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iBioSim/docs/OldTutorial/GridTest.xml

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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<comp:listOfExternalModelDefinitions xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
<comp:externalModelDefinition comp:source="file:case00987.xml" comp:id="case00987"/>
</comp:listOfExternalModelDefinitions>
<model id="GridTest" metaid="iBioSim1">
<comp:listOfSubmodels xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
<comp:submodel comp:modelRef="case00987" comp:id="GRID__case00987">
<annotation>
<array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/><array:array array:size="1" xmlns:array="http://www.fakeuri.com"/> </annotation>
</comp:submodel>
</comp:listOfSubmodels>
<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:listOfAdditionalGraphicalObjects>
<layout:generalGlyph layout:reference="C1" layout:id="Glyph__C1">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C2" layout:id="Glyph__C2">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C3" layout:id="Glyph__C3">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C4" layout:id="Glyph__C4">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C5" layout:id="Glyph__C5">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C6" layout:id="Glyph__C6">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C7" layout:id="Glyph__C7">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C8" layout:id="Glyph__C8">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:reference="C9" layout:id="Glyph__C9">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:generalGlyph>
</layout:listOfAdditionalGraphicalObjects>
<layout:listOfTextGlyphs>
<layout:textGlyph layout:graphicalObject="Glyph__C1" layout:id="TextGlyph__C1" layout:text="C1">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C2" layout:id="TextGlyph__C2" layout:text="C2">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C3" layout:id="TextGlyph__C3" layout:text="C3">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="30"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C4" layout:id="TextGlyph__C4" layout:text="C4">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C5" layout:id="TextGlyph__C5" layout:text="C5">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C6" layout:id="TextGlyph__C6" layout:text="C6">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="100"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C7" layout:id="TextGlyph__C7" layout:text="C7">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C8" layout:id="TextGlyph__C8" layout:text="C8">
<layout:boundingBox>
<layout:position layout:x="140" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:graphicalObject="Glyph__C9" layout:id="TextGlyph__C9" layout:text="C9">
<layout:boundingBox>
<layout:position layout:x="250" layout:y="170"/>
<layout:dimensions layout:width="80" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
</layout:listOfTextGlyphs>
</layout:layout>
</layout:listOfLayouts>
<listOfCompartments>
<compartment id="Grid" constant="true" spatialDimensions="3" size="1">
<annotation>
<ibiosim:ibiosim ibiosim:grid="(3,3)" xmlns:ibiosim="http://www.fakeuri.com"/> </annotation>
</compartment>
</listOfCompartments>
<listOfParameters>
<parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim2" value="0.5"/>
<parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim3" value="1"/>
<parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim4" value="0.0033"/>
<parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim5" value="1"/>
<parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim6" value="0.033"/>
<parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim7" value="1"/>
<parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim8" value="1"/>
<parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim9" value="1"/>
<parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim10" value="0.05"/>
<parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim11" value="1"/>
<parameter id="kmdiff_f" constant="true" name="Forward membrane diffusion rate" metaid="iBioSim12" value="1"/>
<parameter id="kmdiff_r" constant="true" name="Reverse membrane diffusion rate" metaid="iBioSim13" value="0.01"/>
<parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim14" value="0.0075"/>
<parameter id="kecd" constant="true" name="Extracellular degradation rate" metaid="iBioSim15" value="0.005"/>
<parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim16" value="2"/>
<parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim17" value="30"/>
<parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim18" value="0.05"/>
<parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim19" value="0.0001"/>
<parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim20" value="2"/>
<parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim21" value="10"/>
<parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim22" value="0.25"/>
<parameter id="kecdiff" constant="true" name="Extracellular diffusion rate" metaid="iBioSim23" value="1"/>
<parameter id="case00987__locations" constant="false" value="0">
<annotation>
<array:array array:C1="(0,0)" array:C2="(0,1)" array:C3="(0,2)" array:C4="(1,0)" array:C5="(1,1)" array:C6="(1,2)" array:C7="(2,0)" array:C8="(2,1)" array:C9="(2,2)" xmlns:array="http://www.fakeuri.com"/> </annotation>
</parameter>
</listOfParameters>
</model>
</sbml>
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