<?xml version="1.0" encoding="UTF-8"?><sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1"> <model name="Locke2005ks_tanh_floweringM3"> <notes> <html xmlns="http://www.w3.org/1999/xhtml"> <body> <p>SBML model of the Model 3 of Arabidopsis flowering model (Domingo et al., Cell 2009) - the photoperiodic pathway (CO attached to the interlocked feedback loop network (redeveloped SBML file of Kevin S) </p> <p/> <p> As per BIOMD0000000055.xml but with revised light function.</p> </body> </html> </notes> <listOfFunctionDefinitions> <functionDefinition id="lightFunction" name="lightFunction"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> t </ci> </bvar> <bvar> <ci> lightOffset </ci> </bvar> <bvar> <ci> lightAmplitude </ci> </bvar> <bvar> <ci> phase </ci> </bvar> <bvar> <ci> photoPeriod </ci> </bvar> <bvar> <ci> cyclePeriod </ci> </bvar> <bvar> <ci> twilightPeriod </ci> </bvar> <apply> <plus/> <apply> <minus/> <apply> <plus/> <ci> lightOffset </ci> <apply> <times/> <cn> 0.5 </cn> <ci> lightAmplitude </ci> <apply> <plus/> <cn type="integer"> 1 </cn> <apply> <tanh/> <apply> <divide/> <apply> <times/> <ci> cyclePeriod </ci> <apply> <minus/> <apply> <divide/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> <ci> cyclePeriod </ci> </apply> <apply> <floor/> <apply> <divide/> <apply> <floor/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> </apply> <ci> cyclePeriod </ci> </apply> </apply> </apply> </apply> <ci> twilightPeriod </ci> </apply> </apply> </apply> </apply> </apply> <apply> <times/> <cn> 0.5 </cn> <ci> lightAmplitude </ci> <apply> <plus/> <cn type="integer"> 1 </cn> <apply> <tanh/> <apply> <divide/> <apply> <minus/> <apply> <times/> <ci> cyclePeriod </ci> <apply> <minus/> <apply> <divide/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> <ci> cyclePeriod </ci> </apply> <apply> <floor/> <apply> <divide/> <apply> <floor/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> </apply> <ci> cyclePeriod </ci> </apply> </apply> </apply> </apply> <ci> photoPeriod </ci> </apply> <ci> twilightPeriod </ci> </apply> </apply> </apply> </apply> </apply> <apply> <times/> <cn> 0.5 </cn> <ci> lightAmplitude </ci> <apply> <plus/> <cn type="integer"> 1 </cn> <apply> <tanh/> <apply> <divide/> <apply> <minus/> <apply> <times/> <ci> cyclePeriod </ci> <apply> <minus/> <apply> <divide/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> <ci> cyclePeriod </ci> </apply> <apply> <floor/> <apply> <divide/> <apply> <floor/> <apply> <plus/> <ci> time </ci> <ci> phase </ci> </apply> </apply> <ci> cyclePeriod </ci> </apply> </apply> </apply> </apply> <ci> cyclePeriod </ci> </apply> <ci> twilightPeriod </ci> </apply> </apply> </apply> </apply> </apply> </lambda> </math> </functionDefinition> </listOfFunctionDefinitions> <listOfCompartments> <compartment id="compartment" name="compartment" size="1"/> </listOfCompartments> <listOfSpecies> <species id="cCOp" name="cCOp" compartment="compartment" initialConcentration="0"/> <species id="cFTm" name="cFTm" compartment="compartment" initialConcentration="0"/> <species id="cLc" name="cLc" compartment="compartment" initialConcentration="0.015"/> <species id="cLm" name="cLm" compartment="compartment" initialConcentration="0.539"/> <species id="cLn" name="cLn" compartment="compartment" initialConcentration="0.0855"/> <species id="cPn" name="cPn" compartment="compartment" initialConcentration="0.835"/> <species id="cTc" name="cTc" compartment="compartment" initialConcentration="8.7"/> <species id="cTm" name="cTm" compartment="compartment" initialConcentration="0.456"/> <species id="cTn" name="cTn" compartment="compartment" initialConcentration="0.4"/> <species id="cXc" name="cXc" compartment="compartment" initialConcentration="1.34"/> <species id="cXm" name="cXm" compartment="compartment" initialConcentration="0.08"/> <species id="cXn" name="cXn" compartment="compartment" initialConcentration="0.4"/> <species id="cYc" name="cYc" compartment="compartment" initialConcentration="0.004"/> <species id="cYm" name="cYm" compartment="compartment" initialConcentration="0.037"/> <species id="cYn" name="cYn" compartment="compartment" initialConcentration="0.013"/> </listOfSpecies> <listOfParameters> <parameter id="q1" name="q1" value="2.4514"/> <parameter id="n1" name="n1" value="5.1694"/> <parameter id="a" name="a" value="3.3064"/> <parameter id="g1" name="g1" value="0.876738488"/> <parameter id="m1" name="m1" value="1.5283"/> <parameter id="k1" name="k1" value="1.817"/> <parameter id="p1" name="p1" value="0.8295"/> <parameter id="r1" name="r1" value="16.8363"/> <parameter id="r2" name="r2" value="0.1687"/> <parameter id="m2" name="m2" value="20.44"/> <parameter id="k2" name="k2" value="1.5644"/> <parameter id="m3" name="m3" value="3.6888"/> <parameter id="k3" name="k3" value="1.2765"/> <parameter id="n2" name="n2" value="3.0087"/> <parameter id="b" name="b" value="1.0258"/> <parameter id="g2" name="g2" value="0.036805783"/> <parameter id="g3" name="g3" value="0.26593318"/> <parameter id="c" name="c" value="1.0258"/> <parameter id="m4" name="m4" value="3.8231"/> <parameter id="k4" name="k4" value="2.5734"/> <parameter id="p2" name="p2" value="4.324"/> <parameter id="r3" name="r3" value="0.3166"/> <parameter id="r4" name="r4" value="2.1509"/> <parameter id="m5" name="m5" value="0.0013"/> <parameter id="m6" name="m6" value="3.1741"/> <parameter id="k5" name="k5" value="2.7454"/> <parameter id="m7" name="m7" value="0.0492"/> <parameter id="m8" name="m8" value="4.0424"/> <parameter id="k6" name="k6" value="0.4033"/> <parameter id="n3" name="n3" value="0.2431"/> <parameter id="d" name="d" value="1.4422"/> <parameter id="g4" name="g4" value="0.538811228"/> <parameter id="m9" name="m9" value="10.1132"/> <parameter id="k7" name="k7" value="6.5585"/> <parameter id="p3" name="p3" value="2.147"/> <parameter id="r5" name="r5" value="1.0352"/> <parameter id="r6" name="r6" value="3.3017"/> <parameter id="m10" name="m10" value="0.2179"/> <parameter id="k8" name="k8" value="0.6632"/> <parameter id="m11" name="m11" value="3.3442"/> <parameter id="k9" name="k9" value="17.1111"/> <parameter id="q2" name="q2" value="2.40178"/> <parameter id="n4" name="n4" value="0.0857"/> <parameter id="n5" name="n5" value="0.1649"/> <parameter id="g5" name="g5" value="1.17803247"/> <parameter id="g6" name="g6" value="0.064455137"/> <parameter id="f" name="f" value="1.0237"/> <parameter id="e" name="e" value="3.6064"/> <parameter id="m12" name="m12" value="4.297"/> <parameter id="k10" name="k10" value="1.7303"/> <parameter id="p4" name="p4" value="0.2485"/> <parameter id="r7" name="r7" value="2.2123"/> <parameter id="r8" name="r8" value="0.2002"/> <parameter id="m13" name="m13" value="0.1347"/> <parameter id="k11" name="k11" value="1.8258"/> <parameter id="m14" name="m14" value="0.6114"/> <parameter id="k12" name="k12" value="1.8066"/> <parameter id="p5" name="p5" value="0.5"/> <parameter id="k13" name="k13" value="1.2"/> <parameter id="q3" name="q3" value="1"/> <parameter id="m15" name="m15" value="1.2"/> <parameter id="lightAmplitude" name="lightAmplitude" value="1"/> <parameter id="lightOffset" name="lightOffset" value="0"/> <parameter id="cyclePeriod" name="cyclePeriod" value="24"/> <parameter id="photoPeriod" name="photoPeriod" value="8"/> <parameter id="phase" name="phase" value="0"/> <parameter id="twilightPeriod" name="twilightPeriod" value="0.0416666667"/> <parameter id="two11_Fch_0" name="two11_Fch_0" value="8"/> <parameter id="four12_Fch_0" name="four12_Fch_0" value="8"/> <parameter id="vCOm" name="vCOm" value="1.1452"/> <parameter id="vCOp" name="vCOp" value="9.2242"/> <parameter id="kCOp" name="kCOp" value="2.0976"/> <parameter id="vCOFT" name="vCOFT" value="0.6683"/> <parameter id="kCOFT" name="kCOFT" value="7.3533"/> <parameter id="vFT" name="vFT" value="1.8674"/> <parameter id="kFT" name="kFT" value="5.3925"/> </listOfParameters> <listOfReactions> <reaction id="one11" name="one11" reversible="false"> <listOfProducts> <speciesReference species="cLm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cPn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> <ci> q1 </ci> <ci> cPn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="two11" name="two11" reversible="false"> <listOfProducts> <speciesReference species="cLm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cXn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> n1 </ci> <apply> <power/> <ci> cXn </ci> <ci> a </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <ci> g1 </ci> <ci> a </ci> </apply> <apply> <power/> <ci> cXn </ci> <ci> a </ci> </apply> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="three11" name="three11" reversible="false"> <listOfReactants> <speciesReference species="cLm"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m1 </ci> <ci> cLm </ci> </apply> <apply> <plus/> <ci> k1 </ci> <ci> cLm </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one12" name="one12" reversible="false"> <listOfProducts> <speciesReference species="cLc"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cLm"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> p1 </ci> <ci> cLm </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three12" name="three12" reversible="false"> <listOfReactants> <speciesReference species="cLn"/> </listOfReactants> <listOfProducts> <speciesReference species="cLc"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r2 </ci> <ci> cLn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="four12" name="four12" reversible="false"> <listOfReactants> <speciesReference species="cLc"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m2 </ci> <ci> cLc </ci> </apply> <apply> <plus/> <ci> k2 </ci> <ci> cLc </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one13" name="one13" reversible="false"> <listOfReactants> <speciesReference species="cLc"/> </listOfReactants> <listOfProducts> <speciesReference species="cLn"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r1 </ci> <ci> cLc </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three13" name="three13" reversible="false"> <listOfReactants> <speciesReference species="cLn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m3 </ci> <ci> cLn </ci> </apply> <apply> <plus/> <ci> k3 </ci> <ci> cLn </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one14" name="one14" reversible="false"> <listOfProducts> <speciesReference species="cTm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cLn"/> <modifierSpeciesReference species="cYn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> n2 </ci> <apply> <power/> <ci> cYn </ci> <ci> b </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <ci> g2 </ci> <ci> b </ci> </apply> <apply> <power/> <ci> cYn </ci> <ci> b </ci> </apply> </apply> </apply> <apply> <divide/> <apply> <power/> <ci> g3 </ci> <ci> c </ci> </apply> <apply> <plus/> <apply> <power/> <ci> g3 </ci> <ci> c </ci> </apply> <apply> <power/> <ci> cLn </ci> <ci> c </ci> </apply> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="two14" name="two14" reversible="false"> <listOfReactants> <speciesReference species="cTm"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m4 </ci> <ci> cTm </ci> </apply> <apply> <plus/> <ci> k4 </ci> <ci> cTm </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one15" name="one15" reversible="false"> <listOfProducts> <speciesReference species="cTc"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cTm"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> p2 </ci> <ci> cTm </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three15" name="three15" reversible="false"> <listOfReactants> <speciesReference species="cTn"/> </listOfReactants> <listOfProducts> <speciesReference species="cTc"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r4 </ci> <ci> cTn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="four15" name="four15" reversible="false"> <listOfReactants> <speciesReference species="cTc"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <plus/> <apply> <times/> <apply> <minus/> <cn type="integer"> 1 </cn> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> </apply> <ci> m5 </ci> </apply> <ci> m6 </ci> </apply> <apply> <divide/> <ci> cTc </ci> <apply> <plus/> <ci> k5 </ci> <ci> cTc </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one16" name="one16" reversible="false"> <listOfReactants> <speciesReference species="cTc"/> </listOfReactants> <listOfProducts> <speciesReference species="cTn"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r3 </ci> <ci> cTc </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three16" name="three16" reversible="false"> <listOfReactants> <speciesReference species="cTn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <plus/> <apply> <times/> <apply> <minus/> <cn type="integer"> 1 </cn> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> </apply> <ci> m7 </ci> </apply> <ci> m8 </ci> </apply> <apply> <divide/> <ci> cTn </ci> <apply> <plus/> <ci> k6 </ci> <ci> cTn </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one17" name="one17" reversible="false"> <listOfProducts> <speciesReference species="cXm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cTn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> n3 </ci> <apply> <power/> <ci> cTn </ci> <ci> d </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <ci> g4 </ci> <ci> d </ci> </apply> <apply> <power/> <ci> cTn </ci> <ci> d </ci> </apply> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="two17" name="two17" reversible="false"> <listOfReactants> <speciesReference species="cXm"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m9 </ci> <ci> cXm </ci> </apply> <apply> <plus/> <ci> k7 </ci> <ci> cXm </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one18" name="one18" reversible="false"> <listOfProducts> <speciesReference species="cXc"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cXm"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> p3 </ci> <ci> cXm </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three18" name="three18" reversible="false"> <listOfReactants> <speciesReference species="cXn"/> </listOfReactants> <listOfProducts> <speciesReference species="cXc"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r6 </ci> <ci> cXn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="four18" name="four18" reversible="false"> <listOfReactants> <speciesReference species="cXc"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m10 </ci> <ci> cXc </ci> </apply> <apply> <plus/> <ci> k8 </ci> <ci> cXc </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one19" name="one19" reversible="false"> <listOfReactants> <speciesReference species="cXc"/> </listOfReactants> <listOfProducts> <speciesReference species="cXn"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r5 </ci> <ci> cXc </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three19" name="three19" reversible="false"> <listOfReactants> <speciesReference species="cXn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m11 </ci> <ci> cXn </ci> </apply> <apply> <plus/> <ci> k9 </ci> <ci> cXn </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one20" name="one20" reversible="false"> <listOfProducts> <speciesReference species="cYm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cLn"/> <modifierSpeciesReference species="cPn"/> <modifierSpeciesReference species="cTn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <plus/> <apply> <times/> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> <ci> q2 </ci> <ci> cPn </ci> </apply> <apply> <divide/> <apply> <times/> <apply> <plus/> <apply> <times/> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> <ci> n4 </ci> </apply> <ci> n5 </ci> </apply> <apply> <power/> <ci> g5 </ci> <ci> e </ci> </apply> </apply> <apply> <plus/> <apply> <power/> <ci> g5 </ci> <ci> e </ci> </apply> <apply> <power/> <ci> cTn </ci> <ci> e </ci> </apply> </apply> </apply> </apply> <apply> <divide/> <apply> <power/> <ci> g6 </ci> <ci> f </ci> </apply> <apply> <plus/> <apply> <power/> <ci> g6 </ci> <ci> f </ci> </apply> <apply> <power/> <ci> cLn </ci> <ci> f </ci> </apply> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="two20" name="two20" reversible="false"> <listOfReactants> <speciesReference species="cYm"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m12 </ci> <ci> cYm </ci> </apply> <apply> <plus/> <ci> k10 </ci> <ci> cYm </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one21" name="one21" reversible="false"> <listOfProducts> <speciesReference species="cYc"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cYm"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> p4 </ci> <ci> cYm </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three21" name="three21" reversible="false"> <listOfReactants> <speciesReference species="cYn"/> </listOfReactants> <listOfProducts> <speciesReference species="cYc"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r8 </ci> <ci> cYn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="four21" name="four21" reversible="false"> <listOfReactants> <speciesReference species="cYc"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m13 </ci> <ci> cYc </ci> </apply> <apply> <plus/> <ci> k11 </ci> <ci> cYc </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one22" name="one22" reversible="false"> <listOfReactants> <speciesReference species="cYc"/> </listOfReactants> <listOfProducts> <speciesReference species="cYn"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> r7 </ci> <ci> cYc </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="three22" name="three22" reversible="false"> <listOfReactants> <speciesReference species="cYn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m14 </ci> <ci> cYn </ci> </apply> <apply> <plus/> <ci> k12 </ci> <ci> cYn </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="one23" name="one23" reversible="false"> <listOfProducts> <speciesReference species="cPn"/> </listOfProducts> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <minus/> <cn type="integer"> 1 </cn> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> </apply> <ci> p5 </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="two23" name="two23" reversible="false"> <listOfReactants> <speciesReference species="cPn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <divide/> <apply> <times/> <ci> m15 </ci> <ci> cPn </ci> </apply> <apply> <plus/> <ci> k13 </ci> <ci> cPn </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="three23" name="three23" reversible="false"> <listOfReactants> <speciesReference species="cPn"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> q3 </ci> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> <ci> cPn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="COpistranslatedfromCOmthatisassumedtobeequaltocTn" name="COpistranslatedfromCOmthatisassumedtobeequaltocTn" reversible="false"> <listOfProducts> <speciesReference species="cCOp"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cTn"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <ci> vCOm </ci> <ci> cTn </ci> </apply> </math> </kineticLaw> </reaction> <reaction id="COpdegradation" name="COpdegradation" reversible="false"> <listOfReactants> <speciesReference species="cCOp"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> compartment </ci> <apply> <minus/> <cn type="integer"> 1 </cn> <apply> <ci> lightFunction </ci> <ci> time </ci> <ci> lightOffset </ci> <ci> lightAmplitude </ci> <ci> phase </ci> <ci> photoPeriod </ci> <ci> cyclePeriod </ci> <ci> twilightPeriod </ci> </apply> </apply> <apply> <divide/> <apply> <times/> <ci> vCOp </ci> <ci> cCOp </ci> </apply> <apply> <plus/> <ci> kCOp </ci> <ci> cCOp </ci> </apply> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="FTinductionbyCOp" name="FTinductionbyCOp" reversible="false"> <listOfProducts> <speciesReference species="cFTm"/> </listOfProducts> <listOfModifiers> <modifierSpeciesReference species="cCOp"/> </listOfModifiers> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <divide/> <apply> <times/> <ci> compartment </ci> <ci> vCOFT </ci> <ci> cCOp </ci> </apply> <apply> <plus/> <ci> kCOFT </ci> <ci> cCOp </ci> </apply> </apply> </math> </kineticLaw> </reaction> <reaction id="FTmdegradation" name="FTmdegradation" reversible="false"> <listOfReactants> <speciesReference species="cFTm"/> </listOfReactants> <kineticLaw> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <divide/> <apply> <times/> <ci> compartment </ci> <ci> vFT </ci> <ci> cFTm </ci> </apply> <apply> <plus/> <ci> kFT </ci> <ci> cFTm </ci> </apply> </apply> </math> </kineticLaw> </reaction> </listOfReactions> </model> </sbml>