfSpeciesGlyphs>
<layout:listOfReactionGlyphs>
<layout:reactionGlyph layout:id="Glyph__R0" layout:reaction="R0">
<layout:boundingBox>
<layout:position layout:x="193" layout:y="139"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__CII" layout:role="substrate" layout:speciesGlyph="Glyph__CII">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="117" layout:y="85"/>
<layout:end layout:x="208" layout:y="154"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__P1" layout:role="substrate" layout:speciesGlyph="Glyph__P1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="327" layout:y="93"/>
<layout:end layout:x="208" layout:y="154"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="Glyph__R0__product__CII_P1" layout:role="product" layout:speciesGlyph="Glyph__CII_P1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="208" layout:y="154"/>
<layout:end layout:x="194" layout:y="220"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
</layout:listOfSpeciesReferenceGlyphs>
</layout:reactionGlyph>
<layout:reactionGlyph layout:id="Glyph__R2" layout:reaction="R2">
<layout:boundingBox>
<layout:position layout:x="270" layout:y="150"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__R2__substrate__CII_P1" layout:role="substrate" layout:speciesGlyph="Glyph__CII_P1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="194" layout:y="220"/>
<layout:end layout:x="285" layout:y="165"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
<layout:speciesReferenceGlyph layout:id="Glyph__R2__product__P1" layout:role="product" layout:speciesGlyph="Glyph__P1">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xsi:type="LineSegment">
<layout:start layout:x="285" layout:y="165"/>
<layout:end layout:x="327" layout:y="93"/>
</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:width="1070" layout:height="425"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__CII" layout:id="TextGlyph__CII" layout:text="CII">
<layout:boundingBox>
<layout:position layout:x="67" layout:y="70"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__CII_P1" layout:id="TextGlyph__CII_P1" layout:text="CII_P1">
<layout:boundingBox>
<layout:position layout:x="144" layout:y="205"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__P1" layout:id="TextGlyph__P1" layout:text="P1">
<layout:boundingBox>
<layout:position layout:x="277" layout:y="78"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__R0" layout:id="TextGlyph__R0" layout:text="R0">
<layout:boundingBox>
<layout:position layout:x="193" layout:y="139"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__R2" layout:id="TextGlyph__R2" layout:text="R2">
<layout:boundingBox>
<layout:position layout:x="270" layout:y="150"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
</layout:listOfTextGlyphs>
</layout:layout>
</layout:listOfLayouts>
<listOfCompartments>
<compartment id="Cell" constant="true" spatialDimensions="3" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="CII" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim1" boundaryCondition="false" compartment="Cell"/>
<species id="CII_P1" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim3" boundaryCondition="false" compartment="Cell"/>
<species id="P1" constant="false" initialAmount="35" hasOnlySubstanceUnits="true" metaid="iBioSim4" boundaryCondition="false" compartment="Cell"/>
</listOfSpecies>
<listOfReactions>
<reaction id="R0" metaid="iBioSim5" reversible="true" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference constant="true" species="CII" stoichiometry="1"/>
<speciesReference constant="true" species="P1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="CII_P1" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<apply>
<times/>
<ci> kf </ci>
<ci> CII </ci>
</apply>
<ci> P1 </ci>
</apply>
<apply>
<times/>
<ci> kr </ci>
<ci> CII_P1 </ci>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kf" metaid="R0___kf" value="1"/>
<localParameter id="kr" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction id="R2" metaid="iBioSim7" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference constant="true" species="CII_P1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference constant="true" species="P1" stoichiometry="1"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kf </ci>
<ci> CII_P1 </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kf" metaid="R2___kf" value="0.002"/>
<localParameter id="kr" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
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