97 lines
3.5 KiB
Text
97 lines
3.5 KiB
Text
// File generated by SBML-to-PRISM converter
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// Original file: SimpleHierchyModel/topModel.xml
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// @GeneticLogicLab
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ctmc
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// const int MAX_AMOUNT = ADD VALUE
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// Compartment size
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const double Cell = 1.0;
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// Model parameters
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const double kr_f = 0.5; // Forward repression binding rate
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const double kr_r = 1.0; // Reverse repression binding rate
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const double ka_f = 0.0033; // Forward activation binding rate
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const double ka_r = 1.0; // Reverse activation binding rate
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const double ko_f = 0.033; // Forward RNAP binding rate
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const double ko_r = 1.0; // Reverse RNAP binding rate
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const double kao_f = 1.0; // Forward activated RNAP binding rate
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const double kao_r = 1.0; // Reverse activated RNAP binding rate
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const double nc = 2.0; // Stoichiometry of binding
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const double nr = 30.0; // Initial RNAP count
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const double ko = 0.05; // Open complex production rate
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const double kb = 1.0E-4; // Basal production rate
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const double ng = 2.0; // Initial promoter count
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const double np = 10.0; // Stoichiometry of production
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const double ka = 0.25; // Activated production rate
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const double kd = 0.0075; // Degradation rate
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const double C1__kr_f = 0.5; // Forward repression binding rate
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const double C1__kr_r = 1.0; // Reverse repression binding rate
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const double C1__ka_f = 0.0033; // Forward activation binding rate
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const double C1__ka_r = 1.0; // Reverse activation binding rate
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const double C1__ko_f = 0.033; // Forward RNAP binding rate
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const double C1__ko_r = 1.0; // Reverse RNAP binding rate
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const double C1__kao_f = 1.0; // Forward activated RNAP binding rate
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const double C1__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double C1__nc = 2.0; // Stoichiometry of binding
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const double C1__nr = 30.0; // Initial RNAP count
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const double C1__ko = 0.05; // Open complex production rate
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const double C1__kb = 1.0E-4; // Basal production rate
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const double C1__ng = 2.0; // Initial promoter count
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const double C1__np = 10.0; // Stoichiometry of production
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const double C1__ka = 0.25; // Activated production rate
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const double C1__kd = 0.0075; // Degradation rate
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// Species S2
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// const int S2_MAX = MAX_AMOUNT;
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module S2
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// S2 : [0..S2_MAX] init 60;
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S2 : int init 60;
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endmodule
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// Species S3
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// const int S3_MAX = MAX_AMOUNT;
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module S3
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// S3 : [0..S3_MAX] init 0;
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S3 : int init 0;
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// C1__Production_P0
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[C1__Production_P0] S3 >= 0 -> (S3'=S3+10);
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// Degradation_S3
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[Degradation_S3] S3 > 0 -> (S3'=S3-1);
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endmodule
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// Species C1__P0
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// const int C1__P0_MAX = MAX_AMOUNT;
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module C1__P0
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// C1__P0 : [0..C1__P0_MAX] init 2;
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C1__P0 : int init 2;
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endmodule
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// Reaction rates
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module reaction_rates
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// C1__Production_P0: -> S3
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[C1__Production_P0] ((C1__P0 * ((((C1__kb * C1__ko_f) / C1__ko_r) * C1__nr) + ((((C1__ka * C1__kao_f) / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) / ((1 + ((C1__ko_f / C1__ko_r) * C1__nr)) + (((C1__kao_f / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) > 0 -> (((C1__P0 * ((((C1__kb * C1__ko_f) / C1__ko_r) * C1__nr) + ((((C1__ka * C1__kao_f) / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc)))) / ((1 + ((C1__ko_f / C1__ko_r) * C1__nr)) + (((C1__kao_f / C1__kao_r) * C1__nr) * pow(((C1__ka_f / C1__ka_r) * S2) , C1__nc))))) : true;
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// Degradation_S3: ->
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[Degradation_S3] (C1__kd * S3) > 0 -> ((C1__kd * S3)) : true;
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endmodule
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// Reward structures (one per species)
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// Reward 1: S2
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rewards "S2" true : S2; endrewards
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// Reward 2: S3
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rewards "S3" true : S3; endrewards
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// Reward 3: C1__P0
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rewards "C1__P0" true : C1__P0; endrewards
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