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Fix typos in tutorial.
Add Tutorial project.
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cjmyers 2013-05-30 18:26:45 +00:00
parent 73beed9c6b
commit cbec16a40f
392 changed files with 17434 additions and 64 deletions
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docs/Tutorial/BioSim.prj Normal file
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#Population Properties
#Thu May 30 12:20:33 MDT 2013
reb2sac.operator.max.concentration.threshold=15
reb2sac.qssa.condition.1=0.1
monte.carlo.simulation.time.step=inf
monte.carlo.simulation.print.interval=10.0
monte.carlo.simulation.runs=1
reb2sac.simulation.method=monteCarlo
simulation.run.termination.decider=constraint
reb2sac.generate.statistics=false
monte.carlo.simulation.random.seed=314159
monte.carlo.simulation.time.limit=2100.0
simulation.printer.tracking.quantity=amount
reb2sac.iSSA.adaptive=true
simulation.printer=tsd.printer
monte.carlo.simulation.min.time.step=0.0
reb2sac.abstraction.method=none
reb2sac.abstraction.method.3.3=kinetic-law-constants-simplifier
reb2sac.abstraction.method.3.2=reversible-to-irreversible-transformer
reb2sac.abstraction.method.3.1=distribute-transformer
reb2sac.iSSA.number.paths=1
reb2sac.rapid.equilibrium.condition.2=0.1
reb2sac.diffusion.stoichiometry.amplification.value=1.0
reb2sac.rapid.equilibrium.condition.1=0.1
monte.carlo.simulation.out.dir=.
selected.simulator=gillespie
reb2sac.iSSA.type=medianPath

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Population.xml

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Executing:
reb2sac --target.encoding=gillespie /Users/myers/research/nobackup/workspace/BioSim/docs//Tutorial/Population/Population.xml
Total Simulation Time: 4.703422 seconds for Population

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#total time-limit C1__CI20 C1__CII50 C2__CI20 C2__CII50 C3__CI20 C3__CII50 C4__CI20 C4__CII50 C5__CI20 C5__CII50 C6__CI20 C6__CII50 C7__CI20 C7__CII50 C8__CI20 C8__CII50 C9__CI20 C9__CII50 C10__CI20 C10__CII50 C11__CI20 C11__CII50 C12__CI20 C12__CII50 C13__CI20 C13__CII50 C14__CI20 C14__CII50 C15__CI20 C15__CII50 C16__CI20 C16__CII50 C17__CI20 C17__CII50 C18__CI20 C18__CII50 C19__CI20 C19__CII50 C20__CI20 C20__CII50 C21__CI20 C21__CII50 C22__CI20 C22__CII50 C23__CI20 C23__CII50 C24__CI20 C24__CII50 C25__CI20 C25__CII50
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

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C17__CII50 82.3876

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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" version="1" layout:required="false" comp:required="true">
<model metaid="iBioSim1" id="lambda" substanceUnits="nanoMole" timeUnits="second" volumeUnits="microLitre" extentUnits="nanoMole">
<listOfFunctionDefinitions>
<functionDefinition id="total" name="Find total molecules">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> x </ci>
</bvar>
<bvar>
<ci> y </ci>
</bvar>
<apply>
<plus/>
<ci> x </ci>
<apply>
<times/>
<cn type="integer"> 2 </cn>
<ci> y </ci>
</apply>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="uniform" name="Uniform distribution">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> a </ci>
</bvar>
<bvar>
<ci> b </ci>
</bvar>
<apply>
<divide/>
<apply>
<plus/>
<ci> a </ci>
<ci> b </ci>
</apply>
<cn type="integer"> 2 </cn>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition id="nanoMole">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-9" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microLitre">
<listOfUnits>
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="iBioSim2" id="CI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim3" id="CI2" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim4" sboTerm="SBO:0000590" id="PR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim6" id="CII" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim7" sboTerm="SBO:0000590" id="PRE" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter metaid="iBioSim10" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
<parameter metaid="iBioSim11" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
<parameter metaid="iBioSim12" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
<parameter metaid="iBioSim13" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
<parameter metaid="iBioSim14" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
<parameter metaid="iBioSim15" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim16" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
<parameter metaid="iBioSim17" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim18" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
<parameter metaid="iBioSim19" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim20" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim21" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim22" id="nr" name="Initial RNAP count" value="30" constant="true"/>
<parameter metaid="iBioSim23" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
<parameter metaid="iBioSim24" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
<parameter metaid="iBioSim25" id="ng" name="Initial promoter count" value="2" constant="true"/>
<parameter metaid="iBioSim26" id="np" name="Stoichiometry of production" value="10" constant="true"/>
<parameter metaid="iBioSim27" id="ka" name="Activated production rate" value="0.25" constant="true"/>
<parameter metaid="iBioSim9" id="CI_total" value="0" units="nanoMole" constant="false"/>
</listOfParameters>
<listOfRules>
<assignmentRule metaid="Total" variable="CI_total">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> total </ci>
<ci> CI </ci>
<ci> CI2 </ci>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfConstraints>
<constraint metaid="CI20">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<leq/>
<ci> CI </ci>
<cn type="integer"> 20 </cn>
</apply>
</math>
</constraint>
<constraint metaid="CII50">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<leq/>
<ci> CII </ci>
<cn type="integer"> 50 </cn>
</apply>
</math>
</constraint>
</listOfConstraints>
<listOfReactions>
<reaction metaid="iBioSim28" sboTerm="SBO:0000179" id="Degradation_CI" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CI" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> CI </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="iBioSim29" sboTerm="SBO:0000177" id="Complex_CI2" reversible="true" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CI" stoichiometry="2" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="CI2" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> kc_f </ci>
<apply>
<power/>
<ci> CI </ci>
<ci> nc </ci>
</apply>
</apply>
<apply>
<times/>
<ci> kc_r </ci>
<ci> CI2 </ci>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kc_f" value="0.1"/>
<localParameter id="kc_r" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction metaid="iBioSim30" sboTerm="SBO:0000179" id="Degradation_CI2" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CI2" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> CI2 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="iBioSim5" sboTerm="SBO:0000589" id="Production_PR" reversible="false" fast="false" compartment="Cell">
<listOfProducts>
<speciesReference species="CII" stoichiometry="10" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000598" species="PR"/>
<modifierSpeciesReference sboTerm="SBO:0000020" species="CI2"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> PR </ci>
<ci> ko </ci>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> kr_CI2_f </ci>
<ci> kr_CI2_r </ci>
</apply>
<ci> CI2 </ci>
</apply>
<ci> nc_CI2_r </ci>
</apply>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="ko" value="0.014"/>
<localParameter id="ko_f" value="0.69422"/>
<localParameter id="ko_r" value="1"/>
<localParameter id="nc_CI2_r" value="1"/>
<localParameter id="kr_CI2_f" value="0.2165"/>
<localParameter id="kr_CI2_r" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction metaid="iBioSim31" sboTerm="SBO:0000179" id="Degradation_CII" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CII" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> CII </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="iBioSim8" sboTerm="SBO:0000589" id="Production_PRE" reversible="false" fast="false" compartment="Cell">
<listOfProducts>
<speciesReference species="CI" stoichiometry="10" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000598" species="PRE"/>
<modifierSpeciesReference sboTerm="SBO:0000459" species="CII"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> PRE </ci>
<apply>
<plus/>
<apply>
<times/>
<ci> kb </ci>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
<apply>
<times/>
<ci> ka </ci>
<apply>
<divide/>
<ci> kao_f </ci>
<ci> kao_r </ci>
</apply>
<ci> nr </ci>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> ka_CII_f </ci>
<ci> ka_CII_r </ci>
</apply>
<ci> CII </ci>
</apply>
<ci> nc_CII_a </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<apply>
<divide/>
<ci> ko_f </ci>
<ci> ko_r </ci>
</apply>
<ci> nr </ci>
</apply>
<apply>
<times/>
<apply>
<divide/>
<ci> kao_f </ci>
<ci> kao_r </ci>
</apply>
<ci> nr </ci>
<apply>
<power/>
<apply>
<times/>
<apply>
<divide/>
<ci> ka_CII_f </ci>
<ci> ka_CII_r </ci>
</apply>
<ci> CII </ci>
</apply>
<ci> nc_CII_a </ci>
</apply>
</apply>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kb" value="4e-05"/>
<localParameter id="ka" value="0.015"/>
<localParameter id="ko_f" value="0.01"/>
<localParameter id="ko_r" value="1"/>
<localParameter id="nc_CII_a" value="1"/>
<localParameter id="ka_CII_f" value="0.00161"/>
<localParameter id="ka_CII_r" value="1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
</listOfReactions>
<listOfEvents>
<event id="CellDivision" useValuesFromTriggerTime="false">
<annotation>
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="Symmetric Division"/>
</annotation>
<trigger initialValue="false" persistent="false">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<true/>
</math>
</trigger>
<delay>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="integer"> 2100 </cn>
</math>
</delay>
<listOfEventAssignments>
<eventAssignment variable="CI">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> CI </ci>
<apply>
<ci> uniform </ci>
<cn type="integer"> 1 </cn>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</eventAssignment>
<eventAssignment variable="CI2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> CI2 </ci>
<apply>
<ci> uniform </ci>
<cn type="integer"> 1 </cn>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</eventAssignment>
<eventAssignment variable="CII">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> CII </ci>
<apply>
<ci> uniform </ci>
<cn type="integer"> 1 </cn>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</eventAssignment>
</listOfEventAssignments>
</event>
</listOfEvents>
<layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
<layout:layout layout:id="iBioSim">
<layout:dimensions layout:width="0" layout:height="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__CI" layout:species="CI">
<layout:boundingBox>
<layout:position layout:x="86" layout:y="50"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__CI2" layout:species="CI2">
<layout:boundingBox>
<layout:position layout:x="103" layout:y="202"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__PR" layout:species="PR">
<layout:boundingBox>
<layout:position layout:x="150" layout:y="340"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
<layout:speciesGlyph layout:id="Glyph__CII" layout:species="CII">
<layout:boundingBox>
<layout:position layout:x="320" layout:y="200"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:speciesGlyph>
</layout:listOfSpeciesGlyphs>
<layout:listOfReactionGlyphs>
<layout:reactionGlyph layout:id="Glyph__CI__complex__CI2">
<layout:boundingBox>
<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="0" layout:height="0"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__CI__product__CI2" layout:speciesGlyph="Glyph__CI2" layout:role="product">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="136" layout:y="65"/>
<layout:end layout:x="153" layout:y="217"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
</layout:listOfSpeciesReferenceGlyphs>
</layout:reactionGlyph>
<layout:reactionGlyph layout:id="Glyph__PR__Production__CII">
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<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="0" layout:height="0"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__PR__product__CII" layout:speciesGlyph="Glyph__CII" layout:role="product">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="200" layout:y="355"/>
<layout:end layout:x="370" layout:y="215"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:speciesReferenceGlyph>
</layout:listOfSpeciesReferenceGlyphs>
</layout:reactionGlyph>
<layout:reactionGlyph layout:id="Glyph__CI2__repression__PR">
<layout:boundingBox>
<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="0" layout:height="0"/>
</layout:boundingBox>
<layout:listOfSpeciesReferenceGlyphs>
<layout:speciesReferenceGlyph layout:id="Glyph__CI2__product__PR" layout:speciesGlyph="Glyph__PR" layout:role="product">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
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<layout:reactionGlyph layout:id="Glyph__CII__repression__CI">
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<layout:position layout:x="0" layout:y="0"/>
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<layout:speciesReferenceGlyph layout:id="Glyph__CII__product__CI" layout:speciesGlyph="Glyph__CI" layout:role="product">
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<layout:textGlyph layout:id="TextGlyph__Cell" layout:text="Cell" layout:graphicalObject="Glyph__Cell">
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<layout:position layout:x="0" layout:y="0"/>
<layout:dimensions layout:width="1070" layout:height="425"/>
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<layout:textGlyph layout:id="TextGlyph__CI" layout:text="CI" layout:graphicalObject="Glyph__CI">
<layout:boundingBox>
<layout:position layout:x="86" layout:y="50"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CI2" layout:text="CI2" layout:graphicalObject="Glyph__CI2">
<layout:boundingBox>
<layout:position layout:x="103" layout:y="202"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__PR" layout:text="PR" layout:graphicalObject="Glyph__PR">
<layout:boundingBox>
<layout:position layout:x="150" layout:y="340"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CII" layout:text="CII" layout:graphicalObject="Glyph__CII">
<layout:boundingBox>
<layout:position layout:x="320" layout:y="200"/>
<layout:dimensions layout:width="100" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CI_total" layout:text="CI_total" layout:graphicalObject="Glyph__CI_total">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="120"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__Total" layout:text="Total" layout:graphicalObject="Glyph__Total">
<layout:boundingBox>
<layout:position layout:x="20" layout:y="200"/>
<layout:dimensions layout:width="50" layout:height="50"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CI20" layout:text="CI20" layout:graphicalObject="Glyph__CI20">
<layout:boundingBox>
<layout:position layout:x="310" layout:y="20"/>
<layout:dimensions layout:width="50" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CellDivision" layout:text="CellDivision" layout:graphicalObject="Glyph__CellDivision">
<layout:boundingBox>
<layout:position layout:x="350" layout:y="90"/>
<layout:dimensions layout:width="75" layout:height="25"/>
</layout:boundingBox>
</layout:textGlyph>
<layout:textGlyph layout:id="TextGlyph__CII50" layout:text="CII50" layout:graphicalObject="Glyph__CII50">
<layout:boundingBox>
<layout:position layout:x="488" layout:y="174"/>
<layout:dimensions layout:width="50" layout:height="40"/>
</layout:boundingBox>
</layout:textGlyph>
</layout:listOfTextGlyphs>
<layout:listOfAdditionalGraphicalObjects>
<layout:generalGlyph layout:id="Glyph__CI_total" layout:reference="CI_total">
<layout:boundingBox>
<layout:position layout:x="30" layout:y="120"/>
<layout:dimensions layout:width="30" layout:height="30"/>
</layout:boundingBox>
</layout:generalGlyph>
<layout:generalGlyph layout:id="Glyph__Total" layout:reference="Total">
<layout:boundingBox>
<layout:position layout:x="20" layout:y="200"/>
<layout:dimensions layout:width="50" layout:height="50"/>
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph layout:id="Glyph__Total__substrate__CI" layout:glyph="Glyph__CI" layout:role="substrate">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="136" layout:y="65"/>
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</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:referenceGlyph>
<layout:referenceGlyph layout:id="Glyph__Total__substrate__CI2" layout:glyph="Glyph__CI2" layout:role="substrate">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
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</layout:curve>
</layout:referenceGlyph>
<layout:referenceGlyph layout:id="Glyph__Total__product__CI_total" layout:glyph="Glyph__CI_total" layout:role="product">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="45" layout:y="225"/>
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</layout:listOfCurveSegments>
</layout:curve>
</layout:referenceGlyph>
</layout:listOfReferenceGlyphs>
</layout:generalGlyph>
<layout:generalGlyph layout:id="Glyph__CI20" layout:reference="CI20">
<layout:boundingBox>
<layout:position layout:x="310" layout:y="20"/>
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<layout:listOfReferenceGlyphs>
<layout:referenceGlyph layout:id="Glyph__CI20__substrate__CI" layout:glyph="Glyph__CI" layout:role="substrate">
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<layout:listOfCurveSegments>
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<layout:generalGlyph layout:id="Glyph__CellDivision" layout:reference="CellDivision">
<layout:boundingBox>
<layout:position layout:x="350" layout:y="90"/>
<layout:dimensions layout:width="75" layout:height="25"/>
</layout:boundingBox>
<layout:listOfReferenceGlyphs>
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CI" layout:glyph="Glyph__CI" layout:role="substrate">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="136" layout:y="65"/>
<layout:end layout:x="387.5" layout:y="102.5"/>
</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:referenceGlyph>
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI" layout:glyph="Glyph__CI" layout:role="product">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="387.5" layout:y="102.5"/>
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</layout:curveSegment>
</layout:listOfCurveSegments>
</layout:curve>
</layout:referenceGlyph>
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CI2" layout:glyph="Glyph__CI2" layout:role="substrate">
<layout:curve>
<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="153" layout:y="217"/>
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</layout:referenceGlyph>
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI2" layout:glyph="Glyph__CI2" layout:role="product">
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<layout:listOfCurveSegments>
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<layout:listOfCurveSegments>
<layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
<layout:start layout:x="387.5" layout:y="102.5"/>
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<layout:position layout:x="488" layout:y="174"/>
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<layout:listOfReferenceGlyphs>
<layout:referenceGlyph layout:id="Glyph__CII50__substrate__CII" layout:glyph="Glyph__CII" layout:role="substrate">
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</model>
</sbml>

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#lambda Properties
#Thu May 30 11:26:28 MDT 2013
file.stem=abs
monte.carlo.simulation.start.index=1
reb2sac.operator.max.concentration.threshold=15
reb2sac.qssa.condition.1=0.1
monte.carlo.simulation.time.step=inf
gcm.abstraction.method.2=operator-site-reduction-abstraction
monte.carlo.simulation.print.interval=10.0
gcm.abstraction.method.1=complex-formation-and-sequestering-abstraction
monte.carlo.simulation.runs=100
reb2sac.simulation.method=monteCarlo
simulation.run.termination.decider=constraint
reb2sac.generate.statistics=false
monte.carlo.simulation.random.seed=314159
monte.carlo.simulation.time.limit=2100.0
simulation.printer.tracking.quantity=amount
reb2sac.iSSA.adaptive=true
simulation.printer=tsd.printer
monte.carlo.simulation.min.time.step=0.0
reb2sac.abstraction.method=abs
reb2sac.abstraction.method.3.3=kinetic-law-constants-simplifier
reb2sac.abstraction.method.3.2=reversible-to-irreversible-transformer
reb2sac.abstraction.method.3.1=distribute-transformer
reb2sac.iSSA.number.paths=1
reb2sac.rapid.equilibrium.condition.2=0.1
reb2sac.diffusion.stoichiometry.amplification.value=1.0
reb2sac.rapid.equilibrium.condition.1=0.1
monte.carlo.simulation.out.dir=.
selected.simulator=gillespie
reb2sac.iSSA.type=medianPath

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<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model metaid="iBioSim1" id="lambda" name="Created by iBioSim flatten routine" substanceUnits="mole" timeUnits="second" volumeUnits="litre" extentUnits="nanoMole">
<listOfFunctionDefinitions>
<functionDefinition id="total" name="Find total molecules">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> x </ci>
</bvar>
<bvar>
<ci> y </ci>
</bvar>
<apply>
<plus/>
<ci> x </ci>
<apply>
<times/>
<cn type="integer"> 2 </cn>
<ci> y </ci>
</apply>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="uniform" name="Uniform distribution">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> a </ci>
</bvar>
<bvar>
<ci> b </ci>
</bvar>
<apply>
<divide/>
<apply>
<plus/>
<ci> a </ci>
<ci> b </ci>
</apply>
<cn type="integer"> 2 </cn>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition id="nanoMole">
<listOfUnits>
<unit kind="mole" exponent="1" scale="-9" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="microLitre">
<listOfUnits>
<unit kind="litre" exponent="1" scale="-3" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u_1_second_n1">
<listOfUnits>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u_1_mole_n1">
<listOfUnits>
<unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="u_1_mole_n1_1_second_n1">
<listOfUnits>
<unit kind="mole" exponent="-1" scale="0" multiplier="1"/>
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species metaid="iBioSim2" id="CI" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim4" sboTerm="SBO:0000590" id="PR" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim6" id="CII" compartment="Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
<species metaid="iBioSim7" sboTerm="SBO:0000590" id="PRE" compartment="Cell" initialAmount="2" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter metaid="iBioSim10" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
<parameter metaid="iBioSim11" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
<parameter metaid="iBioSim12" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
<parameter metaid="iBioSim13" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
<parameter metaid="iBioSim14" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
<parameter metaid="iBioSim15" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim16" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
<parameter metaid="iBioSim17" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim18" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
<parameter metaid="iBioSim19" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim20" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim21" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
<parameter metaid="iBioSim22" id="nr" name="Initial RNAP count" value="30" constant="true"/>
<parameter metaid="iBioSim23" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
<parameter metaid="iBioSim24" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
<parameter metaid="iBioSim25" id="ng" name="Initial promoter count" value="2" constant="true"/>
<parameter metaid="iBioSim26" id="np" name="Stoichiometry of production" value="10" constant="true"/>
<parameter metaid="iBioSim27" id="ka" name="Activated production rate" value="0.25" constant="true"/>
<parameter metaid="iBioSim9" id="CI_total" value="0" units="nanoMole" constant="false"/>
</listOfParameters>
<listOfReactions>
<reaction id="Degradation_CI" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CI" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> CI </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction id="Degradation_CII" reversible="false" fast="false" compartment="Cell">
<listOfReactants>
<speciesReference species="CII" stoichiometry="1" constant="true"/>
</listOfReactants>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd </ci>
<ci> CII </ci>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction id="R_abstracted_production_PRE" reversible="false" fast="false" compartment="Cell">
<listOfProducts>
<speciesReference species="CI" stoichiometry="10" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="CII"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> ng__PRE </ci>
<apply>
<plus/>
<apply>
<times/>
<ci> kb__PRE </ci>
<ci> Ko__PRE </ci>
<ci> RNAP </ci>
</apply>
<apply>
<times/>
<ci> ka__CII_PRE </ci>
<ci> RNAP </ci>
<apply>
<power/>
<apply>
<times/>
<ci> Ka__CII_PRE </ci>
<ci> CII </ci>
</apply>
<ci> nc__CII_PRE </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> Ko__PRE </ci>
<ci> RNAP </ci>
</apply>
<apply>
<times/>
<ci> Kao__PRE </ci>
<ci> RNAP </ci>
<apply>
<power/>
<apply>
<times/>
<ci> Ka__CII_PRE </ci>
<ci> CII </ci>
</apply>
<ci> nc__CII_PRE </ci>
</apply>
</apply>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="RNAP" value="30" units="u_1_mole_n1"/>
<localParameter id="ng__PRE" value="2" units="u_1_mole_n1"/>
<localParameter id="kb__PRE" value="4e-05" units="u_1_second_n1"/>
<localParameter id="Ko__PRE" value="0.01" units="u_1_mole_n1"/>
<localParameter id="Kao__PRE" value="1" units="u_1_mole_n1"/>
<localParameter id="nc__CII_PRE" value="1" units="dimensionless"/>
<localParameter id="Ka__CII_PRE" value="0.00161" units="u_1_mole_n1"/>
<localParameter id="ka__CII_PRE" value="0.015" units="u_1_second_n1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
<reaction id="R_abstracted_production_PR" reversible="false" fast="false" compartment="Cell">
<listOfProducts>
<speciesReference species="CII" stoichiometry="10" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="CI"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> ko__PR </ci>
<ci> ng__PR </ci>
<ci> Ko__PR </ci>
<ci> RNAP </ci>
</apply>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<times/>
<ci> Ko__PR </ci>
<ci> RNAP </ci>
</apply>
<apply>
<power/>
<apply>
<times/>
<ci> Kr__CI2_PR </ci>
<apply>
<power/>
<apply>
<divide/>
<ci> kf_c__CI2 </ci>
<apply>
<plus/>
<ci> kr_c__CI2 </ci>
<ci> kd__CI2 </ci>
</apply>
</apply>
<apply>
<minus/>
<ci> nc__CI_CI2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<power/>
<ci> CI </ci>
<ci> nc__CI_CI2 </ci>
</apply>
</apply>
<ci> nc__CI2_PR </ci>
</apply>
</apply>
</apply>
</math>
<listOfLocalParameters>
<localParameter id="RNAP" value="30" units="u_1_mole_n1"/>
<localParameter id="ng__PR" value="2" units="u_1_mole_n1"/>
<localParameter id="Ko__PR" value="0.69422" units="u_1_mole_n1"/>
<localParameter id="ko__PR" value="0.014" units="u_1_second_n1"/>
<localParameter id="kf_c__CI2" value="0.1" units="u_1_mole_n1_1_second_n1"/>
<localParameter id="kd__CI2" value="0.0075" units="u_1_second_n1"/>
<localParameter id="kr_c__CI2" value="1" units="u_1_second_n1"/>
<localParameter id="nc__CI_CI2" value="2" units="dimensionless"/>
<localParameter id="nc__CI2_PR" value="1" units="dimensionless"/>
<localParameter id="Kr__CI2_PR" value="0.2165" units="u_1_mole_n1"/>
</listOfLocalParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

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Executing:
reb2sac --target.encoding=gillespie /Users/myers/research/nobackup/workspace/BioSim/docs/Tutorial/lambda/abs/lambda.xml
Total Simulation Time: 1.605304 second for lambda abs

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docs/Tutorial/lambda/abs/run-1.tsd Normal file
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docs/Tutorial/lambda/abs/run-10.tsd Normal file
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docs/Tutorial/lambda/abs/run-100.tsd Normal file
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docs/Tutorial/lambda/abs/run-11.tsd Normal file
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docs/Tutorial/lambda/abs/run-12.tsd Normal file
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docs/Tutorial/lambda/abs/run-13.tsd Normal file
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docs/Tutorial/lambda/abs/run-14.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-15.tsd Normal file
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docs/Tutorial/lambda/abs/run-16.tsd Normal file
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docs/Tutorial/lambda/abs/run-17.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-18.tsd Normal file
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docs/Tutorial/lambda/abs/run-19.tsd Normal file
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docs/Tutorial/lambda/abs/run-2.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-20.tsd Normal file
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docs/Tutorial/lambda/abs/run-21.tsd Normal file
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docs/Tutorial/lambda/abs/run-22.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-23.tsd Normal file
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docs/Tutorial/lambda/abs/run-24.tsd Normal file
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docs/Tutorial/lambda/abs/run-25.tsd Normal file
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docs/Tutorial/lambda/abs/run-26.tsd Normal file
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docs/Tutorial/lambda/abs/run-27.tsd Normal file
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docs/Tutorial/lambda/abs/run-28.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-29.tsd Normal file
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docs/Tutorial/lambda/abs/run-3.tsd Normal file
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docs/Tutorial/lambda/abs/run-30.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-31.tsd Normal file
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docs/Tutorial/lambda/abs/run-32.tsd Normal file
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docs/Tutorial/lambda/abs/run-33.tsd Normal file
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1
docs/Tutorial/lambda/abs/run-34.tsd Normal file
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docs/Tutorial/lambda/abs/run-35.tsd Normal file
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docs/Tutorial/lambda/abs/run-36.tsd Normal file
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docs/Tutorial/lambda/abs/run-37.tsd Normal file
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docs/Tutorial/lambda/abs/run-38.tsd Normal file
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docs/Tutorial/lambda/abs/run-39.tsd Normal file
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docs/Tutorial/lambda/abs/run-4.tsd Normal file
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docs/Tutorial/lambda/abs/run-40.tsd Normal file
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docs/Tutorial/lambda/abs/run-41.tsd Normal file
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docs/Tutorial/lambda/abs/run-42.tsd Normal file
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docs/Tutorial/lambda/abs/run-43.tsd Normal file
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docs/Tutorial/lambda/abs/run-44.tsd Normal file
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docs/Tutorial/lambda/abs/run-45.tsd Normal file
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docs/Tutorial/lambda/abs/run-46.tsd Normal file
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docs/Tutorial/lambda/abs/run-47.tsd Normal file
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docs/Tutorial/lambda/abs/run-48.tsd Normal file
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docs/Tutorial/lambda/abs/run-49.tsd Normal file
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docs/Tutorial/lambda/abs/run-5.tsd Normal file
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docs/Tutorial/lambda/abs/run-50.tsd Normal file
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docs/Tutorial/lambda/abs/run-51.tsd Normal file
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docs/Tutorial/lambda/abs/run-52.tsd Normal file
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docs/Tutorial/lambda/abs/run-53.tsd Normal file
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docs/Tutorial/lambda/abs/run-54.tsd Normal file
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docs/Tutorial/lambda/abs/run-55.tsd Normal file
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docs/Tutorial/lambda/abs/run-56.tsd Normal file
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docs/Tutorial/lambda/abs/run-57.tsd Normal file
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docs/Tutorial/lambda/abs/run-58.tsd Normal file
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docs/Tutorial/lambda/abs/run-59.tsd Normal file
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docs/Tutorial/lambda/abs/run-6.tsd Normal file
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docs/Tutorial/lambda/abs/run-60.tsd Normal file
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docs/Tutorial/lambda/abs/run-61.tsd Normal file
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docs/Tutorial/lambda/abs/run-62.tsd Normal file
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docs/Tutorial/lambda/abs/run-63.tsd Normal file
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docs/Tutorial/lambda/abs/run-64.tsd Normal file
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docs/Tutorial/lambda/abs/run-65.tsd Normal file
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docs/Tutorial/lambda/abs/run-66.tsd Normal file
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docs/Tutorial/lambda/abs/run-67.tsd Normal file
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docs/Tutorial/lambda/abs/run-68.tsd Normal file
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docs/Tutorial/lambda/abs/run-69.tsd Normal file
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docs/Tutorial/lambda/abs/run-7.tsd Normal file
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docs/Tutorial/lambda/abs/run-70.tsd Normal file
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docs/Tutorial/lambda/abs/run-71.tsd Normal file
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docs/Tutorial/lambda/abs/run-72.tsd Normal file
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docs/Tutorial/lambda/abs/run-73.tsd Normal file
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docs/Tutorial/lambda/abs/run-74.tsd Normal file
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docs/Tutorial/lambda/abs/run-75.tsd Normal file
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docs/Tutorial/lambda/abs/run-76.tsd Normal file
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docs/Tutorial/lambda/abs/run-77.tsd Normal file
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docs/Tutorial/lambda/abs/run-78.tsd Normal file
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docs/Tutorial/lambda/abs/run-79.tsd Normal file
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docs/Tutorial/lambda/abs/run-8.tsd Normal file
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docs/Tutorial/lambda/abs/run-80.tsd Normal file
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docs/Tutorial/lambda/abs/run-81.tsd Normal file
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