Updated tutorial for synthetic biology focus using Genetic Toggle Switch example.
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cjmyers
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docs/OldTutorial/BioSim.prj
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docs/OldTutorial/BioSim.prj
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docs/OldTutorial/Divide.xml
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docs/OldTutorial/Divide.xml
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<parameter metaid="iBioSim5" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
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<parameter metaid="iBioSim8" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
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<parameter metaid="iBioSim9" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
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<parameter metaid="iBioSim10" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
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<parameter metaid="iBioSim11" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
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164
docs/OldTutorial/GridTest.xml
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docs/OldTutorial/GridTest.xml
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<?xml version='1.0' encoding='UTF-8' standalone='no'?>
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<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
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<model id="GridTest" metaid="iBioSim1">
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<parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim3" value="1"/>
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<parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim5" value="1"/>
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<parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim7" value="1"/>
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<parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim8" value="1"/>
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<parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim9" value="1"/>
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<parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim11" value="1"/>
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<parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim17" value="30"/>
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<parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim18" value="0.05"/>
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<parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim19" value="0.0001"/>
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<parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim21" value="10"/>
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<parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim22" value="0.25"/>
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<parameter id="kecdiff" constant="true" name="Extracellular diffusion rate" metaid="iBioSim23" value="1"/>
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<parameter id="case00987__locations" constant="false" value="0">
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662
docs/OldTutorial/MODEL_01186.xml
Normal file
662
docs/OldTutorial/MODEL_01186.xml
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<body xmlns="http://www.w3.org/1999/xhtml">
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<html:p> <html:span style="font-family: Courier New,Courier,monospace;">Maximize single objective function, hard bounds.</html:span>
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</html:p>
|
||||
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||||
|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<unitDefinition id="length" name="length">
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<unitDefinition id="time" name="time">
|
||||
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|
||||
<unit scale="0" exponent="1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="mole"/>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="gram"/>
|
||||
<unit scale="0" exponent="-1" multiplier="0.00027777" kind="second"/>
|
||||
</listOfUnits>
|
||||
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|
||||
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|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="false" name="Cell" size="1"/>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<species id="C" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="C" metaid="meta_C" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="D" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="D" metaid="meta_D" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="E" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="E" metaid="meta_E" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="F" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="F" metaid="meta_F" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="G" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="G" metaid="meta_G" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="H" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="H" metaid="meta_H" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="I" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="I" metaid="meta_I" boundaryCondition="false" compartment="Cell"/>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<html:p>subsystem: C3</html:p>
|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<html:p>subsystem: C3</html:p>
|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
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|
||||
</reaction>
|
||||
<reaction id="R07" name="R07" metaid="meta_R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
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|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R01" name="R01" metaid="meta_R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="X" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R17" name="R17" metaid="meta_R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R03" name="R03" metaid="meta_R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R02" name="R02" metaid="meta_R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R05" name="R05" metaid="meta_R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R04" name="R04" metaid="meta_R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R10" name="R10" metaid="meta_R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R06" name="R06" metaid="meta_R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R09" name="R09" metaid="meta_R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R08" name="R08" metaid="meta_R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R11" name="R11" metaid="meta_R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R18" name="R18" metaid="meta_R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R19" name="R19" metaid="meta_R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R26" name="R26" metaid="meta_R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Y" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R25" name="R25" metaid="meta_R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
<speciesReference constant="false" species="T" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="0.5"/>
|
||||
<speciesReference constant="false" species="U" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R24" name="R24" metaid="meta_R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R23" name="R23" metaid="meta_R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R22" name="R22" metaid="meta_R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R21" name="R21" metaid="meta_R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R20" name="R20" metaid="meta_R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
21
docs/OldTutorial/MODEL_01186/MODEL_01186.prb
Normal file
21
docs/OldTutorial/MODEL_01186/MODEL_01186.prb
Normal file
|
|
@ -0,0 +1,21 @@
|
|||
#Probability Data
|
||||
#Mon Oct 28 15:15:03 MDT 2013
|
||||
visibleLegend=true
|
||||
gradient=false
|
||||
species.number.1=1
|
||||
species.number.0=0
|
||||
species.paint.1=Blue
|
||||
species.directory.1=
|
||||
species.paint.0=Red
|
||||
x.axis=
|
||||
species.directory.0=
|
||||
shadow=false
|
||||
y.axis=Percent
|
||||
plot.range.grid.line.paint=-4144960
|
||||
chart.background.paint=-1118482
|
||||
species.name.1=R01
|
||||
species.id.1=R01
|
||||
species.name.0=Objective
|
||||
species.id.0=Objective
|
||||
plot.background.paint=-1
|
||||
title=MODEL_01186 simulation results
|
||||
27
docs/OldTutorial/MODEL_01186/MODEL_01186.properties
Normal file
27
docs/OldTutorial/MODEL_01186/MODEL_01186.properties
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
#MODEL_01186 Properties
|
||||
#Mon Oct 28 15:15:03 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=1.0
|
||||
monte.carlo.simulation.runs=1
|
||||
reb2sac.simulation.method=FBA
|
||||
ode.simulation.time.limit=100.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
monte.carlo.simulation.time.limit=100.0
|
||||
simulation.printer.tracking.quantity=amount
|
||||
simulation.printer=tsd.printer
|
||||
monte.carlo.simulation.min.time.step=0.0
|
||||
ode.simulation.absolute.error=1.0E-4
|
||||
ode.simulation.print.interval=1.0
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
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=rkf45
|
||||
2
docs/OldTutorial/MODEL_01186/MODEL_01186.sim
Normal file
2
docs/OldTutorial/MODEL_01186/MODEL_01186.sim
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
MODEL_01186.xml
|
||||
|
||||
673
docs/OldTutorial/MODEL_01186/MODEL_01186.xml
Normal file
673
docs/OldTutorial/MODEL_01186/MODEL_01186.xml
Normal file
|
|
@ -0,0 +1,673 @@
|
|||
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:html="http://www.w3.org/1999/xhtml" level="3" fbc:required="false" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" version="1">
|
||||
<model id="MODEL_01186" name="Created by iBioSim flatten routine" metaid="meta_MODEL_01186" substanceUnits="mole" volumeUnits="litre">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p> <html:span style="font-family: Courier New,Courier,monospace;">Maximize single objective function, hard bounds.</html:span>
|
||||
</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
||||
<rdf:Description rdf:about="#meta_MODEL_01186">
|
||||
<dc:creator>
|
||||
<rdf:Bag>
|
||||
<rdf:li rdf:parseType="Resource">
|
||||
<vCard:N rdf:parseType="Resource">
|
||||
<vCard:Family>Olivier</vCard:Family>
|
||||
<vCard:Given>Brett</vCard:Given>
|
||||
</vCard:N>
|
||||
<vCard:EMAIL>bgoli@users.sourceforge.net</vCard:EMAIL>
|
||||
<vCard:ORG rdf:parseType="Resource">
|
||||
<vCard:Orgname>VU university Amsterdam</vCard:Orgname>
|
||||
</vCard:ORG>
|
||||
</rdf:li>
|
||||
</rdf:Bag>
|
||||
</dc:creator>
|
||||
<dcterms:created rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T11:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:created>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T10:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-28T21:14:39Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-28T21:14:52Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-28T21:14:53Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</annotation>
|
||||
<fbc:listOfFluxBounds xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1">
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c0"/>
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c1"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c2"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c3"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c4"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c5"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c6"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c7"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c8"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c9"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c10"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c11"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c12"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="1" fbc:operation="lessEqual" fbc:id="c13"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c14"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c15"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c16"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c17"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c18"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c19"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c20"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c21"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c22"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c23"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c24"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c25"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c26"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c27"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c28"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c29"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c30"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c31"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c32"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c33"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c34"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c35"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c36"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c37"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c38"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c39"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c40"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c41"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c42"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c43"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c44"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c45"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c46"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c47"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c48"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c49"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c50"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c51"/>
|
||||
</fbc:listOfFluxBounds>
|
||||
<fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" fbc:activeObjective="OBJF">
|
||||
<fbc:objective fbc:type="maximize" fbc:id="OBJF">
|
||||
<fbc:listOfFluxObjectives>
|
||||
<fbc:fluxObjective fbc:reaction="R26" fbc:coefficient="1"/>
|
||||
</fbc:listOfFluxObjectives>
|
||||
</fbc:objective>
|
||||
</fbc:listOfObjectives>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="substance" name="substance">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="mole"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="area" name="area">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="2" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="volume" name="volume">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="litre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="length" name="length">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="time" name="time">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="mole"/>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="gram"/>
|
||||
<unit scale="0" exponent="-1" multiplier="0.00027777" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="false" name="Cell" size="1"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="A" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="A" metaid="meta_A" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="B" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="B" metaid="meta_B" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="C" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="C" metaid="meta_C" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="D" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="D" metaid="meta_D" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="E" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="E" metaid="meta_E" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="F" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="F" metaid="meta_F" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="G" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="G" metaid="meta_G" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="H" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="H" metaid="meta_H" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="I" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="I" metaid="meta_I" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="J" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="J" metaid="meta_J" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="K" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="K" metaid="meta_K" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="L" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="L" metaid="meta_L" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="M" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="M" metaid="meta_M" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="N" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="N" metaid="meta_N" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="O" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="O" metaid="meta_O" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="P" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="P" metaid="meta_P" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="Q" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Q" metaid="meta_Q" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="R" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="R" metaid="meta_R" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="S" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="S" metaid="meta_S" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="T" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="T" metaid="meta_T" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="U" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="U" metaid="meta_U" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="X" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="X" metaid="meta_X" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="Y" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Y" metaid="meta_Y" boundaryCondition="true" compartment="Cell"/>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction id="R16" name="R16" metaid="meta_R16" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R14" name="R14" metaid="meta_R14" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R15" name="R15" metaid="meta_R15" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R12" name="R12" metaid="meta_R12" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R07" name="R07" metaid="meta_R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R13" name="R13" metaid="meta_R13" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R01" name="R01" metaid="meta_R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="X" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R17" name="R17" metaid="meta_R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R03" name="R03" metaid="meta_R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R02" name="R02" metaid="meta_R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R05" name="R05" metaid="meta_R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R04" name="R04" metaid="meta_R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R10" name="R10" metaid="meta_R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R06" name="R06" metaid="meta_R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R09" name="R09" metaid="meta_R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R08" name="R08" metaid="meta_R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R11" name="R11" metaid="meta_R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R18" name="R18" metaid="meta_R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R19" name="R19" metaid="meta_R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R26" name="R26" metaid="meta_R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Y" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R25" name="R25" metaid="meta_R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
<speciesReference constant="false" species="T" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="0.5"/>
|
||||
<speciesReference constant="false" species="U" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R24" name="R24" metaid="meta_R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R23" name="R23" metaid="meta_R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R22" name="R22" metaid="meta_R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R21" name="R21" metaid="meta_R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R20" name="R20" metaid="meta_R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
3
docs/OldTutorial/MODEL_01186/log.txt
Normal file
3
docs/OldTutorial/MODEL_01186/log.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
Total Simulation Time: 0.356126 seconds for MODEL_01186
|
||||
|
||||
|
||||
2
docs/OldTutorial/MODEL_01186/sim-rep.txt
Normal file
2
docs/OldTutorial/MODEL_01186/sim-rep.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
#total Objective R19 R17 R18 R15 R16 R13 R14 R11 R12 R10 R26 R25 R24 R23 R22 R21 R20 R06 R07 R08 R09 R02 R03 R04 R05 R01
|
||||
100 1.0 0.0996 0.6016 0.6016 0.3984 0.6016 0.3984 0.2988 0.5 1.0 0.5 1.0 0.0 260.8256 -259.8256 1.0 0.0996 0.0996 0.5 0.5 0.5 0.5 0.6667 0.3333 0.3333 1.0 1.0
|
||||
658
docs/OldTutorial/MODEL_01187.xml
Normal file
658
docs/OldTutorial/MODEL_01187.xml
Normal file
|
|
@ -0,0 +1,658 @@
|
|||
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:html="http://www.w3.org/1999/xhtml" level="3" fbc:required="false" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" version="1">
|
||||
<model id="MODEL_01187" metaid="meta_MODEL_01187">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p> <html:span style="font-family: Courier New,Courier,monospace;">Minimize single objective function, hard bounds.</html:span>
|
||||
</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
||||
<rdf:Description rdf:about="#meta_MODEL_01187">
|
||||
<dc:creator>
|
||||
<rdf:Bag>
|
||||
<rdf:li rdf:parseType="Resource">
|
||||
<vCard:N rdf:parseType="Resource">
|
||||
<vCard:Family>Olivier</vCard:Family>
|
||||
<vCard:Given>Brett</vCard:Given>
|
||||
</vCard:N>
|
||||
<vCard:EMAIL>bgoli@users.sourceforge.net</vCard:EMAIL>
|
||||
<vCard:ORG rdf:parseType="Resource">
|
||||
<vCard:Orgname>VU university Amsterdam</vCard:Orgname>
|
||||
</vCard:ORG>
|
||||
</rdf:li>
|
||||
</rdf:Bag>
|
||||
</dc:creator>
|
||||
<dcterms:created rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T11:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:created>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T10:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-25T22:25:29Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</annotation>
|
||||
<fbc:listOfFluxBounds xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1">
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c0"/>
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c1"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c2"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c3"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c4"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c5"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c6"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c7"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c8"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c9"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c10"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c11"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c12"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="1" fbc:operation="lessEqual" fbc:id="c13"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c14"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c15"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c16"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c17"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c18"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c19"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c20"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c21"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c22"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c23"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c24"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c25"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c26"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c27"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c28"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c29"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c30"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c31"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c32"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c33"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c34"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c35"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c36"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c37"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c38"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c39"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c40"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c41"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c42"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c43"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c44"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c45"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c46"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c47"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c48"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c49"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c50"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c51"/>
|
||||
</fbc:listOfFluxBounds>
|
||||
<fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" fbc:activeObjective="OBJF">
|
||||
<fbc:objective fbc:type="minimize" fbc:id="OBJF"/>
|
||||
</fbc:listOfObjectives>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="substance" name="substance">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="mole"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="area" name="area">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="2" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="volume" name="volume">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="litre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="length" name="length">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="time" name="time">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="mole"/>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="gram"/>
|
||||
<unit scale="0" exponent="-1" multiplier="0.00027777" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="false" name="Cell" size="1"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="A" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="A" metaid="meta_A" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="B" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="B" metaid="meta_B" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="C" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="C" metaid="meta_C" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="D" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="D" metaid="meta_D" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="E" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="E" metaid="meta_E" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="F" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="F" metaid="meta_F" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="G" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="G" metaid="meta_G" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="H" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="H" metaid="meta_H" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="I" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="I" metaid="meta_I" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="J" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="J" metaid="meta_J" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="K" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="K" metaid="meta_K" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="L" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="L" metaid="meta_L" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="M" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="M" metaid="meta_M" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="N" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="N" metaid="meta_N" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="O" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="O" metaid="meta_O" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="P" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="P" metaid="meta_P" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="Q" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Q" metaid="meta_Q" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="R" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="R" metaid="meta_R" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="S" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="S" metaid="meta_S" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="T" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="T" metaid="meta_T" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="U" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="U" metaid="meta_U" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="X" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="X" metaid="meta_X" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="Y" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Y" metaid="meta_Y" boundaryCondition="true" compartment="Cell"/>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction id="R16" name="R16" metaid="meta_R16" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R14" name="R14" metaid="meta_R14" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R15" name="R15" metaid="meta_R15" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R12" name="R12" metaid="meta_R12" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R07" name="R07" metaid="meta_R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R13" name="R13" metaid="meta_R13" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R01" name="R01" metaid="meta_R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="X" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R17" name="R17" metaid="meta_R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R03" name="R03" metaid="meta_R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R02" name="R02" metaid="meta_R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R05" name="R05" metaid="meta_R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R04" name="R04" metaid="meta_R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R10" name="R10" metaid="meta_R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R06" name="R06" metaid="meta_R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R09" name="R09" metaid="meta_R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R08" name="R08" metaid="meta_R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R11" name="R11" metaid="meta_R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R18" name="R18" metaid="meta_R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R19" name="R19" metaid="meta_R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R26" name="R26" metaid="meta_R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Y" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R25" name="R25" metaid="meta_R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
<speciesReference constant="false" species="T" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="0.5"/>
|
||||
<speciesReference constant="false" species="U" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R24" name="R24" metaid="meta_R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R23" name="R23" metaid="meta_R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R22" name="R22" metaid="meta_R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R21" name="R21" metaid="meta_R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R20" name="R20" metaid="meta_R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
19
docs/OldTutorial/MODEL_01187/MODEL_01187.grf
Normal file
19
docs/OldTutorial/MODEL_01187/MODEL_01187.grf
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
#Graph Data
|
||||
#Fri Oct 25 16:20:04 MDT 2013
|
||||
visibleLegend=true
|
||||
x.axis=time
|
||||
auto.resize=true
|
||||
y.max=
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
x.max=
|
||||
plot.background.paint=-1
|
||||
y.axis=amount
|
||||
chart.background.paint=-1118482
|
||||
x.scale=
|
||||
LogY=false
|
||||
LogX=false
|
||||
title=MODEL_01187 simulation results
|
||||
plot.range.grid.line.paint=-4144960
|
||||
y.min=
|
||||
y.scale=
|
||||
x.min=
|
||||
26
docs/OldTutorial/MODEL_01187/MODEL_01187.prb
Normal file
26
docs/OldTutorial/MODEL_01187/MODEL_01187.prb
Normal file
|
|
@ -0,0 +1,26 @@
|
|||
#Probability Data
|
||||
#Fri Oct 25 16:20:04 MDT 2013
|
||||
visibleLegend=true
|
||||
gradient=false
|
||||
species.number.2=2
|
||||
species.number.1=1
|
||||
species.number.0=0
|
||||
species.paint.2=Green
|
||||
species.directory.2=
|
||||
species.paint.1=Blue
|
||||
species.directory.1=
|
||||
species.paint.0=Red
|
||||
x.axis=
|
||||
species.directory.0=
|
||||
shadow=false
|
||||
y.axis=Percent
|
||||
plot.range.grid.line.paint=-4144960
|
||||
chart.background.paint=-1118482
|
||||
species.id.2=R02
|
||||
species.name.2=R02
|
||||
species.name.1=R01
|
||||
species.id.1=R01
|
||||
species.name.0=Objective
|
||||
species.id.0=Objective
|
||||
plot.background.paint=-1
|
||||
title=MODEL_01187 simulation results
|
||||
27
docs/OldTutorial/MODEL_01187/MODEL_01187.properties
Normal file
27
docs/OldTutorial/MODEL_01187/MODEL_01187.properties
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
#MODEL_01187 Properties
|
||||
#Fri Oct 25 16:20:04 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=1.0
|
||||
monte.carlo.simulation.runs=1
|
||||
reb2sac.simulation.method=FBA
|
||||
ode.simulation.time.limit=100.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
monte.carlo.simulation.time.limit=100.0
|
||||
simulation.printer.tracking.quantity=amount
|
||||
simulation.printer=tsd.printer
|
||||
monte.carlo.simulation.min.time.step=0.0
|
||||
ode.simulation.absolute.error=1.0E-4
|
||||
ode.simulation.print.interval=1.0
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
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=rkf45
|
||||
2
docs/OldTutorial/MODEL_01187/MODEL_01187.sim
Normal file
2
docs/OldTutorial/MODEL_01187/MODEL_01187.sim
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
MODEL_01187.xml
|
||||
|
||||
669
docs/OldTutorial/MODEL_01187/MODEL_01187.xml
Normal file
669
docs/OldTutorial/MODEL_01187/MODEL_01187.xml
Normal file
|
|
@ -0,0 +1,669 @@
|
|||
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:html="http://www.w3.org/1999/xhtml" level="3" fbc:required="false" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" version="1">
|
||||
<model id="MODEL_01187" name="Created by iBioSim flatten routine" metaid="meta_MODEL_01187" substanceUnits="mole" volumeUnits="litre">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p> <html:span style="font-family: Courier New,Courier,monospace;">Minimize single objective function, hard bounds.</html:span>
|
||||
</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
||||
<rdf:Description rdf:about="#meta_MODEL_01187">
|
||||
<dc:creator>
|
||||
<rdf:Bag>
|
||||
<rdf:li rdf:parseType="Resource">
|
||||
<vCard:N rdf:parseType="Resource">
|
||||
<vCard:Family>Olivier</vCard:Family>
|
||||
<vCard:Given>Brett</vCard:Given>
|
||||
</vCard:N>
|
||||
<vCard:EMAIL>bgoli@users.sourceforge.net</vCard:EMAIL>
|
||||
<vCard:ORG rdf:parseType="Resource">
|
||||
<vCard:Orgname>VU university Amsterdam</vCard:Orgname>
|
||||
</vCard:ORG>
|
||||
</rdf:li>
|
||||
</rdf:Bag>
|
||||
</dc:creator>
|
||||
<dcterms:created rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T11:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:created>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T10:05:21Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-25T22:18:57Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-25T22:19:14Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-25T22:19:17Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</annotation>
|
||||
<fbc:listOfFluxBounds xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1">
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c0"/>
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c1"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c2"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c3"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c4"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c5"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c6"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c7"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c8"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c9"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c10"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c11"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c12"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="1" fbc:operation="lessEqual" fbc:id="c13"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c14"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c15"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c16"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c17"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c18"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c19"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c20"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c21"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c22"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c23"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c24"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c25"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c26"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c27"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c28"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c29"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c30"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c31"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c32"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c33"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c34"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c35"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c36"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c37"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c38"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c39"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c40"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c41"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c42"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c43"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c44"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c45"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c46"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c47"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c48"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c49"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c50"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c51"/>
|
||||
</fbc:listOfFluxBounds>
|
||||
<fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" fbc:activeObjective="OBJF">
|
||||
<fbc:objective fbc:type="minimize" fbc:id="OBJF"/>
|
||||
</fbc:listOfObjectives>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="substance" name="substance">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="mole"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="area" name="area">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="2" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="volume" name="volume">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="litre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="length" name="length">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="time" name="time">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="mole"/>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="gram"/>
|
||||
<unit scale="0" exponent="-1" multiplier="0.00027777" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="false" name="Cell" size="1"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="A" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="A" metaid="meta_A" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="B" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="B" metaid="meta_B" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="C" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="C" metaid="meta_C" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="D" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="D" metaid="meta_D" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="E" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="E" metaid="meta_E" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="F" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="F" metaid="meta_F" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="G" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="G" metaid="meta_G" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="H" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="H" metaid="meta_H" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="I" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="I" metaid="meta_I" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="J" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="J" metaid="meta_J" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="K" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="K" metaid="meta_K" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="L" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="L" metaid="meta_L" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="M" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="M" metaid="meta_M" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="N" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="N" metaid="meta_N" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="O" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="O" metaid="meta_O" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="P" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="P" metaid="meta_P" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="Q" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Q" metaid="meta_Q" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="R" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="R" metaid="meta_R" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="S" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="S" metaid="meta_S" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="T" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="T" metaid="meta_T" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="U" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="U" metaid="meta_U" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="X" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="X" metaid="meta_X" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="Y" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Y" metaid="meta_Y" boundaryCondition="true" compartment="Cell"/>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction id="R16" name="R16" metaid="meta_R16" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R14" name="R14" metaid="meta_R14" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R15" name="R15" metaid="meta_R15" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R12" name="R12" metaid="meta_R12" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R07" name="R07" metaid="meta_R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R13" name="R13" metaid="meta_R13" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R01" name="R01" metaid="meta_R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="X" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R17" name="R17" metaid="meta_R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R03" name="R03" metaid="meta_R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R02" name="R02" metaid="meta_R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R05" name="R05" metaid="meta_R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R04" name="R04" metaid="meta_R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R10" name="R10" metaid="meta_R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R06" name="R06" metaid="meta_R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R09" name="R09" metaid="meta_R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R08" name="R08" metaid="meta_R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R11" name="R11" metaid="meta_R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R18" name="R18" metaid="meta_R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R19" name="R19" metaid="meta_R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R26" name="R26" metaid="meta_R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Y" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R25" name="R25" metaid="meta_R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
<speciesReference constant="false" species="T" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="0.5"/>
|
||||
<speciesReference constant="false" species="U" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R24" name="R24" metaid="meta_R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R23" name="R23" metaid="meta_R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R22" name="R22" metaid="meta_R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R21" name="R21" metaid="meta_R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R20" name="R20" metaid="meta_R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
3
docs/OldTutorial/MODEL_01187/log.txt
Normal file
3
docs/OldTutorial/MODEL_01187/log.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
Total Simulation Time: 0.05902 seconds for MODEL_01187
|
||||
|
||||
|
||||
1
docs/OldTutorial/MODEL_01187/schematic_preferences.json
Normal file
1
docs/OldTutorial/MODEL_01187/schematic_preferences.json
Normal file
|
|
@ -0,0 +1 @@
|
|||
[]
|
||||
2
docs/OldTutorial/MODEL_01187/sim-rep.txt
Normal file
2
docs/OldTutorial/MODEL_01187/sim-rep.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
#total Objective R19 R17 R18 R15 R16 R13 R14 R11 R12 R10 R26 R25 R24 R23 R22 R21 R20 R06 R07 R08 R09 R02 R03 R04 R05 R01
|
||||
100 0.0 0.0884 0.5343 0.5343 0.3534 0.5343 0.3534 0.2651 0.4439 0.8877 0.4439 0.9173 0.0591 260.798 -259.9103 0.8877 0.0884 0.0884 0.4439 0.4439 0.4439 0.4439 0.5918 0.2959 0.2959 0.8877 0.9469
|
||||
983
docs/OldTutorial/MODEL_01196.xml
Normal file
983
docs/OldTutorial/MODEL_01196.xml
Normal file
|
|
@ -0,0 +1,983 @@
|
|||
<?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" xmlns:html="http://www.w3.org/1999/xhtml" level="3" 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" version="1" layout:required="false">
|
||||
<model id="MODEL_01196" metaid="meta_MODEL_01196">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p> <html:span style="font-family: Courier New,Courier,monospace;">Infeasible solution, should return a nan</html:span>
|
||||
</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<rdf:RDF xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">
|
||||
<rdf:Description rdf:about="#meta_MODEL_01196">
|
||||
<dc:creator>
|
||||
<rdf:Bag>
|
||||
<rdf:li rdf:parseType="Resource">
|
||||
<vCard:N rdf:parseType="Resource">
|
||||
<vCard:Family>Olivier</vCard:Family>
|
||||
<vCard:Given>Brett</vCard:Given>
|
||||
</vCard:N>
|
||||
<vCard:EMAIL>bgoli@users.sourceforge.net</vCard:EMAIL>
|
||||
<vCard:ORG rdf:parseType="Resource">
|
||||
<vCard:Orgname>VU university Amsterdam</vCard:Orgname>
|
||||
</vCard:ORG>
|
||||
</rdf:li>
|
||||
</rdf:Bag>
|
||||
</dc:creator>
|
||||
<dcterms:created rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T11:05:22Z</dcterms:W3CDTF>
|
||||
</dcterms:created>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T10:05:22Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2013-10-31T23:16:18Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
</rdf:Description>
|
||||
</rdf:RDF> </annotation>
|
||||
<fbc:listOfFluxBounds xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1">
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c0"/>
|
||||
<fbc:fluxBound fbc:reaction="R16" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c1"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c2"/>
|
||||
<fbc:fluxBound fbc:reaction="R03" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c3"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c4"/>
|
||||
<fbc:fluxBound fbc:reaction="R02" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c5"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c6"/>
|
||||
<fbc:fluxBound fbc:reaction="R05" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c7"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="2" fbc:operation="greaterEqual" fbc:id="c8"/>
|
||||
<fbc:fluxBound fbc:reaction="R07" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c9"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c10"/>
|
||||
<fbc:fluxBound fbc:reaction="R04" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c11"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c12"/>
|
||||
<fbc:fluxBound fbc:reaction="R01" fbc:value="1" fbc:operation="lessEqual" fbc:id="c13"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c14"/>
|
||||
<fbc:fluxBound fbc:reaction="R17" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c15"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c16"/>
|
||||
<fbc:fluxBound fbc:reaction="R14" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c17"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c18"/>
|
||||
<fbc:fluxBound fbc:reaction="R15" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c19"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c20"/>
|
||||
<fbc:fluxBound fbc:reaction="R12" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c21"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c22"/>
|
||||
<fbc:fluxBound fbc:reaction="R13" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c23"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c24"/>
|
||||
<fbc:fluxBound fbc:reaction="R10" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c25"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c26"/>
|
||||
<fbc:fluxBound fbc:reaction="R11" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c27"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c28"/>
|
||||
<fbc:fluxBound fbc:reaction="R09" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c29"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c30"/>
|
||||
<fbc:fluxBound fbc:reaction="R08" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c31"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c32"/>
|
||||
<fbc:fluxBound fbc:reaction="R06" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c33"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c34"/>
|
||||
<fbc:fluxBound fbc:reaction="R18" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c35"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c36"/>
|
||||
<fbc:fluxBound fbc:reaction="R19" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c37"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c38"/>
|
||||
<fbc:fluxBound fbc:reaction="R26" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c39"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c40"/>
|
||||
<fbc:fluxBound fbc:reaction="R25" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c41"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c42"/>
|
||||
<fbc:fluxBound fbc:reaction="R24" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c43"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c44"/>
|
||||
<fbc:fluxBound fbc:reaction="R23" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c45"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="0" fbc:operation="greaterEqual" fbc:id="c46"/>
|
||||
<fbc:fluxBound fbc:reaction="R22" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c47"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c48"/>
|
||||
<fbc:fluxBound fbc:reaction="R21" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c49"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="-1000" fbc:operation="greaterEqual" fbc:id="c50"/>
|
||||
<fbc:fluxBound fbc:reaction="R20" fbc:value="1000" fbc:operation="lessEqual" fbc:id="c51"/>
|
||||
</fbc:listOfFluxBounds>
|
||||
<fbc:listOfObjectives xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" fbc:activeObjective="OBJF">
|
||||
<fbc:objective fbc:type="maximize" fbc:id="OBJF">
|
||||
<fbc:listOfFluxObjectives>
|
||||
<fbc:fluxObjective fbc:reaction="R26" fbc:coefficient="1"/>
|
||||
</fbc:listOfFluxObjectives>
|
||||
</fbc:objective>
|
||||
</fbc:listOfObjectives>
|
||||
<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="560" layout:height="390"/>
|
||||
<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__A" layout:species="A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__D" layout:species="D">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="160"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__E" layout:species="E">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__F" layout:species="F">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="120" layout:y="240"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__G" layout:species="G">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="140" layout:y="280"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__H" layout:species="H">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="160" layout:y="320"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__I" layout:species="I">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="180" layout:y="360"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__J" layout:species="J">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="200" layout:y="0"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__K" layout:species="K">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="220" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__L" layout:species="L">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="240" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__M" layout:species="M">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="260" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__N" layout:species="N">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="280" layout:y="160"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__O" layout:species="O">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="300" layout:y="200"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__P" layout:species="P">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="320" layout:y="240"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__Q" layout:species="Q">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="340" layout:y="280"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__R" layout:species="R">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="360" layout:y="320"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__S" layout:species="S">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="550" layout:y="380"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__T" layout:species="T">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="400" layout:y="0"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__U" layout:species="U">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="420" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__X" layout:species="X">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="440" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__Y" layout:species="Y">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="460" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
</layout:listOfSpeciesGlyphs>
|
||||
<layout:listOfReactionGlyphs>
|
||||
<layout:reactionGlyph layout:id="Glyph__R25" layout:reaction="R25">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="480" layout:y="160"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__R25__substrate__A" layout:role="substrate" layout:speciesGlyph="Glyph__A"/>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__R25__substrate__T" layout:role="substrate" layout:speciesGlyph="Glyph__T"/>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__R25__product__S" layout:role="product" layout:speciesGlyph="Glyph__S"/>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__R25__product__U" layout:role="product" layout:speciesGlyph="Glyph__U"/>
|
||||
</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__A" layout:id="TextGlyph__A" layout:text="A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__B" layout:id="TextGlyph__B" layout:text="B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__C" layout:id="TextGlyph__C" layout:text="C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__D" layout:id="TextGlyph__D" layout:text="D">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="160"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__E" layout:id="TextGlyph__E" layout:text="E">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__F" layout:id="TextGlyph__F" layout:text="F">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="120" layout:y="240"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__G" layout:id="TextGlyph__G" layout:text="G">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="140" layout:y="280"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__H" layout:id="TextGlyph__H" layout:text="H">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="160" layout:y="320"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__I" layout:id="TextGlyph__I" layout:text="I">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="180" layout:y="360"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__J" layout:id="TextGlyph__J" layout:text="J">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="200" layout:y="0"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__K" layout:id="TextGlyph__K" layout:text="K">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="220" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__L" layout:id="TextGlyph__L" layout:text="L">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="240" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__M" layout:id="TextGlyph__M" layout:text="M">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="260" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__N" layout:id="TextGlyph__N" layout:text="N">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="280" layout:y="160"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__O" layout:id="TextGlyph__O" layout:text="O">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="300" layout:y="200"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__P" layout:id="TextGlyph__P" layout:text="P">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="320" layout:y="240"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__Q" layout:id="TextGlyph__Q" layout:text="Q">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="340" layout:y="280"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__R" layout:id="TextGlyph__R" layout:text="R">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="360" layout:y="320"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__S" layout:id="TextGlyph__S" layout:text="S">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="550" layout:y="380"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__T" layout:id="TextGlyph__T" layout:text="T">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="400" layout:y="0"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__U" layout:id="TextGlyph__U" layout:text="U">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="420" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__X" layout:id="TextGlyph__X" layout:text="X">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="440" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__Y" layout:id="TextGlyph__Y" layout:text="Y">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="460" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__R25" layout:id="TextGlyph__R25" layout:text="R25">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="480" layout:y="160"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="substance" name="substance">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="mole"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="area" name="area">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="2" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="volume" name="volume">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="litre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="length" name="length">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="metre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="time" name="time">
|
||||
<listOfUnits>
|
||||
<unit scale="0" exponent="1" multiplier="1" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="mole"/>
|
||||
<unit scale="0" exponent="-1" multiplier="1" kind="gram"/>
|
||||
<unit scale="0" exponent="-1" multiplier="0.00027777" kind="second"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="false" name="Cell" size="1">
|
||||
<annotation>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="A" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="A" metaid="meta_A" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="B" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="B" metaid="meta_B" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="C" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="C" metaid="meta_C" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="D" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="D" metaid="meta_D" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="E" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="E" metaid="meta_E" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="F" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="F" metaid="meta_F" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="G" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="G" metaid="meta_G" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="H" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="H" metaid="meta_H" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="I" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="I" metaid="meta_I" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="J" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="J" metaid="meta_J" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="K" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="K" metaid="meta_K" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="L" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="L" metaid="meta_L" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="M" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="M" metaid="meta_M" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="N" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="N" metaid="meta_N" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="O" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="O" metaid="meta_O" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="P" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="P" metaid="meta_P" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="Q" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Q" metaid="meta_Q" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="R" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="R" metaid="meta_R" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="S" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="S" metaid="meta_S" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="T" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="T" metaid="meta_T" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="U" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="U" metaid="meta_U" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="X" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="X" metaid="meta_X" boundaryCondition="true" compartment="Cell"/>
|
||||
<species id="Y" fbc:charge="1" initialConcentration="0" fbc:chemicalFormula="C2H6O" constant="false" hasOnlySubstanceUnits="false" name="Y" metaid="meta_Y" boundaryCondition="true" compartment="Cell"/>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction id="R16" name="R16" metaid="meta_R16" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="M" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R14" name="R14" metaid="meta_R14" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R15" name="R15" metaid="meta_R15" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R12" name="R12" metaid="meta_R12" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R07" name="R07" metaid="meta_R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R13" name="R13" metaid="meta_R13" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="J" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R01" name="R01" metaid="meta_R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="X" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R17" name="R17" metaid="meta_R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R03" name="R03" metaid="meta_R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
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|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R02" name="R02" metaid="meta_R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R05" name="R05" metaid="meta_R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R04" name="R04" metaid="meta_R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="C" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R10" name="R10" metaid="meta_R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R06" name="R06" metaid="meta_R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="E" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R09" name="R09" metaid="meta_R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="D" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="G" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R08" name="R08" metaid="meta_R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="F" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R11" name="R11" metaid="meta_R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="H" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="I" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R18" name="R18" metaid="meta_R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="N" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R19" name="R19" metaid="meta_R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="K" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R26" name="R26" metaid="meta_R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="Y" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R25" name="R25" metaid="meta_R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="A" stoichiometry="1"/>
|
||||
<speciesReference constant="false" species="T" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="0.5"/>
|
||||
<speciesReference constant="false" species="U" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R23" name="R23" metaid="meta_R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R22" name="R22" metaid="meta_R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="Q" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R21" name="R21" metaid="meta_R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="L" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R20" name="R20" metaid="meta_R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="O" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="P" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction id="R24" name="R24" metaid="meta_R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference constant="false" species="R" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="false" species="S" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
19
docs/OldTutorial/MODEL_01196/MODEL_01196.grf
Normal file
19
docs/OldTutorial/MODEL_01196/MODEL_01196.grf
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
#Graph Data
|
||||
#Mon Jun 17 15:21:31 MDT 2013
|
||||
visibleLegend=true
|
||||
x.axis=time
|
||||
auto.resize=true
|
||||
y.max=
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
x.max=
|
||||
plot.background.paint=-1
|
||||
y.axis=amount
|
||||
chart.background.paint=-1118482
|
||||
x.scale=
|
||||
LogY=false
|
||||
LogX=false
|
||||
title=MODEL_01196 simulation results
|
||||
plot.range.grid.line.paint=-4144960
|
||||
y.min=
|
||||
y.scale=
|
||||
x.min=
|
||||
11
docs/OldTutorial/MODEL_01196/MODEL_01196.prb
Normal file
11
docs/OldTutorial/MODEL_01196/MODEL_01196.prb
Normal file
|
|
@ -0,0 +1,11 @@
|
|||
#Probability Data
|
||||
#Mon Jun 17 15:21:31 MDT 2013
|
||||
visibleLegend=true
|
||||
x.axis=
|
||||
plot.background.paint=-1
|
||||
y.axis=Percent
|
||||
chart.background.paint=-1118482
|
||||
title=MODEL_01196 simulation results
|
||||
gradient=false
|
||||
plot.range.grid.line.paint=-4144960
|
||||
shadow=false
|
||||
27
docs/OldTutorial/MODEL_01196/MODEL_01196.properties
Normal file
27
docs/OldTutorial/MODEL_01196/MODEL_01196.properties
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
#MODEL_01196 Properties
|
||||
#Mon Jun 17 15:21:31 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=1.0
|
||||
monte.carlo.simulation.runs=1
|
||||
reb2sac.simulation.method=FBA
|
||||
ode.simulation.time.limit=100.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
monte.carlo.simulation.time.limit=100.0
|
||||
simulation.printer.tracking.quantity=amount
|
||||
simulation.printer=tsd.printer
|
||||
monte.carlo.simulation.min.time.step=0.0
|
||||
ode.simulation.absolute.error=1.0E-9
|
||||
ode.simulation.print.interval=1.0
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
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=rkf45
|
||||
2
docs/OldTutorial/MODEL_01196/MODEL_01196.sim
Normal file
2
docs/OldTutorial/MODEL_01196/MODEL_01196.sim
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
MODEL_01196.xml
|
||||
|
||||
638
docs/OldTutorial/MODEL_01196/MODEL_01196.xml
Normal file
638
docs/OldTutorial/MODEL_01196/MODEL_01196.xml
Normal file
|
|
@ -0,0 +1,638 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" xmlns:html="http://www.w3.org/1999/xhtml" level="3" version="1" fbc:required="false">
|
||||
<model metaid="meta_MODEL_01196" id="MODEL_01196" name="Created by iBioSim flatten routine" substanceUnits="mole" volumeUnits="litre">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>
|
||||
<html:span style="font-family: Courier New,Courier,monospace;">Infeasible solution, should return a nan</html:span>
|
||||
</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
|
||||
<rdf:Description rdf:about="#meta_MODEL_01196">
|
||||
<dc:creator>
|
||||
<rdf:Bag>
|
||||
<rdf:li rdf:parseType="Resource">
|
||||
<vCard:N rdf:parseType="Resource">
|
||||
<vCard:Family>Olivier</vCard:Family>
|
||||
<vCard:Given>Brett</vCard:Given>
|
||||
</vCard:N>
|
||||
<vCard:EMAIL>bgoli@users.sourceforge.net</vCard:EMAIL>
|
||||
<vCard:ORG rdf:parseType="Resource">
|
||||
<vCard:Orgname>VU university Amsterdam</vCard:Orgname>
|
||||
</vCard:ORG>
|
||||
</rdf:li>
|
||||
</rdf:Bag>
|
||||
</dc:creator>
|
||||
<dcterms:created rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T11:05:22Z</dcterms:W3CDTF>
|
||||
</dcterms:created>
|
||||
<dcterms:modified rdf:parseType="Resource">
|
||||
<dcterms:W3CDTF>2012-12-21T10:05:22Z</dcterms:W3CDTF>
|
||||
</dcterms:modified>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</annotation>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="substance" name="substance">
|
||||
<listOfUnits>
|
||||
<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="area" name="area">
|
||||
<listOfUnits>
|
||||
<unit kind="metre" exponent="2" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="volume" name="volume">
|
||||
<listOfUnits>
|
||||
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="length" name="length">
|
||||
<listOfUnits>
|
||||
<unit kind="metre" exponent="1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="time" name="time">
|
||||
<listOfUnits>
|
||||
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="mmol_per_gDW_per_hr" name="mmol_per_gDW_per_hr">
|
||||
<listOfUnits>
|
||||
<unit kind="mole" exponent="1" scale="-3" multiplier="1"/>
|
||||
<unit kind="gram" exponent="-1" scale="0" multiplier="1"/>
|
||||
<unit kind="second" exponent="-1" scale="0" multiplier="0.00027777"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" name="Cell" size="1" constant="false"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species metaid="meta_A" id="A" name="A" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_B" id="B" name="B" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_C" id="C" name="C" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_D" id="D" name="D" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_E" id="E" name="E" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_F" id="F" name="F" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_G" id="G" name="G" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_H" id="H" name="H" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_I" id="I" name="I" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_J" id="J" name="J" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_K" id="K" name="K" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_L" id="L" name="L" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_M" id="M" name="M" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_N" id="N" name="N" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_O" id="O" name="O" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_P" id="P" name="P" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_Q" id="Q" name="Q" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_R" id="R" name="R" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_S" id="S" name="S" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_T" id="T" name="T" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_U" id="U" name="U" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_X" id="X" name="X" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
<species metaid="meta_Y" id="Y" name="Y" compartment="Cell" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false" fbc:charge="1" fbc:chemicalFormula="C2H6O"/>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction metaid="meta_R16" id="R16" name="R16" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="J" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="M" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R14" id="R14" name="R14" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="K" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="L" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R15" id="R15" name="R15" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="L" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="Q" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R12" id="R12" name="R12" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="I" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="J" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R07" id="R07" name="R07" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="E" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="F" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R13" id="R13" name="R13" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="J" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="K" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R01" id="R01" name="R01" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="X" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="A" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R17" id="R17" name="R17" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="M" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="N" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R03" id="R03" name="R03" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="A" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="C" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R02" id="R02" name="R02" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="A" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="B" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R05" id="R05" name="R05" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="B" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="D" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R04" id="R04" name="R04" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C1</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C1"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="C" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="B" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R10" id="R10" name="R10" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="G" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="H" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R06" id="R06" name="R06" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="D" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="E" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R09" id="R09" name="R09" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="D" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="G" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R08" id="R08" name="R08" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="F" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="I" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R11" id="R11" name="R11" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C2</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C2"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="H" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="I" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R18" id="R18" name="R18" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="N" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="Q" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R19" id="R19" name="R19" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="K" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="O" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R26" id="R26" name="R26" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="S" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="Y" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R25" id="R25" name="R25" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="A" stoichiometry="1" constant="false"/>
|
||||
<speciesReference species="T" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="S" stoichiometry="0.5" constant="false"/>
|
||||
<speciesReference species="U" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R23" id="R23" name="R23" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="R" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="S" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R22" id="R22" name="R22" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: L</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="L"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="Q" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="R" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R21" id="R21" name="R21" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="P" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="L" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R20" id="R20" name="R20" reversible="true" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C3</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C3"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="O" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="P" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
<reaction metaid="meta_R24" id="R24" name="R24" reversible="false" fast="false">
|
||||
<notes>
|
||||
<body xmlns:html="http://www.w3.org/1999/xhtml">
|
||||
<html:p>subsystem: C4</html:p>
|
||||
</body>
|
||||
</notes>
|
||||
<annotation>
|
||||
<listOfKeyValueData xmlns="http://pysces.sourceforge.net/KeyValueData">
|
||||
<data id="subsystem" type="string" value="C4"/>
|
||||
</listOfKeyValueData>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="R" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="S" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
<fbc:listOfFluxBounds>
|
||||
<fbc:fluxBound fbc:id="c0" fbc:reaction="R16" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c1" fbc:reaction="R16" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c2" fbc:reaction="R03" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c3" fbc:reaction="R03" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c4" fbc:reaction="R02" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c5" fbc:reaction="R02" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c6" fbc:reaction="R05" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c7" fbc:reaction="R05" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c8" fbc:reaction="R07" fbc:operation="greaterEqual" fbc:value="2"/>
|
||||
<fbc:fluxBound fbc:id="c9" fbc:reaction="R07" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c10" fbc:reaction="R04" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c11" fbc:reaction="R04" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c12" fbc:reaction="R01" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c13" fbc:reaction="R01" fbc:operation="lessEqual" fbc:value="1"/>
|
||||
<fbc:fluxBound fbc:id="c14" fbc:reaction="R17" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c15" fbc:reaction="R17" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c16" fbc:reaction="R14" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c17" fbc:reaction="R14" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c18" fbc:reaction="R15" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c19" fbc:reaction="R15" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c20" fbc:reaction="R12" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c21" fbc:reaction="R12" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c22" fbc:reaction="R13" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c23" fbc:reaction="R13" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c24" fbc:reaction="R10" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c25" fbc:reaction="R10" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c26" fbc:reaction="R11" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c27" fbc:reaction="R11" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c28" fbc:reaction="R09" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c29" fbc:reaction="R09" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c30" fbc:reaction="R08" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c31" fbc:reaction="R08" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c32" fbc:reaction="R06" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c33" fbc:reaction="R06" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c34" fbc:reaction="R18" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c35" fbc:reaction="R18" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c36" fbc:reaction="R19" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c37" fbc:reaction="R19" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c38" fbc:reaction="R26" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c39" fbc:reaction="R26" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c40" fbc:reaction="R25" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c41" fbc:reaction="R25" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c42" fbc:reaction="R24" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c43" fbc:reaction="R24" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c44" fbc:reaction="R23" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c45" fbc:reaction="R23" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c46" fbc:reaction="R22" fbc:operation="greaterEqual" fbc:value="0"/>
|
||||
<fbc:fluxBound fbc:id="c47" fbc:reaction="R22" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c48" fbc:reaction="R21" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c49" fbc:reaction="R21" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
<fbc:fluxBound fbc:id="c50" fbc:reaction="R20" fbc:operation="greaterEqual" fbc:value="-1000"/>
|
||||
<fbc:fluxBound fbc:id="c51" fbc:reaction="R20" fbc:operation="lessEqual" fbc:value="1000"/>
|
||||
</fbc:listOfFluxBounds>
|
||||
<fbc:listOfObjectives fbc:activeObjective="OBJF">
|
||||
<fbc:objective fbc:id="OBJF" fbc:type="maximize">
|
||||
<fbc:listOfFluxObjectives>
|
||||
<fbc:fluxObjective fbc:reaction="R26" fbc:coefficient="1"/>
|
||||
</fbc:listOfFluxObjectives>
|
||||
</fbc:objective>
|
||||
</fbc:listOfObjectives>
|
||||
</model>
|
||||
</sbml>
|
||||
3
docs/OldTutorial/MODEL_01196/log.txt
Normal file
3
docs/OldTutorial/MODEL_01196/log.txt
Normal file
|
|
@ -0,0 +1,3 @@
|
|||
Total Simulation Time: 0.02813 seconds for MODEL_01196
|
||||
|
||||
|
||||
1
docs/OldTutorial/MODEL_01196/schematic_preferences.json
Normal file
1
docs/OldTutorial/MODEL_01196/schematic_preferences.json
Normal file
|
|
@ -0,0 +1 @@
|
|||
[]
|
||||
466
docs/OldTutorial/Population.xml
Normal file
466
docs/OldTutorial/Population.xml
Normal file
|
|
@ -0,0 +1,466 @@
|
|||
<?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="Population">
|
||||
<listOfFunctionDefinitions>
|
||||
<functionDefinition id="get2DArrayElement" name="get2DArrayElement">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<lambda>
|
||||
<bvar>
|
||||
<ci> a </ci>
|
||||
</bvar>
|
||||
<bvar>
|
||||
<ci> b </ci>
|
||||
</bvar>
|
||||
<bvar>
|
||||
<ci> c </ci>
|
||||
</bvar>
|
||||
<ci> a </ci>
|
||||
</lambda>
|
||||
</math>
|
||||
</functionDefinition>
|
||||
</listOfFunctionDefinitions>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Grid" spatialDimensions="3" size="1" constant="true">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species metaid="iBioSim26" id="CII" compartment="Grid" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
</species>
|
||||
</listOfSpecies>
|
||||
<listOfParameters>
|
||||
<parameter metaid="iBioSim2" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
|
||||
<parameter metaid="iBioSim3" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim4" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
|
||||
<parameter metaid="iBioSim5" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim6" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
|
||||
<parameter metaid="iBioSim7" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim8" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim9" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim10" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim11" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim12" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim13" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
|
||||
<parameter metaid="iBioSim14" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
|
||||
<parameter metaid="iBioSim15" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
|
||||
<parameter metaid="iBioSim16" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim17" id="nr" name="Initial RNAP count" value="30" constant="true"/>
|
||||
<parameter metaid="iBioSim18" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim19" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
|
||||
<parameter metaid="iBioSim20" id="ng" name="Initial promoter count" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim21" id="np" name="Stoichiometry of production" value="10" constant="true"/>
|
||||
<parameter metaid="iBioSim22" id="ka" name="Activated production rate" value="0.25" constant="true"/>
|
||||
<parameter metaid="iBioSim23" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim24" id="lambda__locations" value="0" constant="false">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:C1="(0,0)"/>
|
||||
</annotation>
|
||||
</parameter>
|
||||
<parameter id="Divide__locations" value="0" constant="false">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:C2="(0,1)"/>
|
||||
</annotation>
|
||||
</parameter>
|
||||
</listOfParameters>
|
||||
<listOfReactions>
|
||||
<reaction metaid="Degradation_CII" sboTerm="SBO:0000179" id="Degradation_CII" reversible="false" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecd </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="kecd" value="0.005" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="Diffusion_CII_Above" id="Diffusion_CII_Above" reversible="true" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<apply>
|
||||
<minus/>
|
||||
<ci> i </ci>
|
||||
<cn type="integer"> 1 </cn>
|
||||
</apply>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> j </ci>
|
||||
<cn type="integer"> 0 </cn>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="Diffusion_CII_Below" id="Diffusion_CII_Below" reversible="true" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> i </ci>
|
||||
<cn type="integer"> 1 </cn>
|
||||
</apply>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> j </ci>
|
||||
<cn type="integer"> 0 </cn>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="Diffusion_CII_Left" id="Diffusion_CII_Left" reversible="true" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> i </ci>
|
||||
<cn type="integer"> 0 </cn>
|
||||
</apply>
|
||||
<apply>
|
||||
<minus/>
|
||||
<ci> j </ci>
|
||||
<cn type="integer"> 1 </cn>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="Diffusion_CII_Right" id="Diffusion_CII_Right" reversible="true" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,2)"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kecdiff </ci>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> i </ci>
|
||||
<cn type="integer"> 0 </cn>
|
||||
</apply>
|
||||
<apply>
|
||||
<plus/>
|
||||
<ci> j </ci>
|
||||
<cn type="integer"> 1 </cn>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="kecdiff" value="1" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="MembraneDiffusion_CII" id="MembraneDiffusion_CII" reversible="true" fast="false" compartment="Grid">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="grid"/>
|
||||
</annotation>
|
||||
<listOfReactants>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="CII" stoichiometry="1" constant="false"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<minus/>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> kmdiff_f </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
<apply>
|
||||
<times/>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> kmdiff_r </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
<apply>
|
||||
<ci> get2DArrayElement </ci>
|
||||
<ci> CII </ci>
|
||||
<ci> i </ci>
|
||||
<ci> j </ci>
|
||||
</apply>
|
||||
</apply>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="i">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="0"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
<localParameter id="j">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</localParameter>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
<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:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:id="TextGlyph__C1" layout:text="C1" layout:graphicalObject="Glyph__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:id="TextGlyph__C2" layout:text="C2" layout:graphicalObject="Glyph__C2">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="140" layout:y="30"/>
|
||||
<layout:dimensions layout:width="80" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
<layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:generalGlyph layout:id="Glyph__C1" layout:reference="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:id="Glyph__C2" layout:reference="C2">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="140" layout:y="30"/>
|
||||
<layout:dimensions layout:width="80" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
</layout:generalGlyph>
|
||||
</layout:listOfAdditionalGraphicalObjects>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<comp:listOfSubmodels>
|
||||
<comp:submodel metaid="iBioSim25" comp:id="GRID__lambda" comp:modelRef="lambda">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
<comp:listOfDeletions>
|
||||
<comp:deletion comp:portRef="rule__Total"/>
|
||||
<comp:deletion comp:portRef="constraint__CI20"/>
|
||||
<comp:deletion comp:portRef="constraint__CII50"/>
|
||||
<comp:deletion comp:portRef="event__CellDivision"/>
|
||||
</comp:listOfDeletions>
|
||||
</comp:submodel>
|
||||
<comp:submodel comp:id="GRID__Divide" comp:modelRef="Divide">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:size="1"/>
|
||||
</annotation>
|
||||
</comp:submodel>
|
||||
</comp:listOfSubmodels>
|
||||
</model>
|
||||
<comp:listOfExternalModelDefinitions>
|
||||
<comp:externalModelDefinition comp:id="lambda" comp:source="file:lambda.xml" comp:md5="9fb1f105f55254ab934bf32ed25a0708"/>
|
||||
<comp:externalModelDefinition comp:id="Divide" comp:source="file:Divide.xml" comp:md5="0a417cb64224a4ab9c9b82acab9082d4"/>
|
||||
</comp:listOfExternalModelDefinitions>
|
||||
</sbml>
|
||||
63
docs/OldTutorial/Population/Population.grf
Normal file
63
docs/OldTutorial/Population/Population.grf
Normal file
|
|
@ -0,0 +1,63 @@
|
|||
#Graph Data
|
||||
#Mon Jun 10 14:26:23 MDT 2013
|
||||
species.filled.2=true
|
||||
species.filled.1=true
|
||||
species.filled.0=true
|
||||
chart.background.paint=-1118482
|
||||
species.connected.3=true
|
||||
plot.background.paint=-1
|
||||
species.connected.2=true
|
||||
species.connected.1=true
|
||||
species.connected.0=true
|
||||
species.xnumber.3=0
|
||||
species.xnumber.2=0
|
||||
y.max=62.7
|
||||
species.id.3=C11__CII (1)
|
||||
species.xnumber.1=0
|
||||
species.id.2=C11__CII (1)
|
||||
species.xnumber.0=0
|
||||
auto.resize=true
|
||||
species.id.1=C10__CII (1)
|
||||
species.number.3=17
|
||||
species.id.0=C10__C1__S0 (1)
|
||||
species.number.2=17
|
||||
species.visible.3=true
|
||||
species.number.1=5
|
||||
species.visible.2=true
|
||||
y.axis=amount
|
||||
species.number.0=0
|
||||
species.visible.1=true
|
||||
species.visible.0=true
|
||||
species.paint.3=Green
|
||||
species.paint.2=Yellow
|
||||
species.directory.3=
|
||||
species.paint.1=Red
|
||||
species.directory.2=
|
||||
species.paint.0=Blue
|
||||
species.directory.1=
|
||||
species.directory.0=
|
||||
x.max=500.0
|
||||
title=Population simulation results
|
||||
y.scale=5.0
|
||||
x.scale=25.0
|
||||
species.shape.3=Triangle
|
||||
species.name.3=C11__CII(\u03C7)
|
||||
y.min=0.0
|
||||
species.shape.2=Diamond
|
||||
species.name.2=C11__CII(1)
|
||||
species.shape.1=Square
|
||||
species.name.1=C10__CII (1)
|
||||
species.name.0=C10__C1__S0 (1)
|
||||
species.shape.0=Circle
|
||||
x.axis=time
|
||||
LogY=false
|
||||
LogX=false
|
||||
plot.range.grid.line.paint=-4144960
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
species.run.number.3=Average
|
||||
species.run.number.2=run-1
|
||||
species.run.number.1=run-1
|
||||
species.run.number.0=run-1
|
||||
visibleLegend=true
|
||||
species.filled.3=true
|
||||
x.min=0.0
|
||||
11
docs/OldTutorial/Population/Population.prb
Normal file
11
docs/OldTutorial/Population/Population.prb
Normal file
|
|
@ -0,0 +1,11 @@
|
|||
#Probability Data
|
||||
#Sun Jun 09 18:21:36 MDT 2013
|
||||
visibleLegend=true
|
||||
x.axis=
|
||||
plot.background.paint=-1
|
||||
y.axis=Percent
|
||||
chart.background.paint=-1118482
|
||||
title=Population simulation results
|
||||
gradient=false
|
||||
plot.range.grid.line.paint=-4144960
|
||||
shadow=false
|
||||
27
docs/OldTutorial/Population/Population.properties
Normal file
27
docs/OldTutorial/Population/Population.properties
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
#Population Properties
|
||||
#Sun Jun 23 12:47:27 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=2
|
||||
reb2sac.simulation.method=Browser
|
||||
ode.simulation.time.limit=500.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
monte.carlo.simulation.time.limit=500.0
|
||||
simulation.printer.tracking.quantity=amount
|
||||
simulation.printer=tsd.printer
|
||||
monte.carlo.simulation.min.time.step=0.0
|
||||
ode.simulation.absolute.error=1.0E-9
|
||||
ode.simulation.print.interval=10.0
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
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=rkf45
|
||||
2
docs/OldTutorial/Population/Population.sim
Normal file
2
docs/OldTutorial/Population/Population.sim
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
Population.xml
|
||||
|
||||
1238
docs/OldTutorial/Population/Population.xhtml
Normal file
1238
docs/OldTutorial/Population/Population.xhtml
Normal file
File diff suppressed because it is too large
Load diff
1153
docs/OldTutorial/Population/Population.xml
Normal file
1153
docs/OldTutorial/Population/Population.xml
Normal file
File diff suppressed because it is too large
Load diff
9
docs/OldTutorial/Population/log.txt
Normal file
9
docs/OldTutorial/Population/log.txt
Normal file
|
|
@ -0,0 +1,9 @@
|
|||
Executing:
|
||||
reb2sac --target.encoding=xhtml --out=Population.xhtml /Users/myers/research/nobackup/workspace/BioSim/docs/Tutorial/Population/Population.xml
|
||||
|
||||
Total Simulation Time: 1.067807 second for Population
|
||||
|
||||
|
||||
Executing:
|
||||
open /Users/myers/research/nobackup/workspace/BioSim/docs/Tutorial/Population/Population.xhtml
|
||||
|
||||
1
docs/OldTutorial/Population/mean.tsd
Normal file
1
docs/OldTutorial/Population/mean.tsd
Normal file
File diff suppressed because one or more lines are too long
1
docs/OldTutorial/Population/percent-term-time.tsd
Normal file
1
docs/OldTutorial/Population/percent-term-time.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time"),(0.0),(10.0),(20.0),(30.0),(40.0),(50.0),(60.0),(70.0),(80.0),(90.0),(100.0),(110.0),(120.0),(130.0),(140.0),(150.0),(160.0),(170.0),(180.0),(190.0),(200.0),(210.0),(220.0),(230.0),(240.0),(250.0),(260.0),(270.0),(280.0),(290.0),(300.0),(310.0),(320.0),(330.0),(340.0),(350.0),(360.0),(370.0),(380.0),(390.0),(400.0),(410.0),(420.0),(430.0),(440.0),(450.0),(460.0),(470.0),(480.0),(490.0),(500.0))
|
||||
1
docs/OldTutorial/Population/run-1.tsd
Normal file
1
docs/OldTutorial/Population/run-1.tsd
Normal file
File diff suppressed because one or more lines are too long
1
docs/OldTutorial/Population/run-2.tsd
Normal file
1
docs/OldTutorial/Population/run-2.tsd
Normal file
File diff suppressed because one or more lines are too long
1
docs/OldTutorial/Population/schematic_preferences.json
Normal file
1
docs/OldTutorial/Population/schematic_preferences.json
Normal file
|
|
@ -0,0 +1 @@
|
|||
[]
|
||||
2
docs/OldTutorial/Population/sim-rep.txt
Normal file
2
docs/OldTutorial/Population/sim-rep.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
#total time-limit
|
||||
2 2
|
||||
1
docs/OldTutorial/Population/standard_deviation.tsd
Normal file
1
docs/OldTutorial/Population/standard_deviation.tsd
Normal file
File diff suppressed because one or more lines are too long
3088
docs/OldTutorial/Population/statistics.txt
Normal file
3088
docs/OldTutorial/Population/statistics.txt
Normal file
File diff suppressed because it is too large
Load diff
1
docs/OldTutorial/Population/term-time.tsd
Normal file
1
docs/OldTutorial/Population/term-time.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time"),(0.0),(10.0),(20.0),(30.0),(40.0),(50.0),(60.0),(70.0),(80.0),(90.0),(100.0),(110.0),(120.0),(130.0),(140.0),(150.0),(160.0),(170.0),(180.0),(190.0),(200.0),(210.0),(220.0),(230.0),(240.0),(250.0),(260.0),(270.0),(280.0),(290.0),(300.0),(310.0),(320.0),(330.0),(340.0),(350.0),(360.0),(370.0),(380.0),(390.0),(400.0),(410.0),(420.0),(430.0),(440.0),(450.0),(460.0),(470.0),(480.0),(490.0),(500.0))
|
||||
0
docs/OldTutorial/Population/term-time.txt
Normal file
0
docs/OldTutorial/Population/term-time.txt
Normal file
1
docs/OldTutorial/Population/variance.tsd
Normal file
1
docs/OldTutorial/Population/variance.tsd
Normal file
File diff suppressed because one or more lines are too long
90
docs/OldTutorial/SweepTest.xml
Normal file
90
docs/OldTutorial/SweepTest.xml
Normal file
|
|
@ -0,0 +1,90 @@
|
|||
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
||||
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
|
||||
<model id="SweepTest" metaid="iBioSim1">
|
||||
<annotation>
|
||||
</annotation>
|
||||
<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: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="0" layout:height="0" 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__S0" layout:species="S0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="156" layout:y="87"/>
|
||||
<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="213" layout:y="183"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__R0__substrate__S0" layout:role="substrate" layout:speciesGlyph="Glyph__S0"/>
|
||||
</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__S0" layout:id="TextGlyph__S0" layout:text="S0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="156" layout:y="87"/>
|
||||
<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="213" layout:y="183"/>
|
||||
<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">
|
||||
<annotation>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="S0" constant="false" initialAmount="100" hasOnlySubstanceUnits="true" metaid="iBioSim2" boundaryCondition="false" compartment="Cell">
|
||||
<annotation>
|
||||
</annotation>
|
||||
</species>
|
||||
</listOfSpecies>
|
||||
<listOfReactions>
|
||||
<reaction id="R0" metaid="iBioSim3" reversible="false" fast="false" compartment="Cell">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="S0" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<ci> kf </ci>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="kf" value="0.1"/>
|
||||
<localParameter id="kr" value="1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
</model>
|
||||
</sbml>
|
||||
1
docs/OldTutorial/SweepTest/SweepTest.sim
Normal file
1
docs/OldTutorial/SweepTest/SweepTest.sim
Normal file
|
|
@ -0,0 +1 @@
|
|||
SweepTest.xml
|
||||
0
docs/OldTutorial/SweepTest/SweepTest.xml
Normal file
0
docs/OldTutorial/SweepTest/SweepTest.xml
Normal file
97
docs/OldTutorial/TestDivide.xml
Normal file
97
docs/OldTutorial/TestDivide.xml
Normal file
|
|
@ -0,0 +1,97 @@
|
|||
<?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="TestDivide">
|
||||
<listOfFunctionDefinitions>
|
||||
<functionDefinition id="get2DArrayElement" name="get2DArrayElement">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<lambda>
|
||||
<bvar>
|
||||
<ci> a </ci>
|
||||
</bvar>
|
||||
<bvar>
|
||||
<ci> b </ci>
|
||||
</bvar>
|
||||
<bvar>
|
||||
<ci> c </ci>
|
||||
</bvar>
|
||||
<ci> a </ci>
|
||||
</lambda>
|
||||
</math>
|
||||
</functionDefinition>
|
||||
</listOfFunctionDefinitions>
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Grid" spatialDimensions="3" size="1" constant="true">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(1,1)"/>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfParameters>
|
||||
<parameter metaid="iBioSim2" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
|
||||
<parameter metaid="iBioSim3" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim4" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
|
||||
<parameter metaid="iBioSim5" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim6" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
|
||||
<parameter metaid="iBioSim7" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim8" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim9" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim10" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim11" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim12" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim13" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
|
||||
<parameter metaid="iBioSim14" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
|
||||
<parameter metaid="iBioSim15" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
|
||||
<parameter metaid="iBioSim16" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim17" id="nr" name="Initial RNAP count" value="30" constant="true"/>
|
||||
<parameter metaid="iBioSim18" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim19" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
|
||||
<parameter metaid="iBioSim20" id="ng" name="Initial promoter count" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim21" id="np" name="Stoichiometry of production" value="10" constant="true"/>
|
||||
<parameter metaid="iBioSim22" id="ka" name="Activated production rate" value="0.25" constant="true"/>
|
||||
<parameter metaid="iBioSim23" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim24" id="Divide__locations" value="0" constant="false">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:C1="(0,0)"/>
|
||||
</annotation>
|
||||
</parameter>
|
||||
</listOfParameters>
|
||||
<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:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:id="TextGlyph__C1" layout:text="C1" layout:graphicalObject="Glyph__C1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="30" layout:y="30"/>
|
||||
<layout:dimensions layout:width="80" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
<layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:generalGlyph layout:id="Glyph__C1" layout:reference="C1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="30" layout:y="30"/>
|
||||
<layout:dimensions layout:width="80" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
</layout:generalGlyph>
|
||||
</layout:listOfAdditionalGraphicalObjects>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<comp:listOfSubmodels>
|
||||
<comp:submodel metaid="iBioSim25" comp:id="GRID__Divide" comp:modelRef="Divide">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:count="1"/>
|
||||
</annotation>
|
||||
</comp:submodel>
|
||||
</comp:listOfSubmodels>
|
||||
</model>
|
||||
<comp:listOfExternalModelDefinitions>
|
||||
<comp:externalModelDefinition comp:id="Divide" comp:source="file:Divide.xml" comp:md5="0a417cb64224a4ab9c9b82acab9082d4"/>
|
||||
</comp:listOfExternalModelDefinitions>
|
||||
</sbml>
|
||||
19
docs/OldTutorial/TestDivide/TestDivide.grf
Normal file
19
docs/OldTutorial/TestDivide/TestDivide.grf
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
#Graph Data
|
||||
#Wed Jun 05 16:52:08 MDT 2013
|
||||
visibleLegend=true
|
||||
x.axis=time
|
||||
auto.resize=true
|
||||
y.max=1.0
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
x.max=1.0
|
||||
plot.background.paint=-1
|
||||
y.axis=amount
|
||||
chart.background.paint=-1118482
|
||||
x.scale=0.1
|
||||
LogY=false
|
||||
LogX=false
|
||||
title=TestDivide simulation results
|
||||
plot.range.grid.line.paint=-4144960
|
||||
y.min=-1.0
|
||||
y.scale=0.1
|
||||
x.min=-1.0
|
||||
27
docs/OldTutorial/TestDivide/TestDivide.properties
Normal file
27
docs/OldTutorial/TestDivide/TestDivide.properties
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
#TestDivide Properties
|
||||
#Tue Jun 04 17:34:33 MDT 2013
|
||||
reb2sac.operator.max.concentration.threshold=15
|
||||
reb2sac.qssa.condition.1=0.1
|
||||
monte.carlo.simulation.time.step=100.0
|
||||
monte.carlo.simulation.print.interval=1.0
|
||||
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=1000.0
|
||||
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=SSA-Direct (Java)
|
||||
reb2sac.iSSA.type=medianPath
|
||||
2
docs/OldTutorial/TestDivide/TestDivide.sim
Normal file
2
docs/OldTutorial/TestDivide/TestDivide.sim
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
TestDivide.xml
|
||||
|
||||
123
docs/OldTutorial/TestDivide/TestDivide.xml
Normal file
123
docs/OldTutorial/TestDivide/TestDivide.xml
Normal file
|
|
@ -0,0 +1,123 @@
|
|||
<?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="TestDivide" name="Created by iBioSim flatten routine" substanceUnits="mole" volumeUnits="litre">
|
||||
<listOfUnitDefinitions>
|
||||
<unitDefinition id="u_1_second_n1">
|
||||
<listOfUnits>
|
||||
<unit kind="second" exponent="-1" scale="0" multiplier="1"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Grid" spatialDimensions="3" size="1" constant="true">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:grid="(4,5)"/>
|
||||
</annotation>
|
||||
</compartment>
|
||||
<compartment id="C1__Cell" spatialDimensions="3" size="1" constant="true"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species metaid="C1__iBioSim2" id="C1__S0" compartment="C1__Cell" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
|
||||
</listOfSpecies>
|
||||
<listOfParameters>
|
||||
<parameter metaid="iBioSim2" id="kr_f" name="Forward repression binding rate" value="0.5" constant="true"/>
|
||||
<parameter metaid="iBioSim3" id="kr_r" name="Reverse repression binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim4" id="ka_f" name="Forward activation binding rate" value="0.0033" constant="true"/>
|
||||
<parameter metaid="iBioSim5" id="ka_r" name="Reverse activation binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim6" id="ko_f" name="Forward RNAP binding rate" value="0.033" constant="true"/>
|
||||
<parameter metaid="iBioSim7" id="ko_r" name="Reverse RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim8" id="kao_f" name="Forward activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim9" id="kao_r" name="Reverse activated RNAP binding rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim10" id="kc_f" name="Forward complex formation rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim11" id="kc_r" name="Reverse complex formation rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim12" id="kmdiff_f" name="Forward membrane diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim13" id="kmdiff_r" name="Reverse membrane diffusion rate" value="0.01" constant="true"/>
|
||||
<parameter metaid="iBioSim14" id="kd" name="Degradation rate" value="0.0075" constant="true"/>
|
||||
<parameter metaid="iBioSim15" id="kecd" name="Extracellular degradation rate" value="0.005" constant="true"/>
|
||||
<parameter metaid="iBioSim16" id="nc" name="Stoichiometry of binding" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim17" id="nr" name="Initial RNAP count" value="30" constant="true"/>
|
||||
<parameter metaid="iBioSim18" id="ko" name="Open complex production rate" value="0.05" constant="true"/>
|
||||
<parameter metaid="iBioSim19" id="kb" name="Basal production rate" value="0.0001" constant="true"/>
|
||||
<parameter metaid="iBioSim20" id="ng" name="Initial promoter count" value="2" constant="true"/>
|
||||
<parameter metaid="iBioSim21" id="np" name="Stoichiometry of production" value="10" constant="true"/>
|
||||
<parameter metaid="iBioSim22" id="ka" name="Activated production rate" value="0.25" constant="true"/>
|
||||
<parameter metaid="iBioSim23" id="kecdiff" name="Extracellular diffusion rate" value="1" constant="true"/>
|
||||
<parameter metaid="iBioSim24" id="Divide__locations" value="0" constant="false">
|
||||
<annotation>
|
||||
<array:array xmlns:array="http://www.fakeuri.com" array:C1="(0,0)"/>
|
||||
</annotation>
|
||||
</parameter>
|
||||
<parameter metaid="C1__iBioSim3" id="C1__kd" name="Degradation rate" value="0.0075" constant="true"/>
|
||||
<parameter metaid="C1__iBioSim4" id="C1__np" name="Stoichiometry of production" value="10" constant="true"/>
|
||||
<parameter metaid="C1__iBioSim5" id="C1__ko" name="Open complex production rate" value="0.05" constant="true"/>
|
||||
</listOfParameters>
|
||||
<listOfReactions>
|
||||
<reaction id="Constitutive_production_C1__S0" reversible="false" fast="false" compartment="Grid">
|
||||
<listOfProducts>
|
||||
<speciesReference species="C1__S0" stoichiometry="10" constant="true"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<ci> kp </ci>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="kp" value="0.05"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="Degradation_C1__S0" reversible="false" fast="false" compartment="Grid">
|
||||
<listOfReactants>
|
||||
<speciesReference species="C1__S0" stoichiometry="1" constant="true"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kd </ci>
|
||||
<ci> C1__S0 </ci>
|
||||
</apply>
|
||||
</math>
|
||||
<listOfLocalParameters>
|
||||
<localParameter id="kd" value="0.0075" units="u_1_second_n1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
<listOfEvents>
|
||||
<event id="C1__SymmetricDivision__event0" 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"> 200 </cn>
|
||||
</math>
|
||||
</delay>
|
||||
</event>
|
||||
<event id="C1__Death__event1" useValuesFromTriggerTime="false">
|
||||
<annotation>
|
||||
<ibiosim:ibiosim xmlns:ibiosim="http://www.fakeuri.com" ibiosim:type="Death"/>
|
||||
</annotation>
|
||||
<trigger initialValue="false" persistent="false">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<gt/>
|
||||
<ci> C1__S0 </ci>
|
||||
<cn type="integer"> 50 </cn>
|
||||
</apply>
|
||||
</math>
|
||||
</trigger>
|
||||
<delay>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<cn type="integer"> 100 </cn>
|
||||
</math>
|
||||
</delay>
|
||||
</event>
|
||||
</listOfEvents>
|
||||
</model>
|
||||
</sbml>
|
||||
0
docs/OldTutorial/TestDivide/log.txt
Normal file
0
docs/OldTutorial/TestDivide/log.txt
Normal file
1
docs/OldTutorial/TestDivide/percent-term-time.tsd
Normal file
1
docs/OldTutorial/TestDivide/percent-term-time.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time"),(0.0),(100.0),(200.0),(300.0),(400.0),(500.0),(600.0),(700.0),(800.0),(900.0),(1000.0))
|
||||
2002
docs/OldTutorial/TestDivide/run-1.dtsd
Normal file
2002
docs/OldTutorial/TestDivide/run-1.dtsd
Normal file
File diff suppressed because it is too large
Load diff
2
docs/OldTutorial/TestDivide/sim-rep.txt
Normal file
2
docs/OldTutorial/TestDivide/sim-rep.txt
Normal file
|
|
@ -0,0 +1,2 @@
|
|||
#total time-limit
|
||||
1 1
|
||||
50
docs/OldTutorial/TestDivide/statistics.txt
Normal file
50
docs/OldTutorial/TestDivide/statistics.txt
Normal file
|
|
@ -0,0 +1,50 @@
|
|||
Parameter Values:
|
||||
kao_f = 1.000000
|
||||
nr = 30.000000
|
||||
C1__np = 10.000000
|
||||
ka_f = 0.003300
|
||||
nc = 2.000000
|
||||
C1__kd = 0.007500
|
||||
kr_f = 0.500000
|
||||
kmdiff_r = 0.010000
|
||||
kc_f = 0.050000
|
||||
t = 0.000000
|
||||
Degradation_C1__S0_kd = 0.007500
|
||||
ng = 2.000000
|
||||
Constitutive_production_C1__S0_kp = 0.050000
|
||||
kmdiff_f = 1.000000
|
||||
kecd = 0.005000
|
||||
ko = 0.050000
|
||||
ko_r = 1.000000
|
||||
kao_r = 1.000000
|
||||
ka = 0.250000
|
||||
kecdiff = 1.000000
|
||||
C1__ko = 0.050000
|
||||
ka_r = 1.000000
|
||||
kb = 0.000100
|
||||
kr_r = 1.000000
|
||||
np = 10.000000
|
||||
time = 0.000000
|
||||
ko_f = 0.033000
|
||||
kc_r = 1.000000
|
||||
kd = 0.007500
|
||||
Divide__locations = 0.000000
|
||||
|
||||
Initial State Vector:
|
||||
C1__S0 = 0.000000
|
||||
|
||||
Initial Reaction Rate Array:
|
||||
0.050000
|
||||
0.000000
|
||||
|
||||
Reaction Rate Equation Array:
|
||||
Constitutive_production_C1__S0_kp
|
||||
Degradation_C1__S0_kd * C1__S0
|
||||
|
||||
Reactant Matrix:
|
||||
0.000000
|
||||
1.000000
|
||||
|
||||
Delta Matrix:
|
||||
10.000000
|
||||
-1.000000
|
||||
1
docs/OldTutorial/TestDivide/term-time.tsd
Normal file
1
docs/OldTutorial/TestDivide/term-time.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time"),(0.0),(100.0),(200.0),(300.0),(400.0),(500.0),(600.0),(700.0),(800.0),(900.0),(1000.0))
|
||||
0
docs/OldTutorial/TestDivide/term-time.txt
Normal file
0
docs/OldTutorial/TestDivide/term-time.txt
Normal file
32
docs/OldTutorial/TopLevel.xml
Normal file
32
docs/OldTutorial/TopLevel.xml
Normal file
|
|
@ -0,0 +1,32 @@
|
|||
<?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="TopLevel">
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" spatialDimensions="3" size="1" constant="true"/>
|
||||
</listOfCompartments>
|
||||
<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:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:id="TextGlyph__Cell" layout:text="Cell" layout:graphicalObject="Glyph__Cell">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="0" layout:y="0"/>
|
||||
<layout:dimensions layout:width="1070" layout:height="425"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<comp:listOfPorts>
|
||||
<comp:port sboTerm="SBO:0000601" comp:idRef="Cell" comp:id="compartment__Cell"/>
|
||||
</comp:listOfPorts>
|
||||
</model>
|
||||
</sbml>
|
||||
165
docs/OldTutorial/case00987.xml
Normal file
165
docs/OldTutorial/case00987.xml
Normal file
|
|
@ -0,0 +1,165 @@
|
|||
<?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" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" version="1" layout:required="false">
|
||||
<model id="case00987" name="case00987" metaid="iBioSim1">
|
||||
<annotation>
|
||||
</annotation>
|
||||
<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="160" layout:height="230" layout:depth="0"/>
|
||||
<layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:generalGlyph layout:reference="_E0" layout:id="Glyph___E0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="140"/>
|
||||
<layout:dimensions layout:width="75" layout:height="25"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfReferenceGlyphs>
|
||||
<layout:referenceGlyph layout:id="Glyph___E0__product__k1" layout:role="product" layout:glyph="Glyph__k1"/>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
<layout:generalGlyph layout:reference="k1" layout:id="Glyph__k1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:generalGlyph>
|
||||
</layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:listOfCompartmentGlyphs>
|
||||
<layout:compartmentGlyph layout:id="Glyph__default_compartment" layout:compartment="default_compartment">
|
||||
<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__A" layout:species="A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
</layout:listOfSpeciesGlyphs>
|
||||
<layout:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__default_compartment" layout:id="TextGlyph__default_compartment" layout:text="default_compartment">
|
||||
<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__A" layout:id="TextGlyph__A" layout:text="A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__B" layout:id="TextGlyph__B" layout:text="B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__C" layout:id="TextGlyph__C" layout:text="C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph___E0" layout:id="TextGlyph___E0" layout:text="_E0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="140"/>
|
||||
<layout:dimensions layout:width="75" layout:height="25"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:graphicalObject="Glyph__k1" layout:id="TextGlyph__k1" layout:text="k1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
<listOfCompartments>
|
||||
<compartment id="default_compartment" constant="true" spatialDimensions="3" sboTerm="SBO:0000410" size="1">
|
||||
<annotation>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="A" constant="false" initialAmount="1" hasOnlySubstanceUnits="true" metaid="iBioSim3" boundaryCondition="false" compartment="default_compartment"/>
|
||||
<species id="B" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim4" boundaryCondition="false" compartment="default_compartment"/>
|
||||
<species id="C" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim5" boundaryCondition="false" compartment="default_compartment"/>
|
||||
</listOfSpecies>
|
||||
<listOfParameters>
|
||||
<parameter id="k1" constant="false" metaid="iBioSim2" value="0"/>
|
||||
</listOfParameters>
|
||||
<listOfReactions>
|
||||
<reaction id="fast" metaid="iBioSim6" reversible="true" fast="true">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="A" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="true" species="B" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> k1 </ci>
|
||||
<ci> A </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="slow" metaid="iBioSim7" reversible="true" fast="false">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="B" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="true" species="C" stoichiometry="1"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> k1 </ci>
|
||||
<ci> B </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
<listOfEvents>
|
||||
<event id="_E0" useValuesFromTriggerTime="true">
|
||||
<trigger persistent="true" initialValue="true">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<gt/>
|
||||
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
|
||||
<cn> 0.99 </cn>
|
||||
</apply>
|
||||
</math>
|
||||
</trigger>
|
||||
<listOfEventAssignments>
|
||||
<eventAssignment variable="k1">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<cn type="integer"> 1 </cn>
|
||||
</math>
|
||||
</eventAssignment>
|
||||
</listOfEventAssignments>
|
||||
</event>
|
||||
</listOfEvents>
|
||||
</model>
|
||||
</sbml>
|
||||
67
docs/OldTutorial/case00987/case00987-sedml.xml
Normal file
67
docs/OldTutorial/case00987/case00987-sedml.xml
Normal file
|
|
@ -0,0 +1,67 @@
|
|||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<sedML xmlns="http://sed-ml.org/" version="1" level="1">
|
||||
<!--This file was generated by jlibsedml, version 1.2.0.-->
|
||||
<listOfSimulations>
|
||||
<uniformTimeCourse id="simulation_1" initialTime="0.0" outputStartTime="0.0" outputEndTime="2.0" numberOfPoints="11">
|
||||
<algorithm kisaoID="KISAO:0000019" />
|
||||
</uniformTimeCourse>
|
||||
</listOfSimulations>
|
||||
<listOfModels>
|
||||
<model id="model_1" language="urn:sedml:language:sbml" source="case00987.xml" />
|
||||
</listOfModels>
|
||||
<listOfTasks>
|
||||
<task id="task_1" modelReference="model_1" simulationReference="simulation_1" />
|
||||
</listOfTasks>
|
||||
<listOfDataGenerators>
|
||||
<dataGenerator id="time_1" name="time">
|
||||
<listOfVariables>
|
||||
<variable id="time" taskReference="task_1" symbol="urn:sedml:symbol:time" />
|
||||
</listOfVariables>
|
||||
<math:math xmlns:math="http://www.w3.org/1998/Math/MathML">
|
||||
<math:ci>time</math:ci>
|
||||
</math:math>
|
||||
</dataGenerator>
|
||||
<dataGenerator id="A_1" name="A">
|
||||
<listOfVariables>
|
||||
<variable id="A" name="A" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='A']" />
|
||||
</listOfVariables>
|
||||
<math:math xmlns:math="http://www.w3.org/1998/Math/MathML">
|
||||
<math:ci>A</math:ci>
|
||||
</math:math>
|
||||
</dataGenerator>
|
||||
<dataGenerator id="B_1" name="B">
|
||||
<listOfVariables>
|
||||
<variable id="B" name="B" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='B']" />
|
||||
</listOfVariables>
|
||||
<math:math xmlns:math="http://www.w3.org/1998/Math/MathML">
|
||||
<math:ci>B</math:ci>
|
||||
</math:math>
|
||||
</dataGenerator>
|
||||
<dataGenerator id="C_1" name="C">
|
||||
<listOfVariables>
|
||||
<variable id="C" name="C" taskReference="task_1" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='C']" />
|
||||
</listOfVariables>
|
||||
<math:math xmlns:math="http://www.w3.org/1998/Math/MathML">
|
||||
<math:ci>C</math:ci>
|
||||
</math:math>
|
||||
</dataGenerator>
|
||||
</listOfDataGenerators>
|
||||
<listOfOutputs>
|
||||
<plot2D id="plot_1" name="Timecourse for test 00987">
|
||||
<listOfCurves>
|
||||
<curve id="c_A_1" name="A" logX="false" logY="false" xDataReference="time_1" yDataReference="A_1" />
|
||||
<curve id="c_B_1" name="B" logX="false" logY="false" xDataReference="time_1" yDataReference="B_1" />
|
||||
<curve id="c_C_1" name="C" logX="false" logY="false" xDataReference="time_1" yDataReference="C_1" />
|
||||
</listOfCurves>
|
||||
</plot2D>
|
||||
<report id="report_1" name="Report for test 00987">
|
||||
<listOfDataSets>
|
||||
<dataSet dataReference="time_1" id="ds_time" label="Time" />
|
||||
<dataSet dataReference="A_1" id="ds_A_1" label="A" />
|
||||
<dataSet dataReference="B_1" id="ds_B_1" label="B" />
|
||||
<dataSet dataReference="C_1" id="ds_C_1" label="C" />
|
||||
</listOfDataSets>
|
||||
</report>
|
||||
</listOfOutputs>
|
||||
</sedML>
|
||||
|
||||
52
docs/OldTutorial/case00987/case00987.grf
Normal file
52
docs/OldTutorial/case00987/case00987.grf
Normal file
|
|
@ -0,0 +1,52 @@
|
|||
#Graph Data
|
||||
#Fri Jun 07 14:29:46 MDT 2013
|
||||
species.filled.2=true
|
||||
species.filled.1=true
|
||||
species.filled.0=true
|
||||
chart.background.paint=-1118482
|
||||
plot.background.paint=-1
|
||||
species.connected.2=true
|
||||
species.connected.1=true
|
||||
species.connected.0=true
|
||||
species.xnumber.2=0
|
||||
y.max=1.0
|
||||
species.xnumber.1=0
|
||||
species.id.2=C (1)
|
||||
species.xnumber.0=0
|
||||
auto.resize=true
|
||||
species.id.1=B (1)
|
||||
species.id.0=A (1)
|
||||
species.number.2=2
|
||||
species.number.1=1
|
||||
species.visible.2=true
|
||||
y.axis=
|
||||
species.number.0=0
|
||||
species.visible.1=true
|
||||
species.visible.0=true
|
||||
species.paint.2=Black
|
||||
species.paint.1=Black
|
||||
species.directory.2=
|
||||
species.paint.0=Black
|
||||
species.directory.1=
|
||||
species.directory.0=
|
||||
x.max=1.0
|
||||
title=Timecourse for test 00987
|
||||
y.scale=0.1
|
||||
x.scale=0.1
|
||||
y.min=0.0
|
||||
species.shape.2=Circle
|
||||
species.name.2=C (1)
|
||||
species.shape.1=Circle
|
||||
species.name.1=B (1)
|
||||
species.name.0=A (1)
|
||||
species.shape.0=Circle
|
||||
x.axis=
|
||||
LogY=false
|
||||
LogX=false
|
||||
plot.range.grid.line.paint=-4144960
|
||||
plot.domain.grid.line.paint=-4144960
|
||||
species.run.number.2=run-1
|
||||
species.run.number.1=run-1
|
||||
species.run.number.0=run-1
|
||||
visibleLegend=true
|
||||
x.min=0.0
|
||||
24
docs/OldTutorial/case00987/case00987.properties
Normal file
24
docs/OldTutorial/case00987/case00987.properties
Normal file
|
|
@ -0,0 +1,24 @@
|
|||
#case00987 Properties
|
||||
#Fri Jun 07 14:29:47 MDT 2013
|
||||
monte.carlo.simulation.start.index=1
|
||||
reb2sac.operator.max.concentration.threshold=15
|
||||
reb2sac.qssa.condition.1=0.1
|
||||
ode.simulation.number.steps=11
|
||||
monte.carlo.simulation.runs=1
|
||||
reb2sac.simulation.method=ODE
|
||||
ode.simulation.time.limit=2.0
|
||||
simulation.run.termination.decider=constraint
|
||||
reb2sac.generate.statistics=false
|
||||
monte.carlo.simulation.random.seed=314159
|
||||
ode.simulation.time.step=inf
|
||||
ode.simulation.out.dir=.
|
||||
simulation.printer.tracking.quantity=amount
|
||||
simulation.printer=tsd.printer
|
||||
ode.simulation.absolute.error=1.0E-9
|
||||
ode.simulation.min.time.step=0.0
|
||||
reb2sac.abstraction.method=none
|
||||
reb2sac.abstraction.method.3.1=kinetic-law-constants-simplifier
|
||||
reb2sac.rapid.equilibrium.condition.2=0.1
|
||||
reb2sac.diffusion.stoichiometry.amplification.value=1.0
|
||||
reb2sac.rapid.equilibrium.condition.1=0.1
|
||||
selected.simulator=rkf45
|
||||
1
docs/OldTutorial/case00987/case00987.sim
Normal file
1
docs/OldTutorial/case00987/case00987.sim
Normal file
|
|
@ -0,0 +1 @@
|
|||
case00987.xml
|
||||
169
docs/OldTutorial/case00987/case00987.xml
Normal file
169
docs/OldTutorial/case00987/case00987.xml
Normal file
|
|
@ -0,0 +1,169 @@
|
|||
<?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="case00987" name="case00987">
|
||||
<listOfCompartments>
|
||||
<compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species metaid="iBioSim3" id="A" compartment="default_compartment" initialAmount="1" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
|
||||
<species metaid="iBioSim4" id="B" compartment="default_compartment" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
|
||||
<species metaid="iBioSim5" id="C" compartment="default_compartment" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
|
||||
</listOfSpecies>
|
||||
<listOfParameters>
|
||||
<parameter metaid="iBioSim2" id="k1" value="0" constant="false"/>
|
||||
</listOfParameters>
|
||||
<listOfReactions>
|
||||
<reaction metaid="iBioSim6" id="fast" reversible="true" fast="true">
|
||||
<listOfReactants>
|
||||
<speciesReference species="A" stoichiometry="1" constant="true"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="B" stoichiometry="1" constant="true"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> k1 </ci>
|
||||
<ci> A </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction metaid="iBioSim7" id="slow" reversible="true" fast="false">
|
||||
<listOfReactants>
|
||||
<speciesReference species="B" stoichiometry="1" constant="true"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference species="C" stoichiometry="1" constant="true"/>
|
||||
</listOfProducts>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> k1 </ci>
|
||||
<ci> B </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
</listOfReactions>
|
||||
<listOfEvents>
|
||||
<event id="_E0" useValuesFromTriggerTime="true">
|
||||
<trigger initialValue="true" persistent="true">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<gt/>
|
||||
<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
|
||||
<cn> 0.99 </cn>
|
||||
</apply>
|
||||
</math>
|
||||
</trigger>
|
||||
<listOfEventAssignments>
|
||||
<eventAssignment variable="k1">
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<cn type="integer"> 1 </cn>
|
||||
</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="160" layout:height="230"/>
|
||||
<layout:listOfCompartmentGlyphs>
|
||||
<layout:compartmentGlyph layout:id="Glyph__default_compartment" layout:compartment="default_compartment">
|
||||
<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__A" layout:species="A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
<layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:speciesGlyph>
|
||||
</layout:listOfSpeciesGlyphs>
|
||||
<layout:listOfTextGlyphs>
|
||||
<layout:textGlyph layout:id="TextGlyph__default_compartment" layout:text="default_compartment" layout:graphicalObject="Glyph__default_compartment">
|
||||
<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:id="TextGlyph__A" layout:text="A" layout:graphicalObject="Glyph__A">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="20" layout:y="40"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:id="TextGlyph__B" layout:text="B" layout:graphicalObject="Glyph__B">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="40" layout:y="80"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:id="TextGlyph__C" layout:text="C" layout:graphicalObject="Glyph__C">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="60" layout:y="120"/>
|
||||
<layout:dimensions layout:width="100" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:id="TextGlyph___E0" layout:text="_E0" layout:graphicalObject="Glyph___E0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="140"/>
|
||||
<layout:dimensions layout:width="75" layout:height="25"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
<layout:textGlyph layout:id="TextGlyph__k1" layout:text="k1" layout:graphicalObject="Glyph__k1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:textGlyph>
|
||||
</layout:listOfTextGlyphs>
|
||||
<layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:generalGlyph layout:id="Glyph___E0" layout:reference="_E0">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="80" layout:y="140"/>
|
||||
<layout:dimensions layout:width="75" layout:height="25"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfReferenceGlyphs>
|
||||
<layout:referenceGlyph layout:id="Glyph___E0__product__k1" layout:glyph="Glyph__k1" 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="117.5" layout:y="152.5"/>
|
||||
<layout:end layout:x="115" layout:y="215"/>
|
||||
</layout:curveSegment>
|
||||
</layout:listOfCurveSegments>
|
||||
</layout:curve>
|
||||
</layout:referenceGlyph>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
<layout:generalGlyph layout:id="Glyph__k1" layout:reference="k1">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="100" layout:y="200"/>
|
||||
<layout:dimensions layout:width="30" layout:height="30"/>
|
||||
</layout:boundingBox>
|
||||
</layout:generalGlyph>
|
||||
</layout:listOfAdditionalGraphicalObjects>
|
||||
</layout:layout>
|
||||
</layout:listOfLayouts>
|
||||
</model>
|
||||
</sbml>
|
||||
6
docs/OldTutorial/case00987/log.txt
Normal file
6
docs/OldTutorial/case00987/log.txt
Normal file
|
|
@ -0,0 +1,6 @@
|
|||
Executing:
|
||||
reb2sac --target.encoding=rkf45 /Users/myers/research/nobackup/workspace/BioSim/docs//Tutorial/case00987/case00987.xml
|
||||
|
||||
Total Simulation Time: 2.412381 seconds for case00987
|
||||
|
||||
|
||||
1
docs/OldTutorial/case00987/run-1.tsd
Normal file
1
docs/OldTutorial/case00987/run-1.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","A","B","C","k1"),(0, 1, 0, 0,0),(0.181818181818, 1, 0, 0,0),(0.363636363636, 1, 0, 0,0),(0.545454545455, 1, 0, 0,0),(0.727272727273, 1, 0, 0,0),(0.909090909091, 1, 0, 0,0),(1.09090909091, 3.33066907388e-16, 0.904024342939, 0.0959856570605,1),(1.27272727273, 3.33066907388e-16, 0.7537329339, 0.2462770661,1),(1.45454545455, 3.33066907388e-16, 0.628427033043, 0.371582966957,1),(1.63636363636, 3.33066907388e-16, 0.523952872556, 0.476057127444,1),(1.81818181818, 3.33066907388e-16, 0.436847236386, 0.563162763614,1),(2, 3.33066907388e-16, 0.36422265805, 0.63578734195,1))
|
||||
25
docs/OldTutorial/case00987/statistics.txt
Normal file
25
docs/OldTutorial/case00987/statistics.txt
Normal file
|
|
@ -0,0 +1,25 @@
|
|||
Parameter Values:
|
||||
t = 0.000000
|
||||
k1 = 0.000000
|
||||
time = 0.000000
|
||||
|
||||
Initial State Vector:
|
||||
A = 1.000000
|
||||
B = 0.000000
|
||||
C = 0.000000
|
||||
|
||||
Initial Reaction Rate Array:
|
||||
0.000000
|
||||
0.000000
|
||||
|
||||
Reaction Rate Equation Array:
|
||||
k1 * A
|
||||
k1 * B
|
||||
|
||||
Reactant Matrix:
|
||||
1.000000 0.000000 0.000000
|
||||
0.000000 1.000000 0.000000
|
||||
|
||||
Delta Matrix:
|
||||
-1.000000 1.000000 0.000000
|
||||
0.000000 -1.000000 1.000000
|
||||
0
docs/OldTutorial/case00987/term-time.txt
Normal file
0
docs/OldTutorial/case00987/term-time.txt
Normal file
644
docs/OldTutorial/lambda.xml
Normal file
644
docs/OldTutorial/lambda.xml
Normal file
|
|
@ -0,0 +1,644 @@
|
|||
<?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" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" comp:required="true" version="1" layout:required="false">
|
||||
<model id="lambda" metaid="iBioSim1" timeUnits="second" extentUnits="nanoMole" substanceUnits="nanoMole" volumeUnits="microLitre">
|
||||
<annotation>
|
||||
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#"><rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:about="#iBioSim1"><mts:DNAComponents><rdf:Seq><rdf:li rdf:resource="http://www.async.ece.utah.edu#comp_9_31_2013_17_14_57_346_iBioSim"/></rdf:Seq></mts:DNAComponents></rdf:Description></rdf:RDF></ModelToSBOL> </annotation>
|
||||
<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="0" layout:height="0"/>
|
||||
<layout:listOfAdditionalGraphicalObjects>
|
||||
<layout:generalGlyph layout:reference="CI_total" layout:id="Glyph__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:reference="Total" layout:id="Glyph__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:role="substrate" layout:glyph="Glyph__CI"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__Total__substrate__CI2" layout:role="substrate" layout:glyph="Glyph__CI2"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__Total__product__CI_total" layout:role="product" layout:glyph="Glyph__CI_total"/>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
<layout:generalGlyph layout:reference="CI20" layout:id="Glyph__CI20">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="310" layout:y="20"/>
|
||||
<layout:dimensions layout:width="50" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfReferenceGlyphs>
|
||||
<layout:referenceGlyph layout:id="Glyph__CI20__substrate__CI" layout:role="substrate" layout:glyph="Glyph__CI"/>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
<layout:generalGlyph layout:reference="CellDivision" layout:id="Glyph__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:role="substrate" layout:glyph="Glyph__CI"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI" layout:role="product" layout:glyph="Glyph__CI"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CI2" layout:role="substrate" layout:glyph="Glyph__CI2"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CI2" layout:role="product" layout:glyph="Glyph__CI2"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__CellDivision__substrate__CII" layout:role="substrate" layout:glyph="Glyph__CII"/>
|
||||
<layout:referenceGlyph layout:id="Glyph__CellDivision__product__CII" layout:role="product" layout:glyph="Glyph__CII"/>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
<layout:generalGlyph layout:reference="CII50" layout:id="Glyph__CII50">
|
||||
<layout:boundingBox>
|
||||
<layout:position layout:x="488" layout:y="174"/>
|
||||
<layout:dimensions layout:width="50" layout:height="40"/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfReferenceGlyphs>
|
||||
<layout:referenceGlyph layout:id="Glyph__CII50__substrate__CII" layout:role="substrate" layout:glyph="Glyph__CII"/>
|
||||
</layout:listOfReferenceGlyphs>
|
||||
</layout:generalGlyph>
|
||||
</layout:listOfAdditionalGraphicalObjects>
|
||||
<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:dimensions/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__CI__product__CI2" layout:role="product" layout:speciesGlyph="Glyph__CI2"/>
|
||||
</layout:listOfSpeciesReferenceGlyphs>
|
||||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__PR__Production__CII">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__PR__product__CII" layout:role="product" layout:speciesGlyph="Glyph__CII"/>
|
||||
</layout:listOfSpeciesReferenceGlyphs>
|
||||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__CI2__repression__PR">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__CI2__product__PR" layout:role="product" layout:speciesGlyph="Glyph__PR"/>
|
||||
</layout:listOfSpeciesReferenceGlyphs>
|
||||
</layout:reactionGlyph>
|
||||
<layout:reactionGlyph layout:id="Glyph__CII__repression__CI">
|
||||
<layout:boundingBox>
|
||||
<layout:position/>
|
||||
<layout:dimensions/>
|
||||
</layout:boundingBox>
|
||||
<layout:listOfSpeciesReferenceGlyphs>
|
||||
<layout:speciesReferenceGlyph layout:id="Glyph__CII__product__CI" layout:role="product" layout:speciesGlyph="Glyph__CI"/>
|
||||
</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__CI" layout:id="TextGlyph__CI" layout:text="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:graphicalObject="Glyph__CI2" layout:id="TextGlyph__CI2" layout:text="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:graphicalObject="Glyph__PR" layout:id="TextGlyph__PR" layout:text="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:graphicalObject="Glyph__CII" layout:id="TextGlyph__CII" layout:text="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:graphicalObject="Glyph__CI_total" layout:id="TextGlyph__CI_total" layout:text="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:graphicalObject="Glyph__Total" layout:id="TextGlyph__Total" layout:text="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:graphicalObject="Glyph__CI20" layout:id="TextGlyph__CI20" layout:text="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:graphicalObject="Glyph__CellDivision" layout:id="TextGlyph__CellDivision" layout:text="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:graphicalObject="Glyph__CII50" layout:id="TextGlyph__CII50" layout:text="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:layout>
|
||||
</layout:listOfLayouts>
|
||||
<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 scale="-9" exponent="1" multiplier="1" kind="mole"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
<unitDefinition id="microLitre">
|
||||
<listOfUnits>
|
||||
<unit scale="-3" exponent="1" multiplier="1" kind="litre"/>
|
||||
</listOfUnits>
|
||||
</unitDefinition>
|
||||
</listOfUnitDefinitions>
|
||||
<listOfCompartments>
|
||||
<compartment id="Cell" constant="true" spatialDimensions="3" size="1">
|
||||
<annotation>
|
||||
</annotation>
|
||||
</compartment>
|
||||
</listOfCompartments>
|
||||
<listOfSpecies>
|
||||
<species id="CI" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim2" boundaryCondition="false" compartment="Cell">
|
||||
<annotation>
|
||||
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
||||
<rdf:Description rdf:about="#iBioSim2">
|
||||
<mts:DNAComponents>
|
||||
<rdf:Seq>
|
||||
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0034"/>
|
||||
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_C0051"/>
|
||||
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
|
||||
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_B0015"/>
|
||||
</rdf:Seq>
|
||||
</mts:DNAComponents>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</ModelToSBOL>
|
||||
</annotation>
|
||||
</species>
|
||||
<species id="CI2" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim3" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="PR" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim4" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
|
||||
<species id="CII" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim6" boundaryCondition="false" compartment="Cell"/>
|
||||
<species id="PRE" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim7" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
|
||||
</listOfSpecies>
|
||||
<listOfParameters>
|
||||
<parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim10" value="0.0075"/>
|
||||
<parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim11" value="0.05"/>
|
||||
<parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim12" value="1"/>
|
||||
<parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim13" value="2"/>
|
||||
<parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim14" value="0.5"/>
|
||||
<parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim15" value="1"/>
|
||||
<parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim16" value="0.0033"/>
|
||||
<parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim17" value="1"/>
|
||||
<parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim18" value="0.033"/>
|
||||
<parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim19" value="1"/>
|
||||
<parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim20" value="1"/>
|
||||
<parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim21" value="1"/>
|
||||
<parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim22" value="30"/>
|
||||
<parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim23" value="0.05"/>
|
||||
<parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim24" value="0.0001"/>
|
||||
<parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim25" value="2"/>
|
||||
<parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim26" value="10"/>
|
||||
<parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim27" value="0.25"/>
|
||||
<parameter id="CI_total" constant="false" metaid="iBioSim9" value="0" units="nanoMole"/>
|
||||
</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 id="Degradation_CI" metaid="iBioSim28" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="CI" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kd </ci>
|
||||
<ci> CI </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="Complex_CI2" metaid="iBioSim29" reversible="true" sboTerm="SBO:0000177" fast="false" compartment="Cell">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="CI" stoichiometry="2"/>
|
||||
</listOfReactants>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="true" species="CI2" stoichiometry="1"/>
|
||||
</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 id="Degradation_CI2" metaid="iBioSim30" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="CI2" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kd </ci>
|
||||
<ci> CI2 </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="Production_PR" metaid="iBioSim5" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
|
||||
<annotation>
|
||||
<ModelToSBOL xmlns="http://sbolstandard.org/modeltosbol/1.0#">
|
||||
<rdf:RDF xmlns:mts="http://sbolstandard.org/modeltosbol/1.0#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
|
||||
<rdf:Description rdf:about="#iBioSim5">
|
||||
<mts:DNAComponents>
|
||||
<rdf:Seq>
|
||||
<rdf:li rdf:resource="http://partsregistry.org/Part:BBa_R0051"/>
|
||||
</rdf:Seq>
|
||||
</mts:DNAComponents>
|
||||
</rdf:Description>
|
||||
</rdf:RDF>
|
||||
</ModelToSBOL>
|
||||
</annotation>
|
||||
<listOfProducts>
|
||||
<speciesReference constant="true" species="CII" stoichiometry="10"/>
|
||||
</listOfProducts>
|
||||
<listOfModifiers>
|
||||
<modifierSpeciesReference species="PR" sboTerm="SBO:0000598"/>
|
||||
<modifierSpeciesReference species="CI2" sboTerm="SBO:0000020"/>
|
||||
</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="nc_CI2_r" value="1"/>
|
||||
<localParameter id="kr_CI2_f" value="0.2165"/>
|
||||
<localParameter id="kr_CI2_r" value="1"/>
|
||||
<localParameter id="ko" value="0.014"/>
|
||||
<localParameter id="ko_f" value="0.69422"/>
|
||||
<localParameter id="ko_r" value="1"/>
|
||||
</listOfLocalParameters>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="Degradation_CII" metaid="iBioSim31" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
|
||||
<listOfReactants>
|
||||
<speciesReference constant="true" species="CII" stoichiometry="1"/>
|
||||
</listOfReactants>
|
||||
<kineticLaw>
|
||||
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
||||
<apply>
|
||||
<times/>
|
||||
<ci> kd </ci>
|
||||
<ci> CII </ci>
|
||||
</apply>
|
||||
</math>
|
||||
</kineticLaw>
|
||||
</reaction>
|
||||
<reaction id="Production_PRE" metaid="iBioSim8" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
|
||||
<listOfProducts>
|
||||
<speciesReference constant="true" species="CI" stoichiometry="10"/>
|
||||
</listOfProducts>
|
||||
<listOfModifiers>
|
||||
<modifierSpeciesReference species="PRE" sboTerm="SBO:0000598"/>
|
||||
<modifierSpeciesReference species="CII" sboTerm="SBO:0000459"/>
|
||||
</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-5"/>
|
||||
<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 ibiosim:type="Symmetric Division" xmlns:ibiosim="http://www.fakeuri.com"/>
|
||||
</annotation>
|
||||
<trigger persistent="false" initialValue="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>
|
||||
</model>
|
||||
</sbml>
|
||||
31
docs/OldTutorial/lambda/abs/lambda.properties
Normal file
31
docs/OldTutorial/lambda/abs/lambda.properties
Normal file
|
|
@ -0,0 +1,31 @@
|
|||
#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
|
||||
291
docs/OldTutorial/lambda/abs/lambda.xml
Normal file
291
docs/OldTutorial/lambda/abs/lambda.xml
Normal file
|
|
@ -0,0 +1,291 @@
|
|||
<?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>
|
||||
6
docs/OldTutorial/lambda/abs/log.txt
Normal file
6
docs/OldTutorial/lambda/abs/log.txt
Normal file
|
|
@ -0,0 +1,6 @@
|
|||
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
|
||||
|
||||
|
||||
1
docs/OldTutorial/lambda/abs/mean.tsd
Normal file
1
docs/OldTutorial/lambda/abs/mean.tsd
Normal file
File diff suppressed because one or more lines are too long
1
docs/OldTutorial/lambda/abs/percent-term-time.tsd
Normal file
1
docs/OldTutorial/lambda/abs/percent-term-time.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time"),(0.0),(10.0),(20.0),(30.0),(40.0),(50.0),(60.0),(70.0),(80.0),(90.0),(100.0),(110.0),(120.0),(130.0),(140.0),(150.0),(160.0),(170.0),(180.0),(190.0),(200.0),(210.0),(220.0),(230.0),(240.0),(250.0),(260.0),(270.0),(280.0),(290.0),(300.0),(310.0),(320.0),(330.0),(340.0),(350.0),(360.0),(370.0),(380.0),(390.0),(400.0),(410.0),(420.0),(430.0),(440.0),(450.0),(460.0),(470.0),(480.0),(490.0),(500.0),(510.0),(520.0),(530.0),(540.0),(550.0),(560.0),(570.0),(580.0),(590.0),(600.0),(610.0),(620.0),(630.0),(640.0),(650.0),(660.0),(670.0),(680.0),(690.0),(700.0),(710.0),(720.0),(730.0),(740.0),(750.0),(760.0),(770.0),(780.0),(790.0),(800.0),(810.0),(820.0),(830.0),(840.0),(850.0),(860.0),(870.0),(880.0),(890.0),(900.0),(910.0),(920.0),(930.0),(940.0),(950.0),(960.0),(970.0),(980.0),(990.0),(1000.0),(1010.0),(1020.0),(1030.0),(1040.0),(1050.0),(1060.0),(1070.0),(1080.0),(1090.0),(1100.0),(1110.0),(1120.0),(1130.0),(1140.0),(1150.0),(1160.0),(1170.0),(1180.0),(1190.0),(1200.0),(1210.0),(1220.0),(1230.0),(1240.0),(1250.0),(1260.0),(1270.0),(1280.0),(1290.0),(1300.0),(1310.0),(1320.0),(1330.0),(1340.0),(1350.0),(1360.0),(1370.0),(1380.0),(1390.0),(1400.0),(1410.0),(1420.0),(1430.0),(1440.0),(1450.0),(1460.0),(1470.0),(1480.0),(1490.0),(1500.0),(1510.0),(1520.0),(1530.0),(1540.0),(1550.0),(1560.0),(1570.0),(1580.0),(1590.0),(1600.0),(1610.0),(1620.0),(1630.0),(1640.0),(1650.0),(1660.0),(1670.0),(1680.0),(1690.0),(1700.0),(1710.0),(1720.0),(1730.0),(1740.0),(1750.0),(1760.0),(1770.0),(1780.0),(1790.0),(1800.0),(1810.0),(1820.0),(1830.0),(1840.0),(1850.0),(1860.0),(1870.0),(1880.0),(1890.0),(1900.0),(1910.0),(1920.0),(1930.0),(1940.0),(1950.0),(1960.0),(1970.0),(1980.0),(1990.0),(2000.0),(2010.0),(2020.0),(2030.0),(2040.0),(2050.0),(2060.0),(2070.0),(2080.0),(2090.0),(2100.0))
|
||||
1
docs/OldTutorial/lambda/abs/run-1.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-1.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-10.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-10.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 0, 2,0),(40, 0, 2, 0, 2,0),(50, 0, 2, 0, 2,0),(60, 0, 2, 10, 2,0),(70, 0, 2, 19, 2,0),(80, 0, 2, 17, 2,0),(90, 0, 2, 16, 2,0),(100, 0, 2, 15, 2,0),(110, 19, 2, 24, 2,0),(120, 28, 2, 21, 2,0),(130, 26, 2, 19, 2,0),(140, 26, 2, 25, 2,0),(150, 25, 2, 23, 2,0),(160, 24, 2, 31, 2,0),(170, 20, 2, 25, 2,0),(180, 20, 2, 33, 2,0),(190, 19, 2, 31, 2,0),(200, 18, 2, 29, 2,0),(210, 18, 2, 28, 2,0),(220, 17, 2, 25, 2,0),(230, 16, 2, 22, 2,0),(240, 15, 2, 19, 2,0),(250, 11, 2, 15, 2,0),(260, 11, 2, 14, 2,0),(270, 10, 2, 12, 2,0),(280, 20, 2, 10, 2,0),(290, 18, 2, 10, 2,0),(300, 15, 2, 9, 2,0),(310, 14, 2, 9, 2,0),(320, 14, 2, 8, 2,0),(330, 11, 2, 8, 2,0),(340, 9, 2, 18, 2,0),(350, 19, 2, 16, 2,0),(360, 28, 2, 24, 2,0),(370, 27, 2, 34, 2,0),(380, 26, 2, 34, 2,0),(390, 25, 2, 31, 2,0),(400, 24, 2, 29, 2,0),(410, 22, 2, 29, 2,0),(420, 21, 2, 28, 2,0),(430, 21, 2, 36, 2,0),(440, 19, 2, 33, 2,0),(450, 16, 2, 32, 2,0),(460, 15, 2, 29, 2,0),(470, 14, 2, 26, 2,0),(480, 12, 2, 35, 2,0),(490, 11, 2, 31, 2,0),(500, 11, 2, 39, 2,0),(510, 18, 2, 43, 2,0),(520, 17, 2, 40, 2,0),(530, 16, 2, 56, 2,0),(540, 15, 2, 51, 2,0),(550, 14, 2, 50, 2,0),(560, 14, 2, 47, 2,0),(570, 14, 2, 53, 2,0),(580, 13, 2, 48, 2,0),(590, 23, 2, 56, 2,0),(600, 32, 2, 54, 2,0),(610, 32, 2, 49, 2,0),(620, 29, 2, 45, 2,0),(630, 28, 2, 42, 2,0),(640, 26, 2, 50, 2,0),(650, 23, 2, 68, 2,0),(660, 30, 2, 64, 2,0),(670, 29, 2, 59, 2,0),(680, 25, 2, 53, 2,0),(690, 22, 2, 51, 2,0),(700, 29, 2, 46, 2,0),(710, 27, 2, 44, 2,0),(720, 26, 2, 43, 2,0),(730, 23, 2, 41, 2,0),(740, 32, 2, 39, 2,0),(750, 41, 2, 37, 2,0),(760, 49, 2, 34, 2,0),(770, 49, 2, 31, 2,0),(780, 47, 2, 28, 2,0),(790, 42, 2, 26, 2,0),(800, 39, 2, 26, 2,0),(810, 32, 2, 23, 2,0),(820, 28, 2, 20, 2,0),(830, 26, 2, 26, 2,0),(840, 26, 2, 31, 2,0),(850, 22, 2, 27, 2,0),(860, 22, 2, 27, 2,0),(870, 19, 2, 27, 2,0),(880, 17, 2, 25, 2,0),(890, 26, 2, 24, 2,0),(900, 24, 2, 24, 2,0),(910, 20, 2, 23, 2,0),(920, 19, 2, 33, 2,0),(930, 18, 2, 32, 2,0),(940, 15, 2, 39, 2,0),(950, 13, 2, 39, 2,0),(960, 12, 2, 39, 2,0),(970, 12, 2, 36, 2,0),(980, 11, 2, 34, 2,0),(990, 21, 2, 41, 2,0),(1000, 20, 2, 39, 2,0),(1010, 20, 2, 37, 2,0),(1020, 20, 2, 44, 2,0),(1030, 19, 2, 43, 2,0),(1040, 18, 2, 46, 2,0),(1050, 16, 2, 41, 2,0),(1060, 24, 2, 37, 2,0),(1070, 22, 2, 36, 2,0),(1080, 20, 2, 33, 2,0),(1090, 18, 2, 32, 2,0),(1100, 17, 2, 40, 2,0),(1110, 17, 2, 37, 2,0),(1120, 16, 2, 34, 2,0),(1130, 15, 2, 32, 2,0),(1140, 14, 2, 41, 2,0),(1150, 14, 2, 39, 2,0),(1160, 12, 2, 34, 2,0),(1170, 10, 2, 31, 2,0),(1180, 19, 2, 31, 2,0),(1190, 18, 2, 30, 2,0),(1200, 18, 2, 29, 2,0),(1210, 25, 2, 26, 2,0),(1220, 21, 2, 34, 2,0),(1230, 18, 2, 31, 2,0),(1240, 17, 2, 30, 2,0),(1250, 13, 2, 27, 2,0),(1260, 9, 2, 26, 2,0),(1270, 19, 2, 25, 2,0),(1280, 18, 2, 23, 2,0),(1290, 16, 2, 21, 2,0),(1300, 25, 2, 17, 2,0),(1310, 23, 2, 16, 2,0),(1320, 22, 2, 22, 2,0),(1330, 20, 2, 28, 2,0),(1340, 20, 2, 25, 2,0),(1350, 19, 2, 22, 2,0),(1360, 17, 2, 22, 2,0),(1370, 16, 2, 22, 2,0),(1380, 16, 2, 19, 2,0),(1390, 16, 2, 18, 2,0),(1400, 16, 2, 26, 2,0),(1410, 13, 2, 22, 2,0),(1420, 12, 2, 31, 2,0),(1430, 11, 2, 30, 2,0),(1440, 10, 2, 38, 2,0),(1450, 10, 2, 46, 2,0),(1460, 10, 2, 42, 2,0),(1470, 8, 2, 41, 2,0),(1480, 8, 2, 35, 2,0),(1490, 8, 2, 43, 2,0),(1500, 18, 2, 42, 2,0),(1510, 17, 2, 41, 2,0),(1520, 16, 2, 38, 2,0),(1530, 15, 2, 33, 2,0),(1540, 25, 2, 31, 2,0),(1550, 22, 2, 28, 2,0),(1560, 21, 2, 28, 2,0),(1570, 19, 2, 26, 2,0),(1580, 19, 2, 22, 2,0),(1590, 17, 2, 30, 2,0),(1600, 16, 2, 26, 2,0),(1610, 16, 2, 36, 2,0),(1620, 14, 2, 43, 2,0),(1630, 12, 2, 37, 2,0),(1640, 12, 2, 34, 2,0),(1650, 21, 2, 31, 2,0),(1660, 20, 2, 30, 2,0),(1670, 30, 2, 28, 2,0),(1680, 24, 2, 26, 2,0),(1690, 24, 2, 26, 2,0),(1700, 23, 2, 25, 2,0),(1710, 22, 2, 29, 2,0),(1720, 22, 2, 26, 2,0),(1730, 21, 2, 24, 2,0),(1740, 20, 2, 31, 2,0),(1750, 18, 2, 30, 2,0),(1760, 15, 2, 25, 2,0),(1770, 12, 2, 30, 2,0),(1780, 11, 2, 29, 2,0),(1790, 11, 2, 29, 2,0),(1800, 9, 2, 26, 2,0),(1810, 9, 2, 35, 2,0),(1820, 9, 2, 41, 2,0),(1830, 8, 2, 38, 2,0),(1840, 7, 2, 37, 2,0),(1850, 7, 2, 36, 2,0),(1860, 7, 2, 33, 2,0),(1870, 7, 2, 42, 2,0),(1880, 16, 2, 36, 2,0),(1890, 15, 2, 34, 2,0),(1900, 14, 2, 32, 2,0),(1910, 13, 2, 32, 2,0),(1920, 11, 2, 28, 2,0),(1930, 11, 2, 23, 2,0),(1940, 11, 2, 21, 2,0),(1950, 21, 2, 19, 2,0),(1960, 18, 2, 19, 2,0),(1970, 17, 2, 18, 2,0),(1980, 17, 2, 17, 2,0),(1990, 16, 2, 25, 2,0),(2000, 15, 2, 23, 2,0),(2010, 13, 2, 41, 2,0),(2020, 12, 2, 39, 2,0),(2030, 11, 2, 38, 2,0),(2040, 11, 2, 45, 2,0),(2050, 11, 2, 42, 2,0),(2060, 9, 2, 37, 2,0),(2070, 9, 2, 33, 2,0),(2080, 8, 2, 29, 2,0),(2090, 8, 2, 28, 2,0),(2100, 8, 2, 24, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-100.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-100.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 10, 2,0),(20, 0, 2, 20, 2,0),(30, 0, 2, 19, 2,0),(40, 0, 2, 18, 2,0),(50, 0, 2, 16, 2,0),(60, 0, 2, 14, 2,0),(70, 0, 2, 22, 2,0),(80, 9, 2, 39, 2,0),(90, 9, 2, 35, 2,0),(100, 8, 2, 61, 2,0),(110, 6, 2, 58, 2,0),(120, 6, 2, 54, 2,0),(130, 6, 2, 51, 2,0),(140, 6, 2, 45, 2,0),(150, 6, 2, 44, 2,0),(160, 15, 2, 43, 2,0),(170, 22, 2, 40, 2,0),(180, 31, 2, 38, 2,0),(190, 27, 2, 37, 2,0),(200, 24, 2, 33, 2,0),(210, 22, 2, 27, 2,0),(220, 19, 2, 26, 2,0),(230, 19, 2, 24, 2,0),(240, 18, 2, 21, 2,0),(250, 17, 2, 21, 2,0),(260, 17, 2, 19, 2,0),(270, 16, 2, 19, 2,0),(280, 16, 2, 25, 2,0),(290, 16, 2, 21, 2,0),(300, 14, 2, 39, 2,0),(310, 13, 2, 45, 2,0),(320, 13, 2, 43, 2,0),(330, 12, 2, 41, 2,0),(340, 11, 2, 40, 2,0),(350, 10, 2, 34, 2,0),(360, 9, 2, 33, 2,0),(370, 8, 2, 32, 2,0),(380, 7, 2, 29, 2,0),(390, 7, 2, 25, 2,0),(400, 17, 2, 31, 2,0),(410, 27, 2, 28, 2,0),(420, 22, 2, 23, 2,0),(430, 22, 2, 21, 2,0),(440, 19, 2, 20, 2,0),(450, 17, 2, 28, 2,0),(460, 17, 2, 27, 2,0),(470, 15, 2, 30, 2,0),(480, 14, 2, 27, 2,0),(490, 13, 2, 25, 2,0),(500, 13, 2, 34, 2,0),(510, 12, 2, 32, 2,0),(520, 10, 2, 31, 2,0),(530, 10, 2, 27, 2,0),(540, 9, 2, 34, 2,0),(550, 8, 2, 33, 2,0),(560, 8, 2, 31, 2,0),(570, 8, 2, 30, 2,0),(580, 8, 2, 28, 2,0),(590, 7, 2, 36, 2,0),(600, 7, 2, 41, 2,0),(610, 7, 2, 39, 2,0),(620, 6, 2, 35, 2,0),(630, 6, 2, 44, 2,0),(640, 5, 2, 39, 2,0),(650, 15, 2, 35, 2,0),(660, 15, 2, 40, 2,0),(670, 13, 2, 38, 2,0),(680, 12, 2, 35, 2,0),(690, 20, 2, 52, 2,0),(700, 18, 2, 51, 2,0),(710, 18, 2, 48, 2,0),(720, 16, 2, 43, 2,0),(730, 16, 2, 41, 2,0),(740, 14, 2, 43, 2,0),(750, 14, 2, 41, 2,0),(760, 13, 2, 39, 2,0),(770, 12, 2, 38, 2,0),(780, 11, 2, 34, 2,0),(790, 10, 2, 31, 2,0),(800, 9, 2, 29, 2,0),(810, 7, 2, 26, 2,0),(820, 5, 2, 34, 2,0),(830, 5, 2, 32, 2,0),(840, 5, 2, 30, 2,0),(850, 5, 2, 38, 2,0),(860, 15, 2, 53, 2,0),(870, 22, 2, 63, 2,0),(880, 20, 2, 61, 2,0),(890, 19, 2, 57, 2,0),(900, 16, 2, 54, 2,0),(910, 16, 2, 48, 2,0),(920, 15, 2, 44, 2,0),(930, 11, 2, 43, 2,0),(940, 11, 2, 42, 2,0),(950, 10, 2, 39, 2,0),(960, 9, 2, 34, 2,0),(970, 8, 2, 32, 2,0),(980, 7, 2, 40, 2,0),(990, 16, 2, 38, 2,0),(1000, 16, 2, 46, 2,0),(1010, 13, 2, 44, 2,0),(1020, 11, 2, 41, 2,0),(1030, 11, 2, 36, 2,0),(1040, 11, 2, 33, 2,0),(1050, 11, 2, 31, 2,0),(1060, 20, 2, 40, 2,0),(1070, 19, 2, 39, 2,0),(1080, 19, 2, 34, 2,0),(1090, 17, 2, 34, 2,0),(1100, 16, 2, 29, 2,0),(1110, 14, 2, 29, 2,0),(1120, 13, 2, 29, 2,0),(1130, 13, 2, 38, 2,0),(1140, 13, 2, 35, 2,0),(1150, 13, 2, 32, 2,0),(1160, 12, 2, 37, 2,0),(1170, 12, 2, 35, 2,0),(1180, 12, 2, 32, 2,0),(1190, 11, 2, 41, 2,0),(1200, 11, 2, 41, 2,0),(1210, 8, 2, 49, 2,0),(1220, 8, 2, 47, 2,0),(1230, 8, 2, 42, 2,0),(1240, 7, 2, 51, 2,0),(1250, 16, 2, 49, 2,0),(1260, 25, 2, 45, 2,0),(1270, 23, 2, 51, 2,0),(1280, 22, 2, 47, 2,0),(1290, 21, 2, 43, 2,0),(1300, 21, 2, 41, 2,0),(1310, 20, 2, 38, 2,0),(1320, 17, 2, 33, 2,0),(1330, 17, 2, 30, 2,0),(1340, 17, 2, 27, 2,0),(1350, 16, 2, 24, 2,0),(1360, 15, 2, 20, 2,0),(1370, 15, 2, 27, 2,0),(1380, 14, 2, 24, 2,0),(1390, 12, 2, 29, 2,0),(1400, 20, 2, 27, 2,0),(1410, 19, 2, 36, 2,0),(1420, 27, 2, 34, 2,0),(1430, 25, 2, 29, 2,0),(1440, 24, 2, 36, 2,0),(1450, 23, 2, 36, 2,0),(1460, 23, 2, 34, 2,0),(1470, 22, 2, 31, 2,0),(1480, 22, 2, 29, 2,0),(1490, 30, 2, 26, 2,0),(1500, 28, 2, 26, 2,0),(1510, 28, 2, 24, 2,0),(1520, 27, 2, 30, 2,0),(1530, 26, 2, 27, 2,0),(1540, 25, 2, 27, 2,0),(1550, 33, 2, 27, 2,0),(1560, 33, 2, 25, 2,0),(1570, 32, 2, 25, 2,0),(1580, 30, 2, 24, 2,0),(1590, 30, 2, 22, 2,0),(1600, 30, 2, 20, 2,0),(1610, 26, 2, 16, 2,0),(1620, 23, 2, 15, 2,0),(1630, 21, 2, 15, 2,0),(1640, 21, 2, 15, 2,0),(1650, 20, 2, 14, 2,0),(1660, 19, 2, 23, 2,0),(1670, 17, 2, 23, 2,0),(1680, 17, 2, 22, 2,0),(1690, 17, 2, 20, 2,0),(1700, 16, 2, 20, 2,0),(1710, 14, 2, 18, 2,0),(1720, 13, 2, 26, 2,0),(1730, 11, 2, 24, 2,0),(1740, 10, 2, 24, 2,0),(1750, 10, 2, 23, 2,0),(1760, 7, 2, 21, 2,0),(1770, 16, 2, 28, 2,0),(1780, 13, 2, 24, 2,0),(1790, 11, 2, 21, 2,0),(1800, 10, 2, 20, 2,0),(1810, 10, 2, 18, 2,0),(1820, 7, 2, 17, 2,0),(1830, 7, 2, 16, 2,0),(1840, 7, 2, 15, 2,0),(1850, 7, 2, 13, 2,0),(1860, 7, 2, 12, 2,0),(1870, 17, 2, 12, 2,0),(1880, 17, 2, 10, 2,0),(1890, 17, 2, 10, 2,0),(1900, 17, 2, 9, 2,0),(1910, 14, 2, 18, 2,0),(1920, 14, 2, 26, 2,0),(1930, 14, 2, 26, 2,0),(1940, 14, 2, 25, 2,0),(1950, 23, 2, 32, 2,0),(1960, 32, 2, 31, 2,0),(1970, 31, 2, 30, 2,0),(1980, 30, 2, 28, 2,0),(1990, 27, 2, 26, 2,0),(2000, 24, 2, 24, 2,0),(2010, 21, 2, 23, 2,0),(2020, 17, 2, 23, 2,0),(2030, 15, 2, 33, 2,0),(2040, 22, 2, 53, 2,0),(2050, 21, 2, 52, 2,0),(2060, 30, 2, 50, 2,0),(2070, 34, 2, 44, 2,0),(2080, 33, 2, 44, 2,0),(2090, 39, 2, 41, 2,0),(2100, 35, 2, 37, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-11.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-11.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-12.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-12.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 10, 2,0),(30, 0, 2, 9, 2,0),(40, 0, 2, 9, 2,0),(50, 0, 2, 9, 2,0),(60, 0, 2, 18, 2,0),(70, 0, 2, 27, 2,0),(80, 0, 2, 25, 2,0),(90, 0, 2, 24, 2,0),(100, 0, 2, 23, 2,0),(110, 0, 2, 23, 2,0),(120, 0, 2, 30, 2,0),(130, 0, 2, 36, 2,0),(140, 0, 2, 36, 2,0),(150, 0, 2, 31, 2,0),(160, 0, 2, 29, 2,0),(170, 0, 2, 29, 2,0),(180, 0, 2, 28, 2,0),(190, 0, 2, 33, 2,0),(200, 0, 2, 40, 2,0),(210, 0, 2, 38, 2,0),(220, 0, 2, 51, 2,0),(230, 0, 2, 41, 2,0),(240, 9, 2, 39, 2,0),(250, 9, 2, 35, 2,0),(260, 8, 2, 33, 2,0),(270, 8, 2, 32, 2,0),(280, 7, 2, 28, 2,0),(290, 6, 2, 37, 2,0),(300, 6, 2, 43, 2,0),(310, 6, 2, 39, 2,0),(320, 5, 2, 39, 2,0),(330, 3, 2, 35, 2,0),(340, 11, 2, 32, 2,0),(350, 8, 2, 40, 2,0),(360, 8, 2, 46, 2,0),(370, 6, 2, 43, 2,0),(380, 5, 2, 40, 2,0),(390, 5, 2, 47, 2,0),(400, 5, 2, 42, 2,0),(410, 14, 2, 39, 2,0),(420, 13, 2, 44, 2,0),(430, 13, 2, 42, 2,0),(440, 13, 2, 40, 2,0),(450, 13, 2, 39, 2,0),(460, 10, 2, 36, 2,0),(470, 9, 2, 34, 2,0),(480, 7, 2, 30, 2,0),(490, 7, 2, 29, 2,0),(500, 7, 2, 26, 2,0),(510, 7, 2, 41, 2,0),(520, 17, 2, 35, 2,0),(530, 17, 2, 43, 2,0),(540, 16, 2, 41, 2,0),(550, 14, 2, 38, 2,0),(560, 13, 2, 38, 2,0),(570, 12, 2, 36, 2,0),(580, 11, 2, 32, 2,0),(590, 10, 2, 30, 2,0),(600, 19, 2, 25, 2,0),(610, 16, 2, 24, 2,0),(620, 16, 2, 20, 2,0),(630, 25, 2, 20, 2,0),(640, 23, 2, 20, 2,0),(650, 22, 2, 19, 2,0),(660, 21, 2, 18, 2,0),(670, 19, 2, 18, 2,0),(680, 19, 2, 16, 2,0),(690, 18, 2, 14, 2,0),(700, 17, 2, 24, 2,0),(710, 17, 2, 33, 2,0),(720, 16, 2, 32, 2,0),(730, 16, 2, 27, 2,0),(740, 16, 2, 24, 2,0),(750, 15, 2, 21, 2,0),(760, 14, 2, 29, 2,0),(770, 22, 2, 26, 2,0),(780, 18, 2, 22, 2,0),(790, 25, 2, 21, 2,0),(800, 32, 2, 18, 2,0),(810, 31, 2, 17, 2,0),(820, 29, 2, 16, 2,0),(830, 27, 2, 16, 2,0),(840, 23, 2, 16, 2,0),(850, 20, 2, 13, 2,0),(860, 17, 2, 13, 2,0),(870, 17, 2, 13, 2,0),(880, 25, 2, 13, 2,0),(890, 24, 2, 13, 2,0),(900, 24, 2, 11, 2,0),(910, 22, 2, 10, 2,0),(920, 21, 2, 9, 2,0),(930, 29, 2, 9, 2,0),(940, 26, 2, 7, 2,0),(950, 23, 2, 6, 2,0),(960, 22, 2, 13, 2,0),(970, 19, 2, 13, 2,0),(980, 19, 2, 12, 2,0),(990, 18, 2, 22, 2,0),(1000, 14, 2, 31, 2,0),(1010, 13, 2, 38, 2,0),(1020, 11, 2, 36, 2,0),(1030, 10, 2, 42, 2,0),(1040, 8, 2, 39, 2,0),(1050, 8, 2, 46, 2,0),(1060, 8, 2, 43, 2,0),(1070, 8, 2, 39, 2,0),(1080, 8, 2, 38, 2,0),(1090, 7, 2, 46, 2,0),(1100, 7, 2, 42, 2,0),(1110, 6, 2, 41, 2,0),(1120, 14, 2, 40, 2,0),(1130, 23, 2, 38, 2,0),(1140, 20, 2, 36, 2,0),(1150, 19, 2, 44, 2,0),(1160, 36, 2, 51, 2,0),(1170, 44, 2, 49, 2,0),(1180, 41, 2, 45, 2,0),(1190, 38, 2, 41, 2,0),(1200, 43, 2, 49, 2,0),(1210, 38, 2, 44, 2,0),(1220, 36, 2, 39, 2,0),(1230, 34, 2, 38, 2,0),(1240, 29, 2, 36, 2,0),(1250, 35, 2, 34, 2,0),(1260, 31, 2, 31, 2,0),(1270, 27, 2, 30, 2,0),(1280, 26, 2, 40, 2,0),(1290, 25, 2, 36, 2,0),(1300, 23, 2, 35, 2,0),(1310, 21, 2, 34, 2,0),(1320, 30, 2, 33, 2,0),(1330, 39, 2, 33, 2,0),(1340, 46, 2, 29, 2,0),(1350, 45, 2, 28, 2,0),(1360, 42, 2, 28, 2,0),(1370, 48, 2, 27, 2,0),(1380, 47, 2, 26, 2,0),(1390, 43, 2, 24, 2,0),(1400, 41, 2, 22, 2,0),(1410, 38, 2, 22, 2,0),(1420, 44, 2, 20, 2,0),(1430, 38, 2, 20, 2,0),(1440, 36, 2, 20, 2,0),(1450, 34, 2, 18, 2,0),(1460, 34, 2, 17, 2,0),(1470, 32, 2, 16, 2,0),(1480, 29, 2, 16, 2,0),(1490, 25, 2, 10, 2,0),(1500, 22, 2, 9, 2,0),(1510, 20, 2, 6, 2,0),(1520, 19, 2, 6, 2,0),(1530, 18, 2, 6, 2,0),(1540, 28, 2, 6, 2,0),(1550, 26, 2, 15, 2,0),(1560, 24, 2, 24, 2,0),(1570, 23, 2, 23, 2,0),(1580, 19, 2, 23, 2,0),(1590, 19, 2, 23, 2,0),(1600, 17, 2, 22, 2,0),(1610, 16, 2, 17, 2,0),(1620, 14, 2, 16, 2,0),(1630, 13, 2, 16, 2,0),(1640, 12, 2, 14, 2,0),(1650, 11, 2, 13, 2,0),(1660, 10, 2, 13, 2,0),(1670, 19, 2, 13, 2,0),(1680, 16, 2, 11, 2,0),(1690, 16, 2, 21, 2,0),(1700, 15, 2, 19, 2,0),(1710, 13, 2, 19, 2,0),(1720, 13, 2, 19, 2,0),(1730, 13, 2, 19, 2,0),(1740, 13, 2, 16, 2,0),(1750, 13, 2, 13, 2,0),(1760, 12, 2, 13, 2,0),(1770, 12, 2, 22, 2,0),(1780, 12, 2, 21, 2,0),(1790, 11, 2, 19, 2,0),(1800, 11, 2, 19, 2,0),(1810, 11, 2, 24, 2,0),(1820, 10, 2, 23, 2,0),(1830, 9, 2, 30, 2,0),(1840, 9, 2, 36, 2,0),(1850, 9, 2, 34, 2,0),(1860, 18, 2, 32, 2,0),(1870, 17, 2, 39, 2,0),(1880, 13, 2, 46, 2,0),(1890, 13, 2, 44, 2,0),(1900, 13, 2, 40, 2,0),(1910, 13, 2, 37, 2,0),(1920, 11, 2, 44, 2,0),(1930, 30, 2, 41, 2,0),(1940, 29, 2, 50, 2,0),(1950, 28, 2, 55, 2,0),(1960, 26, 2, 50, 2,0),(1970, 24, 2, 45, 2,0),(1980, 23, 2, 43, 2,0),(1990, 21, 2, 42, 2,0),(2000, 18, 2, 40, 2,0),(2010, 16, 2, 37, 2,0),(2020, 15, 2, 34, 2,0),(2030, 13, 2, 31, 2,0),(2040, 13, 2, 25, 2,0),(2050, 12, 2, 25, 2,0),(2060, 11, 2, 35, 2,0),(2070, 9, 2, 30, 2,0),(2080, 7, 2, 29, 2,0),(2090, 7, 2, 29, 2,0),(2100, 7, 2, 27, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-13.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-13.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 8, 2,0),(20, 0, 2, 7, 2,0),(30, 0, 2, 7, 2,0),(40, 0, 2, 7, 2,0),(50, 0, 2, 17, 2,0),(60, 0, 2, 25, 2,0),(70, 0, 2, 22, 2,0),(80, 0, 2, 20, 2,0),(90, 0, 2, 28, 2,0),(100, 9, 2, 45, 2,0),(110, 9, 2, 41, 2,0),(120, 7, 2, 36, 2,0),(130, 7, 2, 34, 2,0),(140, 7, 2, 38, 2,0),(150, 5, 2, 46, 2,0),(160, 4, 2, 45, 2,0),(170, 3, 2, 43, 2,0),(180, 3, 2, 39, 2,0),(190, 3, 2, 45, 2,0),(200, 3, 2, 43, 2,0),(210, 13, 2, 40, 2,0),(220, 10, 2, 46, 2,0),(230, 9, 2, 42, 2,0),(240, 9, 2, 50, 2,0),(250, 18, 2, 47, 2,0),(260, 17, 2, 43, 2,0),(270, 13, 2, 48, 2,0),(280, 23, 2, 51, 2,0),(290, 32, 2, 47, 2,0),(300, 30, 2, 46, 2,0),(310, 27, 2, 42, 2,0),(320, 25, 2, 48, 2,0),(330, 23, 2, 45, 2,0),(340, 23, 2, 37, 2,0),(350, 22, 2, 33, 2,0),(360, 31, 2, 30, 2,0),(370, 30, 2, 26, 2,0),(380, 27, 2, 32, 2,0),(390, 25, 2, 28, 2,0),(400, 31, 2, 27, 2,0),(410, 30, 2, 24, 2,0),(420, 29, 2, 22, 2,0),(430, 28, 2, 19, 2,0),(440, 34, 2, 28, 2,0),(450, 31, 2, 27, 2,0),(460, 28, 2, 35, 2,0),(470, 28, 2, 33, 2,0),(480, 27, 2, 31, 2,0),(490, 24, 2, 38, 2,0),(500, 21, 2, 36, 2,0),(510, 17, 2, 33, 2,0),(520, 14, 2, 33, 2,0),(530, 12, 2, 31, 2,0),(540, 10, 2, 29, 2,0),(550, 10, 2, 25, 2,0),(560, 10, 2, 31, 2,0),(570, 8, 2, 30, 2,0),(580, 7, 2, 30, 2,0),(590, 6, 2, 28, 2,0),(600, 6, 2, 25, 2,0),(610, 6, 2, 33, 2,0),(620, 6, 2, 32, 2,0),(630, 6, 2, 29, 2,0),(640, 6, 2, 26, 2,0),(650, 6, 2, 26, 2,0),(660, 6, 2, 25, 2,0),(670, 15, 2, 32, 2,0),(680, 15, 2, 30, 2,0),(690, 14, 2, 28, 2,0),(700, 14, 2, 25, 2,0),(710, 13, 2, 23, 2,0),(720, 13, 2, 21, 2,0),(730, 10, 2, 20, 2,0),(740, 9, 2, 17, 2,0),(750, 8, 2, 17, 2,0),(760, 8, 2, 14, 2,0),(770, 8, 2, 13, 2,0),(780, 8, 2, 10, 2,0),(790, 8, 2, 17, 2,0),(800, 8, 2, 17, 2,0),(810, 8, 2, 17, 2,0),(820, 7, 2, 26, 2,0),(830, 7, 2, 26, 2,0),(840, 6, 2, 23, 2,0),(850, 14, 2, 18, 2,0),(860, 14, 2, 17, 2,0),(870, 11, 2, 15, 2,0),(880, 10, 2, 13, 2,0),(890, 20, 2, 12, 2,0),(900, 18, 2, 10, 2,0),(910, 18, 2, 19, 2,0),(920, 18, 2, 28, 2,0),(930, 18, 2, 25, 2,0),(940, 17, 2, 24, 2,0),(950, 17, 2, 22, 2,0),(960, 14, 2, 20, 2,0),(970, 13, 2, 30, 2,0),(980, 13, 2, 25, 2,0),(990, 9, 2, 23, 2,0),(1000, 9, 2, 21, 2,0),(1010, 19, 2, 20, 2,0),(1020, 18, 2, 19, 2,0),(1030, 18, 2, 19, 2,0),(1040, 18, 2, 17, 2,0),(1050, 17, 2, 26, 2,0),(1060, 25, 2, 26, 2,0),(1070, 22, 2, 25, 2,0),(1080, 18, 2, 23, 2,0),(1090, 17, 2, 23, 2,0),(1100, 16, 2, 22, 2,0),(1110, 15, 2, 21, 2,0),(1120, 13, 2, 21, 2,0),(1130, 13, 2, 18, 2,0),(1140, 11, 2, 17, 2,0),(1150, 9, 2, 16, 2,0),(1160, 9, 2, 25, 2,0),(1170, 9, 2, 34, 2,0),(1180, 8, 2, 33, 2,0),(1190, 8, 2, 31, 2,0),(1200, 8, 2, 38, 2,0),(1210, 8, 2, 37, 2,0),(1220, 7, 2, 36, 2,0),(1230, 7, 2, 35, 2,0),(1240, 17, 2, 32, 2,0),(1250, 16, 2, 30, 2,0),(1260, 15, 2, 27, 2,0),(1270, 13, 2, 26, 2,0),(1280, 12, 2, 24, 2,0),(1290, 9, 2, 32, 2,0),(1300, 9, 2, 29, 2,0),(1310, 8, 2, 28, 2,0),(1320, 8, 2, 36, 2,0),(1330, 7, 2, 33, 2,0),(1340, 7, 2, 31, 2,0),(1350, 6, 2, 46, 2,0),(1360, 4, 2, 65, 2,0),(1370, 4, 2, 62, 2,0),(1380, 4, 2, 56, 2,0),(1390, 4, 2, 51, 2,0),(1400, 4, 2, 59, 2,0),(1410, 3, 2, 69, 2,0),(1420, 3, 2, 64, 2,0),(1430, 2, 2, 68, 2,0),(1440, 2, 2, 63, 2,0),(1450, 2, 2, 68, 2,0),(1460, 2, 2, 58, 2,0),(1470, 2, 2, 55, 2,0),(1480, 11, 2, 51, 2,0),(1490, 18, 2, 50, 2,0),(1500, 17, 2, 58, 2,0),(1510, 15, 2, 64, 2,0),(1520, 14, 2, 55, 2,0),(1530, 12, 2, 52, 2,0),(1540, 11, 2, 58, 2,0),(1550, 11, 2, 65, 2,0),(1560, 10, 2, 73, 2,0),(1570, 10, 2, 65, 2,0),(1580, 10, 2, 61, 2,0),(1590, 9, 2, 55, 2,0),(1600, 9, 2, 50, 2,0),(1610, 8, 2, 47, 2,0),(1620, 6, 2, 43, 2,0),(1630, 6, 2, 40, 2,0),(1640, 6, 2, 45, 2,0),(1650, 6, 2, 41, 2,0),(1660, 6, 2, 39, 2,0),(1670, 6, 2, 37, 2,0),(1680, 6, 2, 36, 2,0),(1690, 5, 2, 33, 2,0),(1700, 5, 2, 51, 2,0),(1710, 4, 2, 48, 2,0),(1720, 14, 2, 53, 2,0),(1730, 13, 2, 61, 2,0),(1740, 12, 2, 69, 2,0),(1750, 12, 2, 65, 2,0),(1760, 19, 2, 59, 2,0),(1770, 18, 2, 56, 2,0),(1780, 16, 2, 62, 2,0),(1790, 15, 2, 55, 2,0),(1800, 13, 2, 49, 2,0),(1810, 12, 2, 46, 2,0),(1820, 12, 2, 44, 2,0),(1830, 11, 2, 40, 2,0),(1840, 21, 2, 37, 2,0),(1850, 21, 2, 35, 2,0),(1860, 20, 2, 32, 2,0),(1870, 19, 2, 31, 2,0),(1880, 15, 2, 41, 2,0),(1890, 14, 2, 37, 2,0),(1900, 13, 2, 45, 2,0),(1910, 19, 2, 43, 2,0),(1920, 18, 2, 42, 2,0),(1930, 18, 2, 49, 2,0),(1940, 16, 2, 44, 2,0),(1950, 16, 2, 42, 2,0),(1960, 16, 2, 40, 2,0),(1970, 15, 2, 37, 2,0),(1980, 15, 2, 44, 2,0),(1990, 13, 2, 40, 2,0),(2000, 12, 2, 35, 2,0),(2010, 10, 2, 28, 2,0),(2020, 10, 2, 26, 2,0),(2030, 10, 2, 22, 2,0),(2040, 10, 2, 39, 2,0),(2050, 9, 2, 38, 2,0),(2060, 9, 2, 46, 2,0),(2070, 7, 2, 44, 2,0),(2080, 7, 2, 40, 2,0),(2090, 7, 2, 39, 2,0),(2100, 7, 2, 33, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-14.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-14.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-15.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-15.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 9, 2,0),(40, 0, 2, 8, 2,0),(50, 0, 2, 8, 2,0),(60, 0, 2, 8, 2,0),(70, 10, 2, 6, 2,0),(80, 10, 2, 6, 2,0),(90, 10, 2, 6, 2,0),(100, 9, 2, 4, 2,0),(110, 8, 2, 22, 2,0),(120, 17, 2, 27, 2,0),(130, 15, 2, 24, 2,0),(140, 14, 2, 22, 2,0),(150, 14, 2, 21, 2,0),(160, 14, 2, 21, 2,0),(170, 12, 2, 27, 2,0),(180, 11, 2, 23, 2,0),(190, 11, 2, 21, 2,0),(200, 10, 2, 29, 2,0),(210, 8, 2, 27, 2,0),(220, 6, 2, 27, 2,0),(230, 6, 2, 22, 2,0),(240, 6, 2, 22, 2,0),(250, 6, 2, 21, 2,0),(260, 5, 2, 19, 2,0),(270, 4, 2, 19, 2,0),(280, 3, 2, 18, 2,0),(290, 2, 2, 17, 2,0),(300, 2, 2, 16, 2,0),(310, 0, 2, 25, 2,0),(320, 0, 2, 24, 2,0),(330, 0, 2, 30, 2,0),(340, 0, 2, 34, 2,0),(350, 10, 2, 32, 2,0),(360, 9, 2, 29, 2,0),(370, 9, 2, 37, 2,0),(380, 8, 2, 39, 2,0),(390, 7, 2, 35, 2,0),(400, 6, 2, 32, 2,0),(410, 16, 2, 30, 2,0),(420, 15, 2, 29, 2,0),(430, 14, 2, 27, 2,0),(440, 14, 2, 34, 2,0),(450, 12, 2, 33, 2,0),(460, 12, 2, 37, 2,0),(470, 10, 2, 32, 2,0),(480, 9, 2, 29, 2,0),(490, 9, 2, 28, 2,0),(500, 8, 2, 26, 2,0),(510, 6, 2, 25, 2,0),(520, 5, 2, 22, 2,0),(530, 5, 2, 21, 2,0),(540, 5, 2, 28, 2,0),(550, 5, 2, 24, 2,0),(560, 4, 2, 24, 2,0),(570, 13, 2, 41, 2,0),(580, 13, 2, 37, 2,0),(590, 13, 2, 34, 2,0),(600, 10, 2, 33, 2,0),(610, 10, 2, 30, 2,0),(620, 10, 2, 26, 2,0),(630, 18, 2, 23, 2,0),(640, 18, 2, 20, 2,0),(650, 18, 2, 17, 2,0),(660, 16, 2, 16, 2,0),(670, 16, 2, 24, 2,0),(680, 16, 2, 22, 2,0),(690, 13, 2, 21, 2,0),(700, 11, 2, 18, 2,0),(710, 9, 2, 17, 2,0),(720, 9, 2, 15, 2,0),(730, 7, 2, 23, 2,0),(740, 5, 2, 22, 2,0),(750, 5, 2, 28, 2,0),(760, 5, 2, 25, 2,0),(770, 5, 2, 32, 2,0),(780, 5, 2, 29, 2,0),(790, 5, 2, 36, 2,0),(800, 5, 2, 34, 2,0),(810, 5, 2, 32, 2,0),(820, 4, 2, 28, 2,0),(830, 3, 2, 27, 2,0),(840, 2, 2, 24, 2,0),(850, 2, 2, 33, 2,0),(860, 2, 2, 30, 2,0),(870, 11, 2, 29, 2,0),(880, 9, 2, 26, 2,0),(890, 9, 2, 35, 2,0),(900, 9, 2, 48, 2,0),(910, 9, 2, 42, 2,0),(920, 7, 2, 36, 2,0),(930, 4, 2, 43, 2,0),(940, 4, 2, 38, 2,0),(950, 4, 2, 33, 2,0),(960, 3, 2, 30, 2,0),(970, 3, 2, 28, 2,0),(980, 3, 2, 26, 2,0),(990, 3, 2, 26, 2,0),(1000, 12, 2, 35, 2,0),(1010, 11, 2, 31, 2,0),(1020, 10, 2, 27, 2,0),(1030, 10, 2, 25, 2,0),(1040, 10, 2, 24, 2,0),(1050, 9, 2, 22, 2,0),(1060, 8, 2, 20, 2,0),(1070, 8, 2, 18, 2,0),(1080, 7, 2, 16, 2,0),(1090, 7, 2, 26, 2,0),(1100, 7, 2, 26, 2,0),(1110, 7, 2, 26, 2,0),(1120, 5, 2, 24, 2,0),(1130, 5, 2, 23, 2,0),(1140, 5, 2, 22, 2,0),(1150, 4, 2, 31, 2,0),(1160, 4, 2, 29, 2,0),(1170, 4, 2, 28, 2,0),(1180, 3, 2, 27, 2,0),(1190, 11, 2, 24, 2,0),(1200, 10, 2, 33, 2,0),(1210, 8, 2, 30, 2,0),(1220, 7, 2, 36, 2,0),(1230, 17, 2, 33, 2,0),(1240, 16, 2, 31, 2,0),(1250, 24, 2, 29, 2,0),(1260, 21, 2, 28, 2,0),(1270, 20, 2, 36, 2,0),(1280, 28, 2, 44, 2,0),(1290, 24, 2, 39, 2,0),(1300, 22, 2, 35, 2,0),(1310, 21, 2, 32, 2,0),(1320, 15, 2, 28, 2,0),(1330, 12, 2, 25, 2,0),(1340, 10, 2, 19, 2,0),(1350, 10, 2, 17, 2,0),(1360, 9, 2, 15, 2,0),(1370, 18, 2, 12, 2,0),(1380, 16, 2, 32, 2,0),(1390, 25, 2, 27, 2,0),(1400, 24, 2, 20, 2,0),(1410, 22, 2, 18, 2,0),(1420, 22, 2, 27, 2,0),(1430, 29, 2, 33, 2,0),(1440, 38, 2, 29, 2,0),(1450, 36, 2, 28, 2,0),(1460, 41, 2, 27, 2,0),(1470, 36, 2, 26, 2,0),(1480, 32, 2, 35, 2,0),(1490, 29, 2, 33, 2,0),(1500, 26, 2, 39, 2,0),(1510, 23, 2, 36, 2,0),(1520, 23, 2, 34, 2,0),(1530, 23, 2, 33, 2,0),(1540, 22, 2, 43, 2,0),(1550, 22, 2, 42, 2,0),(1560, 20, 2, 46, 2,0),(1570, 27, 2, 50, 2,0),(1580, 27, 2, 48, 2,0),(1590, 23, 2, 44, 2,0),(1600, 20, 2, 40, 2,0),(1610, 19, 2, 43, 2,0),(1620, 16, 2, 39, 2,0),(1630, 14, 2, 34, 2,0),(1640, 12, 2, 30, 2,0),(1650, 11, 2, 23, 2,0),(1660, 10, 2, 19, 2,0),(1670, 10, 2, 15, 2,0),(1680, 10, 2, 15, 2,0),(1690, 8, 2, 14, 2,0),(1700, 7, 2, 23, 2,0),(1710, 6, 2, 32, 2,0),(1720, 4, 2, 31, 2,0),(1730, 4, 2, 29, 2,0),(1740, 4, 2, 36, 2,0),(1750, 13, 2, 34, 2,0),(1760, 13, 2, 33, 2,0),(1770, 23, 2, 30, 2,0),(1780, 21, 2, 24, 2,0),(1790, 20, 2, 24, 2,0),(1800, 18, 2, 22, 2,0),(1810, 16, 2, 31, 2,0),(1820, 16, 2, 28, 2,0),(1830, 14, 2, 25, 2,0),(1840, 22, 2, 25, 2,0),(1850, 20, 2, 21, 2,0),(1860, 20, 2, 18, 2,0),(1870, 18, 2, 17, 2,0),(1880, 25, 2, 17, 2,0),(1890, 21, 2, 16, 2,0),(1900, 20, 2, 16, 2,0),(1910, 17, 2, 15, 2,0),(1920, 15, 2, 25, 2,0),(1930, 14, 2, 24, 2,0),(1940, 13, 2, 22, 2,0),(1950, 18, 2, 18, 2,0),(1960, 17, 2, 17, 2,0),(1970, 27, 2, 17, 2,0),(1980, 27, 2, 16, 2,0),(1990, 23, 2, 15, 2,0),(2000, 21, 2, 15, 2,0),(2010, 21, 2, 14, 2,0),(2020, 21, 2, 14, 2,0),(2030, 20, 2, 14, 2,0),(2040, 16, 2, 11, 2,0),(2050, 16, 2, 20, 2,0),(2060, 16, 2, 20, 2,0),(2070, 14, 2, 18, 2,0),(2080, 14, 2, 17, 2,0),(2090, 13, 2, 17, 2,0),(2100, 13, 2, 15, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-16.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-16.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 0, 2,0),(40, 0, 2, 0, 2,0),(50, 0, 2, 9, 2,0),(60, 0, 2, 9, 2,0),(70, 0, 2, 9, 2,0),(80, 0, 2, 18, 2,0),(90, 0, 2, 17, 2,0),(100, 0, 2, 15, 2,0),(110, 0, 2, 15, 2,0),(120, 0, 2, 13, 2,0),(130, 0, 2, 21, 2,0),(140, 0, 2, 18, 2,0),(150, 0, 2, 17, 2,0),(160, 0, 2, 16, 2,0),(170, 0, 2, 15, 2,0),(180, 0, 2, 24, 2,0),(190, 0, 2, 22, 2,0),(200, 0, 2, 29, 2,0),(210, 0, 2, 29, 2,0),(220, 9, 2, 33, 2,0),(230, 8, 2, 42, 2,0),(240, 8, 2, 41, 2,0),(250, 7, 2, 39, 2,0),(260, 5, 2, 47, 2,0),(270, 5, 2, 48, 2,0),(280, 5, 2, 41, 2,0),(290, 5, 2, 39, 2,0),(300, 5, 2, 44, 2,0),(310, 5, 2, 41, 2,0),(320, 3, 2, 38, 2,0),(330, 13, 2, 36, 2,0),(340, 12, 2, 31, 2,0),(350, 12, 2, 26, 2,0),(360, 11, 2, 35, 2,0),(370, 21, 2, 31, 2,0),(380, 31, 2, 28, 2,0),(390, 29, 2, 37, 2,0),(400, 36, 2, 36, 2,0),(410, 32, 2, 33, 2,0),(420, 42, 2, 30, 2,0),(430, 39, 2, 30, 2,0),(440, 44, 2, 37, 2,0),(450, 43, 2, 36, 2,0),(460, 41, 2, 34, 2,0),(470, 38, 2, 32, 2,0),(480, 34, 2, 30, 2,0),(490, 31, 2, 27, 2,0),(500, 29, 2, 25, 2,0),(510, 25, 2, 23, 2,0),(520, 25, 2, 21, 2,0),(530, 24, 2, 20, 2,0),(540, 20, 2, 20, 2,0),(550, 19, 2, 30, 2,0),(560, 18, 2, 25, 2,0),(570, 16, 2, 25, 2,0),(580, 13, 2, 24, 2,0),(590, 13, 2, 24, 2,0),(600, 13, 2, 43, 2,0),(610, 32, 2, 42, 2,0),(620, 29, 2, 39, 2,0),(630, 28, 2, 35, 2,0),(640, 27, 2, 34, 2,0),(650, 25, 2, 30, 2,0),(660, 22, 2, 28, 2,0),(670, 21, 2, 25, 2,0),(680, 20, 2, 22, 2,0),(690, 18, 2, 18, 2,0),(700, 18, 2, 17, 2,0),(710, 18, 2, 15, 2,0),(720, 28, 2, 12, 2,0),(730, 37, 2, 12, 2,0),(740, 34, 2, 21, 2,0),(750, 33, 2, 21, 2,0),(760, 32, 2, 20, 2,0),(770, 32, 2, 19, 2,0),(780, 28, 2, 16, 2,0),(790, 26, 2, 23, 2,0),(800, 25, 2, 23, 2,0),(810, 24, 2, 22, 2,0),(820, 23, 2, 22, 2,0),(830, 22, 2, 21, 2,0),(840, 21, 2, 20, 2,0),(850, 20, 2, 18, 2,0),(860, 20, 2, 18, 2,0),(870, 18, 2, 25, 2,0),(880, 18, 2, 33, 2,0),(890, 27, 2, 30, 2,0),(900, 26, 2, 26, 2,0),(910, 24, 2, 24, 2,0),(920, 22, 2, 31, 2,0),(930, 19, 2, 37, 2,0),(940, 19, 2, 35, 2,0),(950, 17, 2, 33, 2,0),(960, 16, 2, 42, 2,0),(970, 15, 2, 40, 2,0),(980, 14, 2, 39, 2,0),(990, 24, 2, 38, 2,0),(1000, 19, 2, 36, 2,0),(1010, 19, 2, 34, 2,0),(1020, 28, 2, 32, 2,0),(1030, 35, 2, 28, 2,0),(1040, 35, 2, 27, 2,0),(1050, 35, 2, 27, 2,0),(1060, 33, 2, 26, 2,0),(1070, 39, 2, 26, 2,0),(1080, 46, 2, 25, 2,0),(1090, 41, 2, 24, 2,0),(1100, 38, 2, 23, 2,0),(1110, 33, 2, 32, 2,0),(1120, 38, 2, 31, 2,0),(1130, 33, 2, 29, 2,0),(1140, 29, 2, 25, 2,0),(1150, 26, 2, 25, 2,0),(1160, 24, 2, 33, 2,0),(1170, 23, 2, 40, 2,0),(1180, 21, 2, 37, 2,0),(1190, 21, 2, 34, 2,0),(1200, 30, 2, 33, 2,0),(1210, 29, 2, 39, 2,0),(1220, 27, 2, 36, 2,0),(1230, 24, 2, 34, 2,0),(1240, 22, 2, 33, 2,0),(1250, 21, 2, 31, 2,0),(1260, 30, 2, 30, 2,0),(1270, 25, 2, 27, 2,0),(1280, 24, 2, 27, 2,0),(1290, 23, 2, 22, 2,0),(1300, 21, 2, 31, 2,0),(1310, 20, 2, 26, 2,0),(1320, 18, 2, 23, 2,0),(1330, 27, 2, 22, 2,0),(1340, 35, 2, 22, 2,0),(1350, 31, 2, 19, 2,0),(1360, 29, 2, 17, 2,0),(1370, 25, 2, 16, 2,0),(1380, 24, 2, 16, 2,0),(1390, 24, 2, 14, 2,0),(1400, 19, 2, 13, 2,0),(1410, 19, 2, 12, 2,0),(1420, 19, 2, 9, 2,0),(1430, 17, 2, 19, 2,0),(1440, 26, 2, 18, 2,0),(1450, 23, 2, 37, 2,0),(1460, 23, 2, 35, 2,0),(1470, 31, 2, 32, 2,0),(1480, 38, 2, 29, 2,0),(1490, 35, 2, 28, 2,0),(1500, 30, 2, 27, 2,0),(1510, 29, 2, 34, 2,0),(1520, 26, 2, 31, 2,0),(1530, 22, 2, 27, 2,0),(1540, 21, 2, 25, 2,0),(1550, 21, 2, 22, 2,0),(1560, 17, 2, 21, 2,0),(1570, 17, 2, 19, 2,0),(1580, 15, 2, 19, 2,0),(1590, 15, 2, 18, 2,0),(1600, 15, 2, 16, 2,0),(1610, 14, 2, 15, 2,0),(1620, 13, 2, 22, 2,0),(1630, 12, 2, 20, 2,0),(1640, 11, 2, 18, 2,0),(1650, 21, 2, 18, 2,0),(1660, 20, 2, 17, 2,0),(1670, 20, 2, 13, 2,0),(1680, 18, 2, 20, 2,0),(1690, 17, 2, 20, 2,0),(1700, 17, 2, 20, 2,0),(1710, 25, 2, 18, 2,0),(1720, 34, 2, 16, 2,0),(1730, 32, 2, 14, 2,0),(1740, 31, 2, 12, 2,0),(1750, 25, 2, 11, 2,0),(1760, 25, 2, 10, 2,0),(1770, 23, 2, 10, 2,0),(1780, 33, 2, 9, 2,0),(1790, 43, 2, 9, 2,0),(1800, 40, 2, 9, 2,0),(1810, 38, 2, 8, 2,0),(1820, 35, 2, 8, 2,0),(1830, 32, 2, 8, 2,0),(1840, 28, 2, 5, 2,0),(1850, 26, 2, 4, 2,0),(1860, 24, 2, 3, 2,0),(1870, 22, 2, 2, 2,0),(1880, 21, 2, 1, 2,0),(1890, 19, 2, 1, 2,0),(1900, 19, 2, 1, 2,0),(1910, 18, 2, 1, 2,0),(1920, 17, 2, 1, 2,0),(1930, 15, 2, 1, 2,0),(1940, 12, 2, 1, 2,0),(1950, 21, 2, 10, 2,0),(1960, 20, 2, 20, 2,0),(1970, 17, 2, 38, 2,0),(1980, 13, 2, 36, 2,0),(1990, 21, 2, 32, 2,0),(2000, 19, 2, 29, 2,0),(2010, 18, 2, 26, 2,0),(2020, 16, 2, 24, 2,0),(2030, 15, 2, 23, 2,0),(2040, 15, 2, 22, 2,0),(2050, 15, 2, 20, 2,0),(2060, 12, 2, 27, 2,0),(2070, 11, 2, 26, 2,0),(2080, 20, 2, 24, 2,0),(2090, 17, 2, 27, 2,0),(2100, 16, 2, 25, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-17.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-17.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-18.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-18.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 0, 2,0),(40, 0, 2, 28, 2,0),(50, 10, 2, 27, 2,0),(60, 10, 2, 24, 2,0),(70, 10, 2, 22, 2,0),(80, 10, 2, 22, 2,0),(90, 9, 2, 20, 2,0),(100, 7, 2, 19, 2,0),(110, 7, 2, 18, 2,0),(120, 16, 2, 16, 2,0),(130, 16, 2, 16, 2,0),(140, 15, 2, 15, 2,0),(150, 14, 2, 15, 2,0),(160, 12, 2, 14, 2,0),(170, 11, 2, 24, 2,0),(180, 20, 2, 23, 2,0),(190, 20, 2, 21, 2,0),(200, 16, 2, 18, 2,0),(210, 15, 2, 16, 2,0),(220, 14, 2, 24, 2,0),(230, 29, 2, 24, 2,0),(240, 26, 2, 31, 2,0),(250, 25, 2, 29, 2,0),(260, 33, 2, 26, 2,0),(270, 40, 2, 24, 2,0),(280, 40, 2, 22, 2,0),(290, 38, 2, 21, 2,0),(300, 37, 2, 19, 2,0),(310, 36, 2, 16, 2,0),(320, 31, 2, 16, 2,0),(330, 29, 2, 15, 2,0),(340, 28, 2, 14, 2,0),(350, 27, 2, 14, 2,0),(360, 37, 2, 14, 2,0),(370, 36, 2, 12, 2,0),(380, 35, 2, 11, 2,0),(390, 33, 2, 11, 2,0),(400, 31, 2, 21, 2,0),(410, 29, 2, 20, 2,0),(420, 27, 2, 19, 2,0),(430, 31, 2, 19, 2,0),(440, 26, 2, 16, 2,0),(450, 25, 2, 34, 2,0),(460, 24, 2, 32, 2,0),(470, 32, 2, 30, 2,0),(480, 32, 2, 28, 2,0),(490, 27, 2, 27, 2,0),(500, 26, 2, 27, 2,0),(510, 24, 2, 33, 2,0),(520, 22, 2, 30, 2,0),(530, 22, 2, 37, 2,0),(540, 20, 2, 45, 2,0),(550, 20, 2, 43, 2,0),(560, 28, 2, 40, 2,0),(570, 26, 2, 37, 2,0),(580, 24, 2, 37, 2,0),(590, 22, 2, 44, 2,0),(600, 32, 2, 41, 2,0),(610, 28, 2, 37, 2,0),(620, 26, 2, 36, 2,0),(630, 26, 2, 32, 2,0),(640, 26, 2, 31, 2,0),(650, 26, 2, 29, 2,0),(660, 26, 2, 26, 2,0),(670, 21, 2, 25, 2,0),(680, 21, 2, 23, 2,0),(690, 18, 2, 22, 2,0),(700, 16, 2, 22, 2,0),(710, 26, 2, 21, 2,0),(720, 25, 2, 17, 2,0),(730, 24, 2, 17, 2,0),(740, 19, 2, 26, 2,0),(750, 16, 2, 22, 2,0),(760, 22, 2, 21, 2,0),(770, 22, 2, 18, 2,0),(780, 19, 2, 16, 2,0),(790, 27, 2, 26, 2,0),(800, 24, 2, 24, 2,0),(810, 23, 2, 24, 2,0),(820, 23, 2, 22, 2,0),(830, 21, 2, 21, 2,0),(840, 18, 2, 19, 2,0),(850, 18, 2, 15, 2,0),(860, 16, 2, 15, 2,0),(870, 14, 2, 13, 2,0),(880, 14, 2, 11, 2,0),(890, 22, 2, 10, 2,0),(900, 21, 2, 10, 2,0),(910, 19, 2, 10, 2,0),(920, 18, 2, 7, 2,0),(930, 17, 2, 7, 2,0),(940, 27, 2, 6, 2,0),(950, 27, 2, 6, 2,0),(960, 25, 2, 6, 2,0),(970, 23, 2, 6, 2,0),(980, 21, 2, 6, 2,0),(990, 18, 2, 6, 2,0),(1000, 16, 2, 6, 2,0),(1010, 15, 2, 5, 2,0),(1020, 14, 2, 5, 2,0),(1030, 13, 2, 5, 2,0),(1040, 12, 2, 14, 2,0),(1050, 12, 2, 14, 2,0),(1060, 11, 2, 24, 2,0),(1070, 10, 2, 21, 2,0),(1080, 9, 2, 19, 2,0),(1090, 9, 2, 29, 2,0),(1100, 9, 2, 29, 2,0),(1110, 6, 2, 27, 2,0),(1120, 6, 2, 23, 2,0),(1130, 5, 2, 23, 2,0),(1140, 14, 2, 31, 2,0),(1150, 13, 2, 28, 2,0),(1160, 12, 2, 25, 2,0),(1170, 12, 2, 25, 2,0),(1180, 12, 2, 21, 2,0),(1190, 12, 2, 19, 2,0),(1200, 9, 2, 18, 2,0),(1210, 8, 2, 26, 2,0),(1220, 8, 2, 20, 2,0),(1230, 7, 2, 19, 2,0),(1240, 6, 2, 16, 2,0),(1250, 5, 2, 16, 2,0),(1260, 5, 2, 11, 2,0),(1270, 4, 2, 11, 2,0),(1280, 3, 2, 10, 2,0),(1290, 2, 2, 18, 2,0),(1300, 2, 2, 17, 2,0),(1310, 2, 2, 25, 2,0),(1320, 1, 2, 22, 2,0),(1330, 11, 2, 21, 2,0),(1340, 11, 2, 20, 2,0),(1350, 10, 2, 20, 2,0),(1360, 9, 2, 20, 2,0),(1370, 9, 2, 19, 2,0),(1380, 9, 2, 17, 2,0),(1390, 9, 2, 17, 2,0),(1400, 9, 2, 16, 2,0),(1410, 9, 2, 36, 2,0),(1420, 9, 2, 32, 2,0),(1430, 9, 2, 39, 2,0),(1440, 9, 2, 38, 2,0),(1450, 8, 2, 34, 2,0),(1460, 8, 2, 31, 2,0),(1470, 17, 2, 39, 2,0),(1480, 15, 2, 37, 2,0),(1490, 23, 2, 34, 2,0),(1500, 23, 2, 32, 2,0),(1510, 21, 2, 27, 2,0),(1520, 20, 2, 24, 2,0),(1530, 20, 2, 32, 2,0),(1540, 19, 2, 42, 2,0),(1550, 18, 2, 40, 2,0),(1560, 18, 2, 38, 2,0),(1570, 16, 2, 37, 2,0),(1580, 14, 2, 33, 2,0),(1590, 23, 2, 32, 2,0),(1600, 33, 2, 25, 2,0),(1610, 32, 2, 24, 2,0),(1620, 29, 2, 24, 2,0),(1630, 28, 2, 21, 2,0),(1640, 26, 2, 20, 2,0),(1650, 35, 2, 19, 2,0),(1660, 43, 2, 18, 2,0),(1670, 41, 2, 17, 2,0),(1680, 48, 2, 15, 2,0),(1690, 48, 2, 14, 2,0),(1700, 42, 2, 13, 2,0),(1710, 37, 2, 21, 2,0),(1720, 37, 2, 20, 2,0),(1730, 33, 2, 20, 2,0),(1740, 29, 2, 18, 2,0),(1750, 28, 2, 27, 2,0),(1760, 25, 2, 27, 2,0),(1770, 45, 2, 24, 2,0),(1780, 38, 2, 22, 2,0),(1790, 37, 2, 20, 2,0),(1800, 34, 2, 20, 2,0),(1810, 31, 2, 18, 2,0),(1820, 28, 2, 17, 2,0),(1830, 27, 2, 16, 2,0),(1840, 24, 2, 25, 2,0),(1850, 21, 2, 23, 2,0),(1860, 21, 2, 21, 2,0),(1870, 20, 2, 19, 2,0),(1880, 19, 2, 17, 2,0),(1890, 29, 2, 14, 2,0),(1900, 27, 2, 14, 2,0),(1910, 26, 2, 24, 2,0),(1920, 24, 2, 22, 2,0),(1930, 21, 2, 20, 2,0),(1940, 19, 2, 18, 2,0),(1950, 27, 2, 27, 2,0),(1960, 21, 2, 23, 2,0),(1970, 20, 2, 21, 2,0),(1980, 17, 2, 29, 2,0),(1990, 15, 2, 35, 2,0),(2000, 11, 2, 31, 2,0),(2010, 10, 2, 28, 2,0),(2020, 19, 2, 27, 2,0),(2030, 15, 2, 36, 2,0),(2040, 12, 2, 31, 2,0),(2050, 10, 2, 30, 2,0),(2060, 19, 2, 29, 2,0),(2070, 17, 2, 28, 2,0),(2080, 27, 2, 26, 2,0),(2090, 25, 2, 24, 2,0),(2100, 34, 2, 23, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-19.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-19.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 10, 2,0),(20, 0, 2, 17, 2,0),(30, 0, 2, 16, 2,0),(40, 0, 2, 15, 2,0),(50, 0, 2, 14, 2,0),(60, 0, 2, 13, 2,0),(70, 0, 2, 12, 2,0),(80, 0, 2, 11, 2,0),(90, 0, 2, 19, 2,0),(100, 10, 2, 27, 2,0),(110, 9, 2, 25, 2,0),(120, 8, 2, 22, 2,0),(130, 7, 2, 19, 2,0),(140, 7, 2, 17, 2,0),(150, 7, 2, 15, 2,0),(160, 6, 2, 21, 2,0),(170, 6, 2, 21, 2,0),(180, 5, 2, 18, 2,0),(190, 4, 2, 25, 2,0),(200, 4, 2, 24, 2,0),(210, 4, 2, 22, 2,0),(220, 3, 2, 20, 2,0),(230, 3, 2, 29, 2,0),(240, 13, 2, 36, 2,0),(250, 11, 2, 42, 2,0),(260, 10, 2, 40, 2,0),(270, 18, 2, 37, 2,0),(280, 24, 2, 35, 2,0),(290, 21, 2, 43, 2,0),(300, 19, 2, 49, 2,0),(310, 18, 2, 48, 2,0),(320, 17, 2, 55, 2,0),(330, 14, 2, 48, 2,0),(340, 13, 2, 44, 2,0),(350, 13, 2, 61, 2,0),(360, 23, 2, 59, 2,0),(370, 21, 2, 56, 2,0),(380, 20, 2, 49, 2,0),(390, 46, 2, 48, 2,0),(400, 42, 2, 47, 2,0),(410, 38, 2, 45, 2,0),(420, 38, 2, 41, 2,0),(430, 37, 2, 37, 2,0),(440, 35, 2, 37, 2,0),(450, 41, 2, 34, 2,0),(460, 38, 2, 32, 2,0),(470, 37, 2, 31, 2,0),(480, 37, 2, 30, 2,0),(490, 34, 2, 27, 2,0),(500, 34, 2, 24, 2,0),(510, 32, 2, 24, 2,0),(520, 30, 2, 20, 2,0),(530, 29, 2, 27, 2,0),(540, 24, 2, 25, 2,0),(550, 21, 2, 21, 2,0),(560, 20, 2, 21, 2,0),(570, 20, 2, 21, 2,0),(580, 20, 2, 21, 2,0),(590, 20, 2, 21, 2,0),(600, 18, 2, 21, 2,0),(610, 27, 2, 20, 2,0),(620, 23, 2, 17, 2,0),(630, 22, 2, 16, 2,0),(640, 18, 2, 15, 2,0),(650, 17, 2, 14, 2,0),(660, 16, 2, 13, 2,0),(670, 16, 2, 13, 2,0),(680, 15, 2, 12, 2,0),(690, 14, 2, 11, 2,0),(700, 12, 2, 11, 2,0),(710, 12, 2, 11, 2,0),(720, 11, 2, 10, 2,0),(730, 11, 2, 10, 2,0),(740, 10, 2, 10, 2,0),(750, 10, 2, 10, 2,0),(760, 10, 2, 9, 2,0),(770, 9, 2, 9, 2,0),(780, 9, 2, 9, 2,0),(790, 6, 2, 19, 2,0),(800, 6, 2, 17, 2,0),(810, 5, 2, 26, 2,0),(820, 5, 2, 25, 2,0),(830, 5, 2, 22, 2,0),(840, 5, 2, 31, 2,0),(850, 13, 2, 29, 2,0),(860, 12, 2, 43, 2,0),(870, 12, 2, 51, 2,0),(880, 11, 2, 48, 2,0),(890, 11, 2, 44, 2,0),(900, 17, 2, 47, 2,0),(910, 17, 2, 45, 2,0),(920, 15, 2, 50, 2,0),(930, 22, 2, 49, 2,0),(940, 41, 2, 54, 2,0),(950, 37, 2, 52, 2,0),(960, 37, 2, 49, 2,0),(970, 34, 2, 46, 2,0),(980, 33, 2, 43, 2,0),(990, 32, 2, 49, 2,0),(1000, 31, 2, 45, 2,0),(1010, 26, 2, 43, 2,0),(1020, 25, 2, 36, 2,0),(1030, 25, 2, 35, 2,0),(1040, 52, 2, 33, 2,0),(1050, 49, 2, 33, 2,0),(1060, 41, 2, 31, 2,0),(1070, 48, 2, 28, 2,0),(1080, 55, 2, 28, 2,0),(1090, 51, 2, 37, 2,0),(1100, 49, 2, 32, 2,0),(1110, 46, 2, 32, 2,0),(1120, 49, 2, 29, 2,0),(1130, 46, 2, 28, 2,0),(1140, 43, 2, 25, 2,0),(1150, 40, 2, 25, 2,0),(1160, 37, 2, 25, 2,0),(1170, 35, 2, 24, 2,0),(1180, 34, 2, 33, 2,0),(1190, 33, 2, 31, 2,0),(1200, 32, 2, 29, 2,0),(1210, 30, 2, 27, 2,0),(1220, 39, 2, 35, 2,0),(1230, 55, 2, 34, 2,0),(1240, 51, 2, 32, 2,0),(1250, 56, 2, 31, 2,0),(1260, 51, 2, 29, 2,0),(1270, 48, 2, 27, 2,0),(1280, 44, 2, 24, 2,0),(1290, 52, 2, 23, 2,0),(1300, 46, 2, 22, 2,0),(1310, 42, 2, 18, 2,0),(1320, 38, 2, 15, 2,0),(1330, 35, 2, 13, 2,0),(1340, 32, 2, 12, 2,0),(1350, 32, 2, 12, 2,0),(1360, 29, 2, 21, 2,0),(1370, 28, 2, 20, 2,0),(1380, 27, 2, 19, 2,0),(1390, 26, 2, 18, 2,0),(1400, 24, 2, 17, 2,0),(1410, 24, 2, 17, 2,0),(1420, 24, 2, 16, 2,0),(1430, 20, 2, 14, 2,0),(1440, 20, 2, 14, 2,0),(1450, 17, 2, 13, 2,0),(1460, 17, 2, 12, 2,0),(1470, 15, 2, 11, 2,0),(1480, 24, 2, 11, 2,0),(1490, 20, 2, 19, 2,0),(1500, 20, 2, 17, 2,0),(1510, 18, 2, 17, 2,0),(1520, 18, 2, 17, 2,0),(1530, 15, 2, 25, 2,0),(1540, 14, 2, 22, 2,0),(1550, 14, 2, 19, 2,0),(1560, 13, 2, 28, 2,0),(1570, 11, 2, 28, 2,0),(1580, 11, 2, 27, 2,0),(1590, 11, 2, 25, 2,0),(1600, 10, 2, 24, 2,0),(1610, 10, 2, 30, 2,0),(1620, 10, 2, 50, 2,0),(1630, 10, 2, 47, 2,0),(1640, 10, 2, 43, 2,0),(1650, 10, 2, 50, 2,0),(1660, 10, 2, 49, 2,0),(1670, 20, 2, 45, 2,0),(1680, 20, 2, 43, 2,0),(1690, 19, 2, 37, 2,0),(1700, 18, 2, 34, 2,0),(1710, 17, 2, 31, 2,0),(1720, 16, 2, 27, 2,0),(1730, 15, 2, 24, 2,0),(1740, 14, 2, 20, 2,0),(1750, 22, 2, 28, 2,0),(1760, 19, 2, 27, 2,0),(1770, 18, 2, 24, 2,0),(1780, 18, 2, 22, 2,0),(1790, 33, 2, 21, 2,0),(1800, 31, 2, 31, 2,0),(1810, 28, 2, 27, 2,0),(1820, 27, 2, 26, 2,0),(1830, 26, 2, 32, 2,0),(1840, 24, 2, 32, 2,0),(1850, 33, 2, 29, 2,0),(1860, 31, 2, 28, 2,0),(1870, 31, 2, 26, 2,0),(1880, 29, 2, 24, 2,0),(1890, 28, 2, 24, 2,0),(1900, 28, 2, 24, 2,0),(1910, 27, 2, 23, 2,0),(1920, 24, 2, 20, 2,0),(1930, 22, 2, 19, 2,0),(1940, 20, 2, 17, 2,0),(1950, 17, 2, 14, 2,0),(1960, 16, 2, 13, 2,0),(1970, 15, 2, 13, 2,0),(1980, 14, 2, 12, 2,0),(1990, 24, 2, 11, 2,0),(2000, 20, 2, 9, 2,0),(2010, 19, 2, 9, 2,0),(2020, 19, 2, 8, 2,0),(2030, 17, 2, 8, 2,0),(2040, 15, 2, 8, 2,0),(2050, 14, 2, 6, 2,0),(2060, 12, 2, 6, 2,0),(2070, 11, 2, 6, 2,0),(2080, 10, 2, 6, 2,0),(2090, 9, 2, 5, 2,0),(2100, 8, 2, 4, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-2.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-2.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-20.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-20.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 18, 2,0),(20, 0, 2, 18, 2,0),(30, 0, 2, 17, 2,0),(40, 0, 2, 17, 2,0),(50, 0, 2, 16, 2,0),(60, 0, 2, 23, 2,0),(70, 0, 2, 21, 2,0),(80, 9, 2, 31, 2,0),(90, 9, 2, 29, 2,0),(100, 9, 2, 27, 2,0),(110, 8, 2, 24, 2,0),(120, 8, 2, 21, 2,0),(130, 8, 2, 19, 2,0),(140, 17, 2, 19, 2,0),(150, 16, 2, 16, 2,0),(160, 16, 2, 16, 2,0),(170, 24, 2, 16, 2,0),(180, 23, 2, 16, 2,0),(190, 21, 2, 16, 2,0),(200, 21, 2, 15, 2,0),(210, 19, 2, 11, 2,0),(220, 17, 2, 21, 2,0),(230, 15, 2, 19, 2,0),(240, 14, 2, 29, 2,0),(250, 12, 2, 28, 2,0),(260, 21, 2, 37, 2,0),(270, 19, 2, 34, 2,0),(280, 19, 2, 32, 2,0),(290, 19, 2, 30, 2,0),(300, 17, 2, 29, 2,0),(310, 16, 2, 26, 2,0),(320, 14, 2, 26, 2,0),(330, 14, 2, 33, 2,0),(340, 11, 2, 32, 2,0),(350, 9, 2, 30, 2,0),(360, 9, 2, 29, 2,0),(370, 9, 2, 37, 2,0),(380, 9, 2, 35, 2,0),(390, 19, 2, 35, 2,0),(400, 18, 2, 43, 2,0),(410, 17, 2, 40, 2,0),(420, 16, 2, 38, 2,0),(430, 16, 2, 37, 2,0),(440, 14, 2, 44, 2,0),(450, 23, 2, 49, 2,0),(460, 21, 2, 45, 2,0),(470, 25, 2, 41, 2,0),(480, 25, 2, 38, 2,0),(490, 23, 2, 36, 2,0),(500, 23, 2, 34, 2,0),(510, 32, 2, 31, 2,0),(520, 31, 2, 30, 2,0),(530, 30, 2, 24, 2,0),(540, 27, 2, 22, 2,0),(550, 25, 2, 22, 2,0),(560, 23, 2, 20, 2,0),(570, 23, 2, 28, 2,0),(580, 19, 2, 35, 2,0),(590, 18, 2, 31, 2,0),(600, 17, 2, 29, 2,0),(610, 17, 2, 28, 2,0),(620, 16, 2, 24, 2,0),(630, 15, 2, 22, 2,0),(640, 15, 2, 29, 2,0),(650, 13, 2, 37, 2,0),(660, 11, 2, 34, 2,0),(670, 10, 2, 31, 2,0),(680, 10, 2, 27, 2,0),(690, 8, 2, 26, 2,0),(700, 8, 2, 25, 2,0),(710, 7, 2, 23, 2,0),(720, 7, 2, 23, 2,0),(730, 7, 2, 30, 2,0),(740, 6, 2, 27, 2,0),(750, 16, 2, 25, 2,0),(760, 25, 2, 23, 2,0),(770, 21, 2, 22, 2,0),(780, 20, 2, 19, 2,0),(790, 36, 2, 18, 2,0),(800, 34, 2, 16, 2,0),(810, 32, 2, 16, 2,0),(820, 38, 2, 14, 2,0),(830, 35, 2, 14, 2,0),(840, 32, 2, 13, 2,0),(850, 32, 2, 12, 2,0),(860, 39, 2, 12, 2,0),(870, 36, 2, 9, 2,0),(880, 36, 2, 19, 2,0),(890, 33, 2, 19, 2,0),(900, 31, 2, 17, 2,0),(910, 39, 2, 27, 2,0),(920, 37, 2, 26, 2,0),(930, 33, 2, 26, 2,0),(940, 32, 2, 24, 2,0),(950, 30, 2, 24, 2,0),(960, 27, 2, 22, 2,0),(970, 25, 2, 19, 2,0),(980, 24, 2, 19, 2,0),(990, 22, 2, 18, 2,0),(1000, 30, 2, 17, 2,0),(1010, 28, 2, 25, 2,0),(1020, 25, 2, 23, 2,0),(1030, 23, 2, 21, 2,0),(1040, 23, 2, 31, 2,0),(1050, 18, 2, 29, 2,0),(1060, 27, 2, 28, 2,0),(1070, 26, 2, 27, 2,0),(1080, 33, 2, 34, 2,0),(1090, 30, 2, 32, 2,0),(1100, 28, 2, 28, 2,0),(1110, 26, 2, 24, 2,0),(1120, 36, 2, 23, 2,0),(1130, 42, 2, 22, 2,0),(1140, 41, 2, 22, 2,0),(1150, 40, 2, 21, 2,0),(1160, 34, 2, 30, 2,0),(1170, 31, 2, 30, 2,0),(1180, 29, 2, 28, 2,0),(1190, 28, 2, 26, 2,0),(1200, 24, 2, 24, 2,0),(1210, 28, 2, 23, 2,0),(1220, 28, 2, 23, 2,0),(1230, 26, 2, 23, 2,0),(1240, 24, 2, 32, 2,0),(1250, 22, 2, 31, 2,0),(1260, 27, 2, 28, 2,0),(1270, 26, 2, 36, 2,0),(1280, 25, 2, 44, 2,0),(1290, 24, 2, 38, 2,0),(1300, 22, 2, 36, 2,0),(1310, 20, 2, 33, 2,0),(1320, 19, 2, 32, 2,0),(1330, 19, 2, 28, 2,0),(1340, 18, 2, 26, 2,0),(1350, 26, 2, 22, 2,0),(1360, 23, 2, 22, 2,0),(1370, 22, 2, 19, 2,0),(1380, 21, 2, 14, 2,0),(1390, 20, 2, 13, 2,0),(1400, 19, 2, 10, 2,0),(1410, 16, 2, 8, 2,0),(1420, 15, 2, 17, 2,0),(1430, 13, 2, 17, 2,0),(1440, 12, 2, 15, 2,0),(1450, 12, 2, 15, 2,0),(1460, 11, 2, 12, 2,0),(1470, 11, 2, 10, 2,0),(1480, 11, 2, 10, 2,0),(1490, 11, 2, 8, 2,0),(1500, 10, 2, 7, 2,0),(1510, 9, 2, 17, 2,0),(1520, 7, 2, 15, 2,0),(1530, 17, 2, 15, 2,0),(1540, 14, 2, 14, 2,0),(1550, 13, 2, 22, 2,0),(1560, 11, 2, 38, 2,0),(1570, 10, 2, 33, 2,0),(1580, 10, 2, 31, 2,0),(1590, 8, 2, 30, 2,0),(1600, 7, 2, 38, 2,0),(1610, 6, 2, 34, 2,0),(1620, 5, 2, 29, 2,0),(1630, 5, 2, 37, 2,0),(1640, 3, 2, 31, 2,0),(1650, 2, 2, 30, 2,0),(1660, 2, 2, 27, 2,0),(1670, 22, 2, 22, 2,0),(1680, 22, 2, 20, 2,0),(1690, 21, 2, 20, 2,0),(1700, 17, 2, 19, 2,0),(1710, 15, 2, 18, 2,0),(1720, 15, 2, 18, 2,0),(1730, 15, 2, 17, 2,0),(1740, 12, 2, 16, 2,0),(1750, 11, 2, 14, 2,0),(1760, 10, 2, 14, 2,0),(1770, 10, 2, 13, 2,0),(1780, 10, 2, 12, 2,0),(1790, 18, 2, 11, 2,0),(1800, 18, 2, 10, 2,0),(1810, 18, 2, 8, 2,0),(1820, 18, 2, 8, 2,0),(1830, 16, 2, 8, 2,0),(1840, 15, 2, 8, 2,0),(1850, 14, 2, 8, 2,0),(1860, 12, 2, 7, 2,0),(1870, 11, 2, 26, 2,0),(1880, 11, 2, 23, 2,0),(1890, 11, 2, 23, 2,0),(1900, 11, 2, 31, 2,0),(1910, 10, 2, 30, 2,0),(1920, 8, 2, 28, 2,0),(1930, 8, 2, 26, 2,0),(1940, 8, 2, 24, 2,0),(1950, 8, 2, 22, 2,0),(1960, 7, 2, 17, 2,0),(1970, 7, 2, 27, 2,0),(1980, 7, 2, 23, 2,0),(1990, 7, 2, 32, 2,0),(2000, 7, 2, 30, 2,0),(2010, 7, 2, 27, 2,0),(2020, 5, 2, 27, 2,0),(2030, 4, 2, 36, 2,0),(2040, 4, 2, 36, 2,0),(2050, 13, 2, 32, 2,0),(2060, 13, 2, 29, 2,0),(2070, 13, 2, 36, 2,0),(2080, 12, 2, 33, 2,0),(2090, 11, 2, 30, 2,0),(2100, 11, 2, 25, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-21.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-21.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 10, 2,0),(40, 0, 2, 19, 2,0),(50, 10, 2, 29, 2,0),(60, 10, 2, 27, 2,0),(70, 19, 2, 36, 2,0),(80, 19, 2, 32, 2,0),(90, 18, 2, 39, 2,0),(100, 16, 2, 36, 2,0),(110, 14, 2, 34, 2,0),(120, 13, 2, 30, 2,0),(130, 21, 2, 27, 2,0),(140, 19, 2, 24, 2,0),(150, 17, 2, 20, 2,0),(160, 16, 2, 19, 2,0),(170, 15, 2, 18, 2,0),(180, 14, 2, 37, 2,0),(190, 13, 2, 35, 2,0),(200, 13, 2, 42, 2,0),(210, 11, 2, 39, 2,0),(220, 11, 2, 36, 2,0),(230, 10, 2, 32, 2,0),(240, 9, 2, 31, 2,0),(250, 8, 2, 40, 2,0),(260, 8, 2, 39, 2,0),(270, 8, 2, 34, 2,0),(280, 7, 2, 51, 2,0),(290, 7, 2, 50, 2,0),(300, 7, 2, 69, 2,0),(310, 17, 2, 76, 2,0),(320, 12, 2, 81, 2,0),(330, 22, 2, 71, 2,0),(340, 22, 2, 78, 2,0),(350, 21, 2, 82, 2,0),(360, 18, 2, 77, 2,0),(370, 17, 2, 79, 2,0),(380, 26, 2, 76, 2,0),(390, 24, 2, 69, 2,0),(400, 31, 2, 64, 2,0),(410, 30, 2, 60, 2,0),(420, 26, 2, 56, 2,0),(430, 25, 2, 52, 2,0),(440, 23, 2, 48, 2,0),(450, 23, 2, 53, 2,0),(460, 22, 2, 49, 2,0),(470, 29, 2, 57, 2,0),(480, 28, 2, 53, 2,0),(490, 28, 2, 51, 2,0),(500, 27, 2, 43, 2,0),(510, 25, 2, 49, 2,0),(520, 22, 2, 41, 2,0),(530, 20, 2, 36, 2,0),(540, 26, 2, 44, 2,0),(550, 26, 2, 41, 2,0),(560, 23, 2, 40, 2,0),(570, 21, 2, 39, 2,0),(580, 20, 2, 37, 2,0),(590, 18, 2, 35, 2,0),(600, 18, 2, 34, 2,0),(610, 16, 2, 32, 2,0),(620, 14, 2, 29, 2,0),(630, 13, 2, 33, 2,0),(640, 13, 2, 32, 2,0),(650, 12, 2, 50, 2,0),(660, 12, 2, 45, 2,0),(670, 10, 2, 43, 2,0),(680, 10, 2, 41, 2,0),(690, 8, 2, 38, 2,0),(700, 6, 2, 33, 2,0),(710, 6, 2, 33, 2,0),(720, 6, 2, 31, 2,0),(730, 6, 2, 27, 2,0),(740, 6, 2, 26, 2,0),(750, 2, 2, 24, 2,0),(760, 1, 2, 23, 2,0),(770, 1, 2, 30, 2,0),(780, 1, 2, 25, 2,0),(790, 1, 2, 35, 2,0),(800, 1, 2, 28, 2,0),(810, 11, 2, 21, 2,0),(820, 21, 2, 20, 2,0),(830, 18, 2, 19, 2,0),(840, 16, 2, 18, 2,0),(850, 22, 2, 17, 2,0),(860, 21, 2, 23, 2,0),(870, 21, 2, 21, 2,0),(880, 21, 2, 29, 2,0),(890, 20, 2, 28, 2,0),(900, 17, 2, 26, 2,0),(910, 35, 2, 24, 2,0),(920, 35, 2, 23, 2,0),(930, 31, 2, 20, 2,0),(940, 29, 2, 20, 2,0),(950, 27, 2, 18, 2,0),(960, 24, 2, 17, 2,0),(970, 24, 2, 15, 2,0),(980, 22, 2, 15, 2,0),(990, 19, 2, 14, 2,0),(1000, 18, 2, 14, 2,0),(1010, 27, 2, 14, 2,0),(1020, 27, 2, 14, 2,0),(1030, 25, 2, 14, 2,0),(1040, 23, 2, 12, 2,0),(1050, 19, 2, 11, 2,0),(1060, 17, 2, 11, 2,0),(1070, 16, 2, 10, 2,0),(1080, 14, 2, 20, 2,0),(1090, 13, 2, 19, 2,0),(1100, 12, 2, 18, 2,0),(1110, 11, 2, 18, 2,0),(1120, 11, 2, 18, 2,0),(1130, 11, 2, 17, 2,0),(1140, 11, 2, 24, 2,0),(1150, 11, 2, 21, 2,0),(1160, 10, 2, 28, 2,0),(1170, 10, 2, 26, 2,0),(1180, 17, 2, 26, 2,0),(1190, 16, 2, 24, 2,0),(1200, 16, 2, 20, 2,0),(1210, 14, 2, 18, 2,0),(1220, 12, 2, 16, 2,0),(1230, 12, 2, 15, 2,0),(1240, 10, 2, 33, 2,0),(1250, 9, 2, 29, 2,0),(1260, 9, 2, 27, 2,0),(1270, 9, 2, 24, 2,0),(1280, 9, 2, 33, 2,0),(1290, 9, 2, 42, 2,0),(1300, 19, 2, 51, 2,0),(1310, 19, 2, 59, 2,0),(1320, 19, 2, 53, 2,0),(1330, 17, 2, 48, 2,0),(1340, 17, 2, 42, 2,0),(1350, 16, 2, 39, 2,0),(1360, 15, 2, 35, 2,0),(1370, 15, 2, 32, 2,0),(1380, 15, 2, 40, 2,0),(1390, 13, 2, 34, 2,0),(1400, 13, 2, 33, 2,0),(1410, 11, 2, 31, 2,0),(1420, 10, 2, 29, 2,0),(1430, 10, 2, 26, 2,0),(1440, 9, 2, 22, 2,0),(1450, 19, 2, 22, 2,0),(1460, 19, 2, 19, 2,0),(1470, 18, 2, 28, 2,0),(1480, 17, 2, 27, 2,0),(1490, 15, 2, 33, 2,0),(1500, 15, 2, 31, 2,0),(1510, 15, 2, 27, 2,0),(1520, 25, 2, 35, 2,0),(1530, 34, 2, 43, 2,0),(1540, 32, 2, 40, 2,0),(1550, 29, 2, 36, 2,0),(1560, 28, 2, 33, 2,0),(1570, 35, 2, 33, 2,0),(1580, 31, 2, 33, 2,0),(1590, 27, 2, 30, 2,0),(1600, 23, 2, 23, 2,0),(1610, 30, 2, 32, 2,0),(1620, 28, 2, 30, 2,0),(1630, 25, 2, 28, 2,0),(1640, 25, 2, 25, 2,0),(1650, 21, 2, 22, 2,0),(1660, 29, 2, 20, 2,0),(1670, 26, 2, 19, 2,0),(1680, 24, 2, 18, 2,0),(1690, 21, 2, 18, 2,0),(1700, 20, 2, 23, 2,0),(1710, 20, 2, 40, 2,0),(1720, 20, 2, 35, 2,0),(1730, 20, 2, 32, 2,0),(1740, 29, 2, 31, 2,0),(1750, 34, 2, 28, 2,0),(1760, 33, 2, 26, 2,0),(1770, 40, 2, 36, 2,0),(1780, 35, 2, 35, 2,0),(1790, 32, 2, 34, 2,0),(1800, 30, 2, 31, 2,0),(1810, 29, 2, 29, 2,0),(1820, 29, 2, 27, 2,0),(1830, 37, 2, 26, 2,0),(1840, 35, 2, 26, 2,0),(1850, 34, 2, 25, 2,0),(1860, 32, 2, 21, 2,0),(1870, 38, 2, 30, 2,0),(1880, 36, 2, 26, 2,0),(1890, 33, 2, 22, 2,0),(1900, 30, 2, 30, 2,0),(1910, 28, 2, 28, 2,0),(1920, 27, 2, 34, 2,0),(1930, 26, 2, 28, 2,0),(1940, 23, 2, 33, 2,0),(1950, 19, 2, 33, 2,0),(1960, 18, 2, 31, 2,0),(1970, 18, 2, 27, 2,0),(1980, 18, 2, 25, 2,0),(1990, 15, 2, 24, 2,0),(2000, 14, 2, 22, 2,0),(2010, 13, 2, 19, 2,0),(2020, 12, 2, 19, 2,0),(2030, 12, 2, 36, 2,0),(2040, 12, 2, 45, 2,0),(2050, 12, 2, 41, 2,0),(2060, 11, 2, 38, 2,0),(2070, 10, 2, 35, 2,0),(2080, 10, 2, 27, 2,0),(2090, 9, 2, 22, 2,0),(2100, 9, 2, 22, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-22.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-22.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-23.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-23.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 10, 2,0),(40, 0, 2, 20, 2,0),(50, 0, 2, 20, 2,0),(60, 0, 2, 17, 2,0),(70, 10, 2, 17, 2,0),(80, 9, 2, 14, 2,0),(90, 8, 2, 12, 2,0),(100, 8, 2, 12, 2,0),(110, 8, 2, 11, 2,0),(120, 8, 2, 10, 2,0),(130, 7, 2, 10, 2,0),(140, 7, 2, 10, 2,0),(150, 7, 2, 9, 2,0),(160, 6, 2, 8, 2,0),(170, 5, 2, 7, 2,0),(180, 4, 2, 7, 2,0),(190, 4, 2, 7, 2,0),(200, 4, 2, 6, 2,0),(210, 4, 2, 6, 2,0),(220, 4, 2, 15, 2,0),(230, 4, 2, 14, 2,0),(240, 4, 2, 20, 2,0),(250, 4, 2, 20, 2,0),(260, 2, 2, 18, 2,0),(270, 2, 2, 37, 2,0),(280, 2, 2, 35, 2,0),(290, 12, 2, 34, 2,0),(300, 12, 2, 31, 2,0),(310, 11, 2, 39, 2,0),(320, 8, 2, 36, 2,0),(330, 8, 2, 36, 2,0),(340, 17, 2, 34, 2,0),(350, 23, 2, 29, 2,0),(360, 23, 2, 27, 2,0),(370, 19, 2, 24, 2,0),(380, 27, 2, 24, 2,0),(390, 36, 2, 21, 2,0),(400, 32, 2, 19, 2,0),(410, 30, 2, 16, 2,0),(420, 29, 2, 15, 2,0),(430, 28, 2, 15, 2,0),(440, 26, 2, 24, 2,0),(450, 22, 2, 21, 2,0),(460, 20, 2, 20, 2,0),(470, 18, 2, 19, 2,0),(480, 18, 2, 17, 2,0),(490, 17, 2, 13, 2,0),(500, 17, 2, 13, 2,0),(510, 16, 2, 12, 2,0),(520, 35, 2, 20, 2,0),(530, 34, 2, 18, 2,0),(540, 32, 2, 17, 2,0),(550, 29, 2, 17, 2,0),(560, 28, 2, 17, 2,0),(570, 23, 2, 17, 2,0),(580, 23, 2, 17, 2,0),(590, 20, 2, 26, 2,0),(600, 16, 2, 23, 2,0),(610, 16, 2, 22, 2,0),(620, 12, 2, 22, 2,0),(630, 21, 2, 19, 2,0),(640, 21, 2, 26, 2,0),(650, 20, 2, 26, 2,0),(660, 19, 2, 44, 2,0),(670, 17, 2, 42, 2,0),(680, 16, 2, 37, 2,0),(690, 15, 2, 34, 2,0),(700, 15, 2, 34, 2,0),(710, 15, 2, 33, 2,0),(720, 13, 2, 32, 2,0),(730, 11, 2, 38, 2,0),(740, 10, 2, 38, 2,0),(750, 9, 2, 37, 2,0),(760, 8, 2, 46, 2,0),(770, 6, 2, 43, 2,0),(780, 6, 2, 40, 2,0),(790, 16, 2, 38, 2,0),(800, 14, 2, 33, 2,0),(810, 14, 2, 31, 2,0),(820, 14, 2, 35, 2,0),(830, 22, 2, 43, 2,0),(840, 21, 2, 38, 2,0),(850, 20, 2, 36, 2,0),(860, 20, 2, 31, 2,0),(870, 19, 2, 30, 2,0),(880, 19, 2, 36, 2,0),(890, 26, 2, 43, 2,0),(900, 25, 2, 50, 2,0),(910, 25, 2, 48, 2,0),(920, 23, 2, 43, 2,0),(930, 22, 2, 38, 2,0),(940, 31, 2, 34, 2,0),(950, 31, 2, 33, 2,0),(960, 28, 2, 29, 2,0),(970, 28, 2, 25, 2,0),(980, 25, 2, 23, 2,0),(990, 25, 2, 30, 2,0),(1000, 25, 2, 26, 2,0),(1010, 22, 2, 24, 2,0),(1020, 21, 2, 33, 2,0),(1030, 19, 2, 31, 2,0),(1040, 17, 2, 30, 2,0),(1050, 14, 2, 28, 2,0),(1060, 14, 2, 27, 2,0),(1070, 13, 2, 36, 2,0),(1080, 11, 2, 34, 2,0),(1090, 11, 2, 32, 2,0),(1100, 21, 2, 32, 2,0),(1110, 21, 2, 31, 2,0),(1120, 21, 2, 51, 2,0),(1130, 31, 2, 48, 2,0),(1140, 30, 2, 45, 2,0),(1150, 38, 2, 61, 2,0),(1160, 35, 2, 56, 2,0),(1170, 31, 2, 53, 2,0),(1180, 28, 2, 49, 2,0),(1190, 35, 2, 46, 2,0),(1200, 32, 2, 38, 2,0),(1210, 40, 2, 34, 2,0),(1220, 39, 2, 29, 2,0),(1230, 38, 2, 35, 2,0),(1240, 35, 2, 29, 2,0),(1250, 31, 2, 29, 2,0),(1260, 29, 2, 29, 2,0),(1270, 26, 2, 28, 2,0),(1280, 20, 2, 27, 2,0),(1290, 18, 2, 36, 2,0),(1300, 18, 2, 34, 2,0),(1310, 18, 2, 31, 2,0),(1320, 17, 2, 27, 2,0),(1330, 16, 2, 27, 2,0),(1340, 15, 2, 25, 2,0),(1350, 14, 2, 35, 2,0),(1360, 13, 2, 33, 2,0),(1370, 13, 2, 31, 2,0),(1380, 12, 2, 38, 2,0),(1390, 12, 2, 35, 2,0),(1400, 22, 2, 34, 2,0),(1410, 27, 2, 42, 2,0),(1420, 25, 2, 38, 2,0),(1430, 32, 2, 30, 2,0),(1440, 30, 2, 30, 2,0),(1450, 30, 2, 28, 2,0),(1460, 26, 2, 28, 2,0),(1470, 32, 2, 26, 2,0),(1480, 30, 2, 24, 2,0),(1490, 25, 2, 24, 2,0),(1500, 25, 2, 23, 2,0),(1510, 23, 2, 20, 2,0),(1520, 23, 2, 28, 2,0),(1530, 21, 2, 25, 2,0),(1540, 20, 2, 22, 2,0),(1550, 18, 2, 30, 2,0),(1560, 17, 2, 28, 2,0),(1570, 33, 2, 26, 2,0),(1580, 29, 2, 24, 2,0),(1590, 27, 2, 23, 2,0),(1600, 25, 2, 21, 2,0),(1610, 21, 2, 21, 2,0),(1620, 20, 2, 21, 2,0),(1630, 19, 2, 19, 2,0),(1640, 18, 2, 17, 2,0),(1650, 17, 2, 26, 2,0),(1660, 17, 2, 35, 2,0),(1670, 15, 2, 45, 2,0),(1680, 15, 2, 44, 2,0),(1690, 14, 2, 43, 2,0),(1700, 13, 2, 40, 2,0),(1710, 23, 2, 39, 2,0),(1720, 22, 2, 38, 2,0),(1730, 20, 2, 37, 2,0),(1740, 19, 2, 35, 2,0),(1750, 16, 2, 33, 2,0),(1760, 14, 2, 30, 2,0),(1770, 24, 2, 29, 2,0),(1780, 23, 2, 25, 2,0),(1790, 30, 2, 24, 2,0),(1800, 30, 2, 22, 2,0),(1810, 39, 2, 21, 2,0),(1820, 38, 2, 21, 2,0),(1830, 38, 2, 16, 2,0),(1840, 47, 2, 14, 2,0),(1850, 42, 2, 12, 2,0),(1860, 40, 2, 10, 2,0),(1870, 37, 2, 20, 2,0),(1880, 33, 2, 20, 2,0),(1890, 31, 2, 18, 2,0),(1900, 31, 2, 27, 2,0),(1910, 28, 2, 24, 2,0),(1920, 27, 2, 23, 2,0),(1930, 25, 2, 30, 2,0),(1940, 35, 2, 27, 2,0),(1950, 35, 2, 24, 2,0),(1960, 31, 2, 22, 2,0),(1970, 29, 2, 20, 2,0),(1980, 27, 2, 19, 2,0),(1990, 27, 2, 17, 2,0),(2000, 27, 2, 16, 2,0),(2010, 24, 2, 15, 2,0),(2020, 24, 2, 15, 2,0),(2030, 22, 2, 14, 2,0),(2040, 20, 2, 14, 2,0),(2050, 16, 2, 12, 2,0),(2060, 13, 2, 12, 2,0),(2070, 13, 2, 11, 2,0),(2080, 13, 2, 9, 2,0),(2090, 12, 2, 7, 2,0),(2100, 12, 2, 7, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-24.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-24.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 0, 2,0),(40, 0, 2, 0, 2,0),(50, 0, 2, 20, 2,0),(60, 0, 2, 19, 2,0),(70, 0, 2, 36, 2,0),(80, 0, 2, 31, 2,0),(90, 0, 2, 39, 2,0),(100, 0, 2, 39, 2,0),(110, 0, 2, 38, 2,0),(120, 0, 2, 33, 2,0),(130, 0, 2, 32, 2,0),(140, 0, 2, 40, 2,0),(150, 0, 2, 36, 2,0),(160, 0, 2, 41, 2,0),(170, 29, 2, 39, 2,0),(180, 27, 2, 38, 2,0),(190, 24, 2, 36, 2,0),(200, 23, 2, 35, 2,0),(210, 21, 2, 32, 2,0),(220, 20, 2, 29, 2,0),(230, 20, 2, 27, 2,0),(240, 19, 2, 37, 2,0),(250, 19, 2, 34, 2,0),(260, 17, 2, 27, 2,0),(270, 14, 2, 26, 2,0),(280, 14, 2, 21, 2,0),(290, 12, 2, 20, 2,0),(300, 9, 2, 29, 2,0),(310, 8, 2, 25, 2,0),(320, 8, 2, 23, 2,0),(330, 8, 2, 20, 2,0),(340, 7, 2, 19, 2,0),(350, 16, 2, 18, 2,0),(360, 14, 2, 17, 2,0),(370, 23, 2, 16, 2,0),(380, 23, 2, 25, 2,0),(390, 20, 2, 41, 2,0),(400, 19, 2, 39, 2,0),(410, 29, 2, 38, 2,0),(420, 28, 2, 33, 2,0),(430, 25, 2, 30, 2,0),(440, 32, 2, 26, 2,0),(450, 30, 2, 26, 2,0),(460, 28, 2, 25, 2,0),(470, 26, 2, 24, 2,0),(480, 21, 2, 24, 2,0),(490, 20, 2, 22, 2,0),(500, 19, 2, 20, 2,0),(510, 19, 2, 26, 2,0),(520, 17, 2, 25, 2,0),(530, 16, 2, 23, 2,0),(540, 14, 2, 32, 2,0),(550, 24, 2, 31, 2,0),(560, 22, 2, 30, 2,0),(570, 20, 2, 25, 2,0),(580, 30, 2, 25, 2,0),(590, 30, 2, 23, 2,0),(600, 36, 2, 22, 2,0),(610, 30, 2, 21, 2,0),(620, 29, 2, 19, 2,0),(630, 24, 2, 28, 2,0),(640, 23, 2, 23, 2,0),(650, 21, 2, 23, 2,0),(660, 31, 2, 22, 2,0),(670, 26, 2, 19, 2,0),(680, 25, 2, 18, 2,0),(690, 24, 2, 14, 2,0),(700, 22, 2, 13, 2,0),(710, 20, 2, 21, 2,0),(720, 30, 2, 19, 2,0),(730, 29, 2, 14, 2,0),(740, 28, 2, 24, 2,0),(750, 28, 2, 22, 2,0),(760, 27, 2, 20, 2,0),(770, 25, 2, 18, 2,0),(780, 25, 2, 17, 2,0),(790, 25, 2, 16, 2,0),(800, 23, 2, 16, 2,0),(810, 22, 2, 15, 2,0),(820, 20, 2, 15, 2,0),(830, 20, 2, 13, 2,0),(840, 18, 2, 12, 2,0),(850, 17, 2, 11, 2,0),(860, 16, 2, 9, 2,0),(870, 14, 2, 7, 2,0),(880, 12, 2, 14, 2,0),(890, 12, 2, 11, 2,0),(900, 12, 2, 21, 2,0),(910, 10, 2, 19, 2,0),(920, 7, 2, 24, 2,0),(930, 6, 2, 22, 2,0),(940, 6, 2, 21, 2,0),(950, 6, 2, 20, 2,0),(960, 6, 2, 19, 2,0),(970, 6, 2, 29, 2,0),(980, 5, 2, 24, 2,0),(990, 5, 2, 20, 2,0),(1000, 15, 2, 19, 2,0),(1010, 15, 2, 16, 2,0),(1020, 14, 2, 15, 2,0),(1030, 13, 2, 15, 2,0),(1040, 12, 2, 14, 2,0),(1050, 11, 2, 23, 2,0),(1060, 11, 2, 23, 2,0),(1070, 11, 2, 30, 2,0),(1080, 10, 2, 38, 2,0),(1090, 9, 2, 42, 2,0),(1100, 8, 2, 39, 2,0),(1110, 8, 2, 38, 2,0),(1120, 8, 2, 42, 2,0),(1130, 7, 2, 38, 2,0),(1140, 7, 2, 32, 2,0),(1150, 6, 2, 31, 2,0),(1160, 15, 2, 39, 2,0),(1170, 13, 2, 38, 2,0),(1180, 12, 2, 34, 2,0),(1190, 12, 2, 31, 2,0),(1200, 20, 2, 30, 2,0),(1210, 19, 2, 38, 2,0),(1220, 17, 2, 36, 2,0),(1230, 16, 2, 34, 2,0),(1240, 15, 2, 32, 2,0),(1250, 15, 2, 31, 2,0),(1260, 12, 2, 31, 2,0),(1270, 21, 2, 26, 2,0),(1280, 21, 2, 25, 2,0),(1290, 18, 2, 24, 2,0),(1300, 17, 2, 23, 2,0),(1310, 17, 2, 30, 2,0),(1320, 17, 2, 29, 2,0),(1330, 16, 2, 28, 2,0),(1340, 15, 2, 36, 2,0),(1350, 15, 2, 32, 2,0),(1360, 14, 2, 30, 2,0),(1370, 14, 2, 29, 2,0),(1380, 14, 2, 26, 2,0),(1390, 14, 2, 25, 2,0),(1400, 14, 2, 23, 2,0),(1410, 13, 2, 22, 2,0),(1420, 11, 2, 20, 2,0),(1430, 11, 2, 19, 2,0),(1440, 11, 2, 19, 2,0),(1450, 9, 2, 25, 2,0),(1460, 9, 2, 22, 2,0),(1470, 6, 2, 22, 2,0),(1480, 6, 2, 19, 2,0),(1490, 6, 2, 18, 2,0),(1500, 5, 2, 16, 2,0),(1510, 5, 2, 16, 2,0),(1520, 2, 2, 14, 2,0),(1530, 2, 2, 12, 2,0),(1540, 2, 2, 12, 2,0),(1550, 12, 2, 11, 2,0),(1560, 12, 2, 10, 2,0),(1570, 12, 2, 20, 2,0),(1580, 12, 2, 20, 2,0),(1590, 12, 2, 19, 2,0),(1600, 10, 2, 17, 2,0),(1610, 20, 2, 16, 2,0),(1620, 29, 2, 16, 2,0),(1630, 24, 2, 16, 2,0),(1640, 18, 2, 26, 2,0),(1650, 16, 2, 25, 2,0),(1660, 15, 2, 25, 2,0),(1670, 15, 2, 21, 2,0),(1680, 13, 2, 20, 2,0),(1690, 11, 2, 18, 2,0),(1700, 10, 2, 17, 2,0),(1710, 10, 2, 17, 2,0),(1720, 10, 2, 27, 2,0),(1730, 8, 2, 24, 2,0),(1740, 8, 2, 31, 2,0),(1750, 8, 2, 29, 2,0),(1760, 8, 2, 36, 2,0),(1770, 7, 2, 35, 2,0),(1780, 7, 2, 33, 2,0),(1790, 7, 2, 30, 2,0),(1800, 5, 2, 28, 2,0),(1810, 4, 2, 28, 2,0),(1820, 4, 2, 28, 2,0),(1830, 4, 2, 22, 2,0),(1840, 4, 2, 19, 2,0),(1850, 4, 2, 19, 2,0),(1860, 4, 2, 18, 2,0),(1870, 4, 2, 28, 2,0),(1880, 4, 2, 25, 2,0),(1890, 4, 2, 23, 2,0),(1900, 4, 2, 22, 2,0),(1910, 14, 2, 28, 2,0),(1920, 14, 2, 26, 2,0),(1930, 23, 2, 24, 2,0),(1940, 19, 2, 20, 2,0),(1950, 17, 2, 28, 2,0),(1960, 17, 2, 28, 2,0),(1970, 25, 2, 28, 2,0),(1980, 23, 2, 24, 2,0),(1990, 23, 2, 22, 2,0),(2000, 33, 2, 21, 2,0),(2010, 29, 2, 20, 2,0),(2020, 28, 2, 19, 2,0),(2030, 26, 2, 25, 2,0),(2040, 24, 2, 24, 2,0),(2050, 21, 2, 21, 2,0),(2060, 20, 2, 20, 2,0),(2070, 18, 2, 29, 2,0),(2080, 17, 2, 26, 2,0),(2090, 17, 2, 26, 2,0),(2100, 16, 2, 34, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-25.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-25.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
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|
||||
1
docs/OldTutorial/lambda/abs/run-26.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-26.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 10, 2,0),(20, 0, 2, 10, 2,0),(30, 0, 2, 10, 2,0),(40, 0, 2, 9, 2,0),(50, 0, 2, 9, 2,0),(60, 0, 2, 9, 2,0),(70, 0, 2, 8, 2,0),(80, 0, 2, 8, 2,0),(90, 0, 2, 8, 2,0),(100, 0, 2, 8, 2,0),(110, 0, 2, 7, 2,0),(120, 0, 2, 16, 2,0),(130, 10, 2, 16, 2,0),(140, 10, 2, 16, 2,0),(150, 10, 2, 13, 2,0),(160, 10, 2, 38, 2,0),(170, 20, 2, 40, 2,0),(180, 28, 2, 38, 2,0),(190, 27, 2, 34, 2,0),(200, 24, 2, 29, 2,0),(210, 23, 2, 29, 2,0),(220, 19, 2, 27, 2,0),(230, 18, 2, 25, 2,0),(240, 25, 2, 22, 2,0),(250, 23, 2, 22, 2,0),(260, 22, 2, 26, 2,0),(270, 21, 2, 25, 2,0),(280, 16, 2, 42, 2,0),(290, 14, 2, 39, 2,0),(300, 13, 2, 36, 2,0),(310, 13, 2, 35, 2,0),(320, 13, 2, 31, 2,0),(330, 13, 2, 30, 2,0),(340, 13, 2, 30, 2,0),(350, 12, 2, 26, 2,0),(360, 21, 2, 24, 2,0),(370, 20, 2, 21, 2,0),(380, 27, 2, 19, 2,0),(390, 26, 2, 18, 2,0),(400, 26, 2, 16, 2,0),(410, 21, 2, 16, 2,0),(420, 21, 2, 23, 2,0),(430, 20, 2, 22, 2,0),(440, 19, 2, 19, 2,0),(450, 16, 2, 19, 2,0),(460, 25, 2, 18, 2,0),(470, 23, 2, 17, 2,0),(480, 21, 2, 16, 2,0),(490, 19, 2, 26, 2,0),(500, 18, 2, 24, 2,0),(510, 26, 2, 22, 2,0),(520, 25, 2, 22, 2,0),(530, 32, 2, 19, 2,0),(540, 30, 2, 18, 2,0),(550, 28, 2, 26, 2,0),(560, 26, 2, 24, 2,0),(570, 24, 2, 22, 2,0),(580, 23, 2, 22, 2,0),(590, 21, 2, 22, 2,0),(600, 19, 2, 21, 2,0),(610, 16, 2, 20, 2,0),(620, 15, 2, 19, 2,0),(630, 14, 2, 19, 2,0),(640, 13, 2, 18, 2,0),(650, 22, 2, 17, 2,0),(660, 31, 2, 16, 2,0),(670, 28, 2, 16, 2,0),(680, 28, 2, 24, 2,0),(690, 27, 2, 20, 2,0),(700, 26, 2, 18, 2,0),(710, 26, 2, 16, 2,0),(720, 25, 2, 16, 2,0),(730, 24, 2, 15, 2,0),(740, 23, 2, 14, 2,0),(750, 22, 2, 23, 2,0),(760, 22, 2, 21, 2,0),(770, 17, 2, 21, 2,0),(780, 16, 2, 30, 2,0),(790, 16, 2, 29, 2,0),(800, 14, 2, 26, 2,0),(810, 14, 2, 23, 2,0),(820, 14, 2, 20, 2,0),(830, 13, 2, 16, 2,0),(840, 13, 2, 15, 2,0),(850, 12, 2, 14, 2,0),(860, 12, 2, 14, 2,0),(870, 12, 2, 13, 2,0),(880, 12, 2, 13, 2,0),(890, 12, 2, 12, 2,0),(900, 12, 2, 11, 2,0),(910, 22, 2, 11, 2,0),(920, 21, 2, 11, 2,0),(930, 21, 2, 21, 2,0),(940, 21, 2, 18, 2,0),(950, 20, 2, 18, 2,0),(960, 18, 2, 16, 2,0),(970, 16, 2, 15, 2,0),(980, 15, 2, 15, 2,0),(990, 22, 2, 15, 2,0),(1000, 20, 2, 14, 2,0),(1010, 20, 2, 24, 2,0),(1020, 17, 2, 34, 2,0),(1030, 25, 2, 33, 2,0),(1040, 21, 2, 33, 2,0),(1050, 20, 2, 30, 2,0),(1060, 18, 2, 37, 2,0),(1070, 15, 2, 33, 2,0),(1080, 14, 2, 42, 2,0),(1090, 14, 2, 38, 2,0),(1100, 21, 2, 47, 2,0),(1110, 18, 2, 45, 2,0),(1120, 17, 2, 43, 2,0),(1130, 15, 2, 52, 2,0),(1140, 15, 2, 55, 2,0),(1150, 13, 2, 53, 2,0),(1160, 12, 2, 50, 2,0),(1170, 30, 2, 46, 2,0),(1180, 28, 2, 54, 2,0),(1190, 24, 2, 61, 2,0),(1200, 21, 2, 56, 2,0),(1210, 18, 2, 52, 2,0),(1220, 16, 2, 51, 2,0),(1230, 32, 2, 47, 2,0),(1240, 28, 2, 41, 2,0),(1250, 27, 2, 50, 2,0),(1260, 26, 2, 58, 2,0),(1270, 26, 2, 53, 2,0),(1280, 31, 2, 59, 2,0),(1290, 29, 2, 63, 2,0),(1300, 27, 2, 58, 2,0),(1310, 26, 2, 55, 2,0),(1320, 28, 2, 61, 2,0),(1330, 26, 2, 56, 2,0),(1340, 34, 2, 55, 2,0),(1350, 32, 2, 53, 2,0),(1360, 32, 2, 61, 2,0),(1370, 42, 2, 56, 2,0),(1380, 38, 2, 64, 2,0),(1390, 34, 2, 60, 2,0),(1400, 31, 2, 56, 2,0),(1410, 28, 2, 53, 2,0),(1420, 27, 2, 50, 2,0),(1430, 27, 2, 46, 2,0),(1440, 26, 2, 43, 2,0),(1450, 24, 2, 42, 2,0),(1460, 23, 2, 39, 2,0),(1470, 23, 2, 38, 2,0),(1480, 23, 2, 36, 2,0),(1490, 19, 2, 33, 2,0),(1500, 16, 2, 30, 2,0),(1510, 24, 2, 37, 2,0),(1520, 23, 2, 37, 2,0),(1530, 31, 2, 35, 2,0),(1540, 29, 2, 34, 2,0),(1550, 29, 2, 33, 2,0),(1560, 27, 2, 33, 2,0),(1570, 24, 2, 33, 2,0),(1580, 23, 2, 31, 2,0),(1590, 22, 2, 28, 2,0),(1600, 19, 2, 26, 2,0),(1610, 18, 2, 26, 2,0),(1620, 27, 2, 26, 2,0),(1630, 26, 2, 22, 2,0),(1640, 25, 2, 20, 2,0),(1650, 23, 2, 20, 2,0),(1660, 22, 2, 20, 2,0),(1670, 20, 2, 20, 2,0),(1680, 19, 2, 20, 2,0),(1690, 16, 2, 19, 2,0),(1700, 16, 2, 29, 2,0),(1710, 25, 2, 27, 2,0),(1720, 22, 2, 26, 2,0),(1730, 21, 2, 26, 2,0),(1740, 20, 2, 26, 2,0),(1750, 20, 2, 25, 2,0),(1760, 18, 2, 24, 2,0),(1770, 17, 2, 32, 2,0),(1780, 17, 2, 32, 2,0),(1790, 25, 2, 29, 2,0),(1800, 25, 2, 26, 2,0),(1810, 23, 2, 25, 2,0),(1820, 23, 2, 24, 2,0),(1830, 23, 2, 24, 2,0),(1840, 22, 2, 22, 2,0),(1850, 22, 2, 19, 2,0),(1860, 29, 2, 15, 2,0),(1870, 28, 2, 15, 2,0),(1880, 26, 2, 14, 2,0),(1890, 22, 2, 13, 2,0),(1900, 28, 2, 12, 2,0),(1910, 26, 2, 12, 2,0),(1920, 25, 2, 21, 2,0),(1930, 24, 2, 19, 2,0),(1940, 22, 2, 16, 2,0),(1950, 22, 2, 14, 2,0),(1960, 21, 2, 14, 2,0),(1970, 21, 2, 14, 2,0),(1980, 19, 2, 12, 2,0),(1990, 17, 2, 21, 2,0),(2000, 16, 2, 20, 2,0),(2010, 16, 2, 18, 2,0),(2020, 15, 2, 17, 2,0),(2030, 14, 2, 14, 2,0),(2040, 14, 2, 12, 2,0),(2050, 23, 2, 12, 2,0),(2060, 19, 2, 12, 2,0),(2070, 19, 2, 11, 2,0),(2080, 17, 2, 11, 2,0),(2090, 17, 2, 10, 2,0),(2100, 16, 2, 8, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-27.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-27.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 10, 2,0),(20, 0, 2, 19, 2,0),(30, 0, 2, 18, 2,0),(40, 0, 2, 16, 2,0),(50, 0, 2, 14, 2,0),(60, 0, 2, 32, 2,0),(70, 0, 2, 30, 2,0),(80, 0, 2, 26, 2,0),(90, 0, 2, 36, 2,0),(100, 10, 2, 35, 2,0),(110, 10, 2, 32, 2,0),(120, 10, 2, 41, 2,0),(130, 9, 2, 48, 2,0),(140, 8, 2, 44, 2,0),(150, 26, 2, 49, 2,0),(160, 25, 2, 44, 2,0),(170, 25, 2, 60, 2,0),(180, 20, 2, 55, 2,0),(190, 19, 2, 52, 2,0),(200, 35, 2, 46, 2,0),(210, 30, 2, 43, 2,0),(220, 28, 2, 39, 2,0),(230, 24, 2, 38, 2,0),(240, 23, 2, 34, 2,0),(250, 22, 2, 41, 2,0),(260, 19, 2, 38, 2,0),(270, 16, 2, 37, 2,0),(280, 15, 2, 34, 2,0),(290, 15, 2, 30, 2,0),(300, 14, 2, 28, 2,0),(310, 13, 2, 26, 2,0),(320, 13, 2, 24, 2,0),(330, 13, 2, 21, 2,0),(340, 12, 2, 21, 2,0),(350, 12, 2, 18, 2,0),(360, 19, 2, 17, 2,0),(370, 18, 2, 25, 2,0),(380, 18, 2, 29, 2,0),(390, 16, 2, 28, 2,0),(400, 14, 2, 28, 2,0),(410, 13, 2, 26, 2,0),(420, 13, 2, 23, 2,0),(430, 10, 2, 21, 2,0),(440, 10, 2, 18, 2,0),(450, 19, 2, 18, 2,0),(460, 17, 2, 18, 2,0),(470, 16, 2, 16, 2,0),(480, 14, 2, 16, 2,0),(490, 13, 2, 16, 2,0),(500, 12, 2, 15, 2,0),(510, 11, 2, 15, 2,0),(520, 11, 2, 14, 2,0),(530, 11, 2, 14, 2,0),(540, 11, 2, 23, 2,0),(550, 10, 2, 23, 2,0),(560, 9, 2, 23, 2,0),(570, 9, 2, 22, 2,0),(580, 8, 2, 21, 2,0),(590, 8, 2, 20, 2,0),(600, 7, 2, 15, 2,0),(610, 7, 2, 13, 2,0),(620, 6, 2, 12, 2,0),(630, 5, 2, 12, 2,0),(640, 4, 2, 12, 2,0),(650, 3, 2, 12, 2,0),(660, 3, 2, 10, 2,0),(670, 3, 2, 9, 2,0),(680, 3, 2, 18, 2,0),(690, 3, 2, 17, 2,0),(700, 2, 2, 17, 2,0),(710, 2, 2, 16, 2,0),(720, 2, 2, 16, 2,0),(730, 2, 2, 13, 2,0),(740, 2, 2, 12, 2,0),(750, 11, 2, 12, 2,0),(760, 10, 2, 20, 2,0),(770, 9, 2, 26, 2,0),(780, 9, 2, 35, 2,0),(790, 8, 2, 32, 2,0),(800, 7, 2, 29, 2,0),(810, 6, 2, 29, 2,0),(820, 5, 2, 27, 2,0),(830, 5, 2, 24, 2,0),(840, 5, 2, 23, 2,0),(850, 13, 2, 22, 2,0),(860, 13, 2, 21, 2,0),(870, 13, 2, 18, 2,0),(880, 13, 2, 18, 2,0),(890, 11, 2, 15, 2,0),(900, 10, 2, 23, 2,0),(910, 10, 2, 23, 2,0),(920, 10, 2, 31, 2,0),(930, 10, 2, 30, 2,0),(940, 7, 2, 29, 2,0),(950, 5, 2, 26, 2,0),(960, 4, 2, 24, 2,0),(970, 14, 2, 24, 2,0),(980, 13, 2, 20, 2,0),(990, 10, 2, 18, 2,0),(1000, 10, 2, 17, 2,0),(1010, 9, 2, 15, 2,0),(1020, 9, 2, 14, 2,0),(1030, 9, 2, 32, 2,0),(1040, 18, 2, 29, 2,0),(1050, 28, 2, 38, 2,0),(1060, 26, 2, 33, 2,0),(1070, 24, 2, 30, 2,0),(1080, 32, 2, 29, 2,0),(1090, 29, 2, 27, 2,0),(1100, 37, 2, 27, 2,0),(1110, 33, 2, 26, 2,0),(1120, 29, 2, 21, 2,0),(1130, 37, 2, 20, 2,0),(1140, 36, 2, 27, 2,0),(1150, 32, 2, 26, 2,0),(1160, 39, 2, 25, 2,0),(1170, 35, 2, 22, 2,0),(1180, 32, 2, 21, 2,0),(1190, 30, 2, 28, 2,0),(1200, 28, 2, 26, 2,0),(1210, 27, 2, 24, 2,0),(1220, 24, 2, 23, 2,0),(1230, 22, 2, 22, 2,0),(1240, 20, 2, 19, 2,0),(1250, 17, 2, 17, 2,0),(1260, 26, 2, 16, 2,0),(1270, 35, 2, 16, 2,0),(1280, 32, 2, 26, 2,0),(1290, 30, 2, 21, 2,0),(1300, 26, 2, 20, 2,0),(1310, 24, 2, 18, 2,0),(1320, 23, 2, 15, 2,0),(1330, 22, 2, 13, 2,0),(1340, 19, 2, 21, 2,0),(1350, 28, 2, 20, 2,0),(1360, 28, 2, 19, 2,0),(1370, 26, 2, 19, 2,0),(1380, 25, 2, 19, 2,0),(1390, 23, 2, 15, 2,0),(1400, 22, 2, 13, 2,0),(1410, 21, 2, 13, 2,0),(1420, 19, 2, 20, 2,0),(1430, 19, 2, 18, 2,0),(1440, 19, 2, 18, 2,0),(1450, 18, 2, 17, 2,0),(1460, 16, 2, 15, 2,0),(1470, 15, 2, 15, 2,0),(1480, 35, 2, 23, 2,0),(1490, 31, 2, 21, 2,0),(1500, 28, 2, 20, 2,0),(1510, 26, 2, 18, 2,0),(1520, 24, 2, 16, 2,0),(1530, 23, 2, 15, 2,0),(1540, 22, 2, 15, 2,0),(1550, 21, 2, 13, 2,0),(1560, 18, 2, 22, 2,0),(1570, 17, 2, 18, 2,0),(1580, 16, 2, 15, 2,0),(1590, 16, 2, 15, 2,0),(1600, 16, 2, 15, 2,0),(1610, 15, 2, 33, 2,0),(1620, 12, 2, 40, 2,0),(1630, 20, 2, 37, 2,0),(1640, 18, 2, 34, 2,0),(1650, 17, 2, 33, 2,0),(1660, 14, 2, 30, 2,0),(1670, 14, 2, 37, 2,0),(1680, 14, 2, 35, 2,0),(1690, 14, 2, 44, 2,0),(1700, 12, 2, 41, 2,0),(1710, 11, 2, 38, 2,0),(1720, 9, 2, 34, 2,0),(1730, 8, 2, 30, 2,0),(1740, 7, 2, 48, 2,0),(1750, 7, 2, 46, 2,0),(1760, 4, 2, 44, 2,0),(1770, 3, 2, 40, 2,0),(1780, 3, 2, 38, 2,0),(1790, 3, 2, 45, 2,0),(1800, 3, 2, 42, 2,0),(1810, 3, 2, 43, 2,0),(1820, 3, 2, 41, 2,0),(1830, 3, 2, 51, 2,0),(1840, 3, 2, 67, 2,0),(1850, 3, 2, 61, 2,0),(1860, 3, 2, 58, 2,0),(1870, 3, 2, 62, 2,0),(1880, 3, 2, 58, 2,0),(1890, 13, 2, 55, 2,0),(1900, 11, 2, 48, 2,0),(1910, 10, 2, 43, 2,0),(1920, 20, 2, 71, 2,0),(1930, 17, 2, 65, 2,0),(1940, 14, 2, 57, 2,0),(1950, 14, 2, 55, 2,0),(1960, 23, 2, 49, 2,0),(1970, 19, 2, 45, 2,0),(1980, 34, 2, 49, 2,0),(1990, 29, 2, 45, 2,0),(2000, 35, 2, 44, 2,0),(2010, 31, 2, 51, 2,0),(2020, 30, 2, 49, 2,0),(2030, 29, 2, 45, 2,0),(2040, 35, 2, 42, 2,0),(2050, 33, 2, 40, 2,0),(2060, 36, 2, 38, 2,0),(2070, 32, 2, 35, 2,0),(2080, 30, 2, 33, 2,0),(2090, 25, 2, 28, 2,0),(2100, 23, 2, 26, 2,0))
|
||||
1
docs/OldTutorial/lambda/abs/run-28.tsd
Normal file
1
docs/OldTutorial/lambda/abs/run-28.tsd
Normal file
|
|
@ -0,0 +1 @@
|
|||
(("time","CI","PR","CII","PRE","CI_total"),(0, 0, 2, 0, 2,0),(10, 0, 2, 0, 2,0),(20, 0, 2, 0, 2,0),(30, 0, 2, 0, 2,0),(40, 0, 2, 0, 2,0),(50, 0, 2, 0, 2,0),(60, 0, 2, 0, 2,0),(70, 0, 2, 0, 2,0),(80, 0, 2, 19, 2,0),(90, 0, 2, 19, 2,0),(100, 0, 2, 18, 2,0),(110, 18, 2, 18, 2,0),(120, 17, 2, 16, 2,0),(130, 15, 2, 25, 2,0),(140, 34, 2, 24, 2,0),(150, 31, 2, 20, 2,0),(160, 40, 2, 19, 2,0),(170, 39, 2, 19, 2,0),(180, 37, 2, 18, 2,0),(190, 35, 2, 18, 2,0),(200, 33, 2, 18, 2,0),(210, 31, 2, 18, 2,0),(220, 29, 2, 18, 2,0),(230, 37, 2, 18, 2,0),(240, 33, 2, 27, 2,0),(250, 32, 2, 26, 2,0),(260, 29, 2, 23, 2,0),(270, 24, 2, 22, 2,0),(280, 24, 2, 20, 2,0),(290, 23, 2, 20, 2,0),(300, 20, 2, 17, 2,0),(310, 20, 2, 15, 2,0),(320, 18, 2, 14, 2,0),(330, 17, 2, 22, 2,0),(340, 15, 2, 20, 2,0),(350, 15, 2, 20, 2,0),(360, 15, 2, 19, 2,0),(370, 15, 2, 19, 2,0),(380, 23, 2, 17, 2,0),(390, 21, 2, 15, 2,0),(400, 17, 2, 15, 2,0),(410, 16, 2, 25, 2,0),(420, 16, 2, 23, 2,0),(430, 14, 2, 29, 2,0),(440, 13, 2, 35, 2,0),(450, 11, 2, 30, 2,0),(460, 20, 2, 37, 2,0),(470, 18, 2, 35, 2,0),(480, 16, 2, 33, 2,0),(490, 15, 2, 30, 2,0),(500, 13, 2, 27, 2,0),(510, 12, 2, 27, 2,0),(520, 11, 2, 24, 2,0),(530, 10, 2, 21, 2,0),(540, 9, 2, 19, 2,0),(550, 7, 2, 18, 2,0),(560, 7, 2, 15, 2,0),(570, 6, 2, 14, 2,0),(580, 6, 2, 13, 2,0),(590, 6, 2, 12, 2,0),(600, 6, 2, 11, 2,0),(610, 13, 2, 20, 2,0),(620, 19, 2, 19, 2,0),(630, 18, 2, 27, 2,0),(640, 16, 2, 26, 2,0),(650, 13, 2, 23, 2,0),(660, 11, 2, 31, 2,0),(670, 10, 2, 28, 2,0),(680, 19, 2, 27, 2,0),(690, 19, 2, 25, 2,0),(700, 18, 2, 24, 2,0),(710, 15, 2, 32, 2,0),(720, 11, 2, 29, 2,0),(730, 8, 2, 28, 2,0),(740, 7, 2, 24, 2,0),(750, 17, 2, 23, 2,0),(760, 26, 2, 18, 2,0),(770, 24, 2, 26, 2,0),(780, 23, 2, 23, 2,0),(790, 19, 2, 51, 2,0),(800, 18, 2, 48, 2,0),(810, 27, 2, 43, 2,0),(820, 26, 2, 40, 2,0),(830, 24, 2, 38, 2,0),(840, 20, 2, 46, 2,0),(850, 18, 2, 45, 2,0),(860, 18, 2, 44, 2,0),(870, 16, 2, 42, 2,0),(880, 15, 2, 39, 2,0),(890, 15, 2, 35, 2,0),(900, 14, 2, 33, 2,0),(910, 13, 2, 39, 2,0),(920, 12, 2, 48, 2,0),(930, 10, 2, 52, 2,0),(940, 10, 2, 55, 2,0),(950, 9, 2, 52, 2,0),(960, 9, 2, 48, 2,0),(970, 27, 2, 44, 2,0),(980, 24, 2, 41, 2,0),(990, 22, 2, 37, 2,0),(1000, 19, 2, 35, 2,0),(1010, 19, 2, 33, 2,0),(1020, 27, 2, 29, 2,0),(1030, 27, 2, 27, 2,0),(1040, 21, 2, 26, 2,0),(1050, 19, 2, 24, 2,0),(1060, 19, 2, 22, 2,0),(1070, 18, 2, 22, 2,0),(1080, 18, 2, 21, 2,0),(1090, 18, 2, 20, 2,0),(1100, 18, 2, 20, 2,0),(1110, 16, 2, 19, 2,0),(1120, 15, 2, 25, 2,0),(1130, 13, 2, 25, 2,0),(1140, 11, 2, 23, 2,0),(1150, 21, 2, 21, 2,0),(1160, 20, 2, 19, 2,0),(1170, 20, 2, 19, 2,0),(1180, 18, 2, 17, 2,0),(1190, 17, 2, 16, 2,0),(1200, 13, 2, 25, 2,0),(1210, 13, 2, 34, 2,0),(1220, 10, 2, 33, 2,0),(1230, 9, 2, 31, 2,0),(1240, 8, 2, 30, 2,0),(1250, 6, 2, 27, 2,0),(1260, 6, 2, 26, 2,0),(1270, 5, 2, 25, 2,0),(1280, 5, 2, 23, 2,0),(1290, 15, 2, 22, 2,0),(1300, 14, 2, 31, 2,0),(1310, 14, 2, 29, 2,0),(1320, 13, 2, 28, 2,0),(1330, 32, 2, 38, 2,0),(1340, 31, 2, 43, 2,0),(1350, 35, 2, 37, 2,0),(1360, 34, 2, 31, 2,0),(1370, 34, 2, 30, 2,0),(1380, 33, 2, 26, 2,0),(1390, 31, 2, 26, 2,0),(1400, 29, 2, 24, 2,0),(1410, 27, 2, 23, 2,0),(1420, 24, 2, 22, 2,0),(1430, 22, 2, 20, 2,0),(1440, 21, 2, 16, 2,0),(1450, 19, 2, 15, 2,0),(1460, 29, 2, 15, 2,0),(1470, 27, 2, 15, 2,0),(1480, 25, 2, 12, 2,0),(1490, 24, 2, 12, 2,0),(1500, 24, 2, 21, 2,0),(1510, 22, 2, 19, 2,0),(1520, 20, 2, 17, 2,0),(1530, 26, 2, 16, 2,0),(1540, 24, 2, 14, 2,0),(1550, 22, 2, 14, 2,0),(1560, 22, 2, 13, 2,0),(1570, 21, 2, 12, 2,0),(1580, 19, 2, 12, 2,0),(1590, 19, 2, 10, 2,0),(1600, 16, 2, 10, 2,0),(1610, 16, 2, 9, 2,0),(1620, 15, 2, 16, 2,0),(1630, 14, 2, 15, 2,0),(1640, 9, 2, 13, 2,0),(1650, 8, 2, 13, 2,0),(1660, 8, 2, 12, 2,0),(1670, 7, 2, 10, 2,0),(1680, 7, 2, 9, 2,0),(1690, 7, 2, 8, 2,0),(1700, 7, 2, 16, 2,0),(1710, 7, 2, 12, 2,0),(1720, 6, 2, 10, 2,0),(1730, 6, 2, 8, 2,0),(1740, 5, 2, 8, 2,0),(1750, 5, 2, 8, 2,0),(1760, 5, 2, 8, 2,0),(1770, 5, 2, 18, 2,0),(1780, 5, 2, 17, 2,0),(1790, 4, 2, 15, 2,0),(1800, 4, 2, 12, 2,0),(1810, 4, 2, 12, 2,0),(1820, 4, 2, 11, 2,0),(1830, 4, 2, 11, 2,0),(1840, 3, 2, 8, 2,0),(1850, 3, 2, 8, 2,0),(1860, 3, 2, 8, 2,0),(1870, 3, 2, 7, 2,0),(1880, 3, 2, 17, 2,0),(1890, 3, 2, 14, 2,0),(1900, 3, 2, 13, 2,0),(1910, 3, 2, 11, 2,0),(1920, 3, 2, 10, 2,0),(1930, 3, 2, 10, 2,0),(1940, 3, 2, 10, 2,0),(1950, 3, 2, 10, 2,0),(1960, 3, 2, 10, 2,0),(1970, 3, 2, 10, 2,0),(1980, 3, 2, 9, 2,0),(1990, 3, 2, 8, 2,0),(2000, 12, 2, 7, 2,0),(2010, 12, 2, 7, 2,0),(2020, 11, 2, 17, 2,0),(2030, 10, 2, 16, 2,0),(2040, 9, 2, 25, 2,0),(2050, 9, 2, 25, 2,0),(2060, 5, 2, 24, 2,0),(2070, 15, 2, 23, 2,0),(2080, 14, 2, 22, 2,0),(2090, 13, 2, 22, 2,0),(2100, 13, 2, 19, 2,0))
|
||||
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