518 lines
34 KiB
Text
518 lines
34 KiB
Text
// File generated by SBML-to-PRISM converter
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// Original file: Circuit0x8E/topModel.xml
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// @GeneticLogicLab
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ctmc
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const int MAX_AMOUNT = 70;
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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 kd = 0.0075; // Degradation rate
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const double kc_f = 0.05; // Forward complex formation rate
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const double kc_r = 1.0; // Reverse complex formation rate
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const double nc = 2.0; // Stoichiometry of binding
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const double topModel_AmtRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
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const double topModel_AmtRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
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const double topModel_AmtRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
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const double topModel_AmtRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
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const double topModel_AmtRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
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const double topModel_AmtRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
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const double topModel_AmtRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
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const double topModel_AmtRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double topModel_AmtRpart_module_sub__nc = 2.0; // Stoichiometry of binding
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const double topModel_AmtRpart_module_sub__nr = 30.0; // Initial RNAP count
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const double topModel_AmtRpart_module_sub__ko = 0.05; // Open complex production rate
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const double topModel_AmtRpart_module_sub__kb = 1.0E-4; // Basal production rate
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const double topModel_AmtRpart_module_sub__ng = 2.0; // Initial promoter count
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const double topModel_AmtRpart_module_sub__np = 10.0; // Stoichiometry of production
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const double topModel_AmtRpart_module_sub__ka = 0.25; // Activated production rate
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const double topModel_YFPpart_module_sub__kr_f = 0.5; // Forward repression binding rate
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const double topModel_YFPpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
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const double topModel_YFPpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
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const double topModel_YFPpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
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const double topModel_YFPpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
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const double topModel_YFPpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
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const double topModel_YFPpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
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const double topModel_YFPpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double topModel_YFPpart_module_sub__nc = 2.0; // Stoichiometry of binding
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const double topModel_YFPpart_module_sub__nr = 30.0; // Initial RNAP count
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const double topModel_YFPpart_module_sub__ko = 0.05; // Open complex production rate
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const double topModel_YFPpart_module_sub__kb = 1.0E-4; // Basal production rate
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const double topModel_YFPpart_module_sub__ng = 2.0; // Initial promoter count
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const double topModel_YFPpart_module_sub__np = 10.0; // Stoichiometry of production
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const double topModel_YFPpart_module_sub__ka = 0.25; // Activated production rate
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const double topModel_BetIpart_module_sub__kr_f = 0.5; // Forward repression binding rate
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const double topModel_BetIpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
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const double topModel_BetIpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
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const double topModel_BetIpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
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const double topModel_BetIpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
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const double topModel_BetIpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
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const double topModel_BetIpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
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const double topModel_BetIpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double topModel_BetIpart_module_sub__nc = 2.0; // Stoichiometry of binding
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const double topModel_BetIpart_module_sub__nr = 30.0; // Initial RNAP count
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const double topModel_BetIpart_module_sub__ko = 0.05; // Open complex production rate
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const double topModel_BetIpart_module_sub__kb = 1.0E-4; // Basal production rate
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const double topModel_BetIpart_module_sub__ng = 2.0; // Initial promoter count
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const double topModel_BetIpart_module_sub__np = 10.0; // Stoichiometry of production
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const double topModel_BetIpart_module_sub__ka = 0.25; // Activated production rate
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const double topModel_PhlFpart_module_sub__kr_f = 0.5; // Forward repression binding rate
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const double topModel_PhlFpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
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const double topModel_PhlFpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
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const double topModel_PhlFpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
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const double topModel_PhlFpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
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const double topModel_PhlFpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
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const double topModel_PhlFpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
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const double topModel_PhlFpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double topModel_PhlFpart_module_sub__nc = 2.0; // Stoichiometry of binding
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const double topModel_PhlFpart_module_sub__nr = 30.0; // Initial RNAP count
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const double topModel_PhlFpart_module_sub__ko = 0.05; // Open complex production rate
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const double topModel_PhlFpart_module_sub__kb = 1.0E-4; // Basal production rate
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const double topModel_PhlFpart_module_sub__ng = 2.0; // Initial promoter count
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const double topModel_PhlFpart_module_sub__np = 10.0; // Stoichiometry of production
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const double topModel_PhlFpart_module_sub__ka = 0.25; // Activated production rate
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const double topModel_HlyIIRpart_module_sub__kr_f = 0.5; // Forward repression binding rate
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const double topModel_HlyIIRpart_module_sub__kr_r = 1.0; // Reverse repression binding rate
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const double topModel_HlyIIRpart_module_sub__ka_f = 0.0033; // Forward activation binding rate
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const double topModel_HlyIIRpart_module_sub__ka_r = 1.0; // Reverse activation binding rate
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const double topModel_HlyIIRpart_module_sub__ko_f = 0.033; // Forward RNAP binding rate
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const double topModel_HlyIIRpart_module_sub__ko_r = 1.0; // Reverse RNAP binding rate
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const double topModel_HlyIIRpart_module_sub__kao_f = 1.0; // Forward activated RNAP binding rate
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const double topModel_HlyIIRpart_module_sub__kao_r = 1.0; // Reverse activated RNAP binding rate
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const double topModel_HlyIIRpart_module_sub__nc = 2.0; // Stoichiometry of binding
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const double topModel_HlyIIRpart_module_sub__nr = 30.0; // Initial RNAP count
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const double topModel_HlyIIRpart_module_sub__ko = 0.05; // Open complex production rate
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const double topModel_HlyIIRpart_module_sub__kb = 1.0E-4; // Basal production rate
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const double topModel_HlyIIRpart_module_sub__ng = 2.0; // Initial promoter count
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const double topModel_HlyIIRpart_module_sub__np = 10.0; // Stoichiometry of production
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const double topModel_HlyIIRpart_module_sub__ka = 0.25; // Activated production rate
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// Species AmtR_protein
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const int AmtR_protein_MAX = MAX_AMOUNT;
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module AmtR_protein
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AmtR_protein : [0..AmtR_protein_MAX] init 70;
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// AmtR_protein : int init 70;
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// AmtR_degradation_interaction
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[AmtR_degradation_interaction] AmtR_protein > 0 -> (AmtR_protein'=AmtR_protein-1);
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// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0
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[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
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// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1
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[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] AmtR_protein <= AmtR_protein_MAX-10 -> (AmtR_protein'=AmtR_protein+10);
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endmodule
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// Species IPTG
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const int IPTG_MAX = MAX_AMOUNT;
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module IPTG
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IPTG : [0..IPTG_MAX] init 0;
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// IPTG : int init 0;
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// Complex_IPTG_LacI_protein
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[Complex_IPTG_LacI_protein] IPTG > 1 -> (IPTG'=IPTG-2);
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endmodule
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// Species Ara_AraC_protein
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const int Ara_AraC_protein_MAX = MAX_AMOUNT;
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module Ara_AraC_protein
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Ara_AraC_protein : [0..Ara_AraC_protein_MAX] init 0;
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// Ara_AraC_protein : int init 0;
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// Ara_AraC_protein_degradation_interaction
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[Ara_AraC_protein_degradation_interaction] Ara_AraC_protein > 0 -> (Ara_AraC_protein'=Ara_AraC_protein-1);
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// Complex_Ara_AraC_protein
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[Complex_Ara_AraC_protein] Ara_AraC_protein <= Ara_AraC_protein_MAX-1 -> (Ara_AraC_protein'=Ara_AraC_protein+1);
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endmodule
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// Species TetR_protein
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const int TetR_protein_MAX = MAX_AMOUNT;
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module TetR_protein
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TetR_protein : [0..TetR_protein_MAX] init 0;
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// TetR_protein : int init 0;
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// Complex_aTc_TetR_protein
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[Complex_aTc_TetR_protein] TetR_protein > 1 -> (TetR_protein'=TetR_protein-2);
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// TetR_degradation_interaction
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[TetR_degradation_interaction] TetR_protein > 0 -> (TetR_protein'=TetR_protein-1);
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endmodule
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// Species LacI_protein
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const int LacI_protein_MAX = MAX_AMOUNT;
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module LacI_protein
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LacI_protein : [0..LacI_protein_MAX] init 0;
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// LacI_protein : int init 0;
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// Complex_IPTG_LacI_protein
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[Complex_IPTG_LacI_protein] LacI_protein > 1 -> (LacI_protein'=LacI_protein-2);
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// LacI_degradation_interaction
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[LacI_degradation_interaction] LacI_protein > 0 -> (LacI_protein'=LacI_protein-1);
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endmodule
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// Species aTc_TetR_protein
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const int aTc_TetR_protein_MAX = MAX_AMOUNT;
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module aTc_TetR_protein
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aTc_TetR_protein : [0..aTc_TetR_protein_MAX] init 0;
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// aTc_TetR_protein : int init 0;
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// Complex_aTc_TetR_protein
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[Complex_aTc_TetR_protein] aTc_TetR_protein <= aTc_TetR_protein_MAX-1 -> (aTc_TetR_protein'=aTc_TetR_protein+1);
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// aTc_TetR_protein_degradation_interaction
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[aTc_TetR_protein_degradation_interaction] aTc_TetR_protein > 0 -> (aTc_TetR_protein'=aTc_TetR_protein-1);
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endmodule
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// Species AraC_protein
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const int AraC_protein_MAX = MAX_AMOUNT;
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module AraC_protein
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AraC_protein : [0..AraC_protein_MAX] init 0;
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// AraC_protein : int init 0;
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// AraC_degradation_interaction
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[AraC_degradation_interaction] AraC_protein > 0 -> (AraC_protein'=AraC_protein-1);
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// Complex_Ara_AraC_protein
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[Complex_Ara_AraC_protein] AraC_protein > 1 -> (AraC_protein'=AraC_protein-2);
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endmodule
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// Species IPTG_LacI_protein
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const int IPTG_LacI_protein_MAX = MAX_AMOUNT;
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module IPTG_LacI_protein
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IPTG_LacI_protein : [0..IPTG_LacI_protein_MAX] init 0;
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// IPTG_LacI_protein : int init 0;
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// IPTG_LacI_protein_degradation_interaction
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[IPTG_LacI_protein_degradation_interaction] IPTG_LacI_protein > 0 -> (IPTG_LacI_protein'=IPTG_LacI_protein-1);
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// Complex_IPTG_LacI_protein
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[Complex_IPTG_LacI_protein] IPTG_LacI_protein <= IPTG_LacI_protein_MAX-1 -> (IPTG_LacI_protein'=IPTG_LacI_protein+1);
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endmodule
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// Species aTc
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const int aTc_MAX = MAX_AMOUNT;
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module aTc
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aTc : [0..aTc_MAX] init 0;
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// aTc : int init 0;
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// Complex_aTc_TetR_protein
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[Complex_aTc_TetR_protein] aTc > 1 -> (aTc'=aTc-2);
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endmodule
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// Species BetI_protein
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const int BetI_protein_MAX = MAX_AMOUNT;
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module BetI_protein
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BetI_protein : [0..BetI_protein_MAX] init 70;
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// BetI_protein : int init 70;
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// BetI_degradation_interaction
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[BetI_degradation_interaction] BetI_protein > 0 -> (BetI_protein'=BetI_protein-1);
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// topModel_BetIpart_module_sub__BetI_protein_interaction_0
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[topModel_BetIpart_module_sub__BetI_protein_interaction_0] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
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// topModel_BetIpart_module_sub__BetI_protein_interaction_1
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[topModel_BetIpart_module_sub__BetI_protein_interaction_1] BetI_protein <= BetI_protein_MAX-10 -> (BetI_protein'=BetI_protein+10);
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endmodule
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// Species HlyIIR_protein
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const int HlyIIR_protein_MAX = MAX_AMOUNT;
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module HlyIIR_protein
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HlyIIR_protein : [0..HlyIIR_protein_MAX] init 0;
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// HlyIIR_protein : int init 0;
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// HlyIIR_degradation_interaction
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[HlyIIR_degradation_interaction] HlyIIR_protein > 0 -> (HlyIIR_protein'=HlyIIR_protein-1);
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// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0
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[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
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// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1
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[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] HlyIIR_protein <= HlyIIR_protein_MAX-10 -> (HlyIIR_protein'=HlyIIR_protein+10);
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endmodule
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// Species PhlF_protein
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const int PhlF_protein_MAX = MAX_AMOUNT;
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module PhlF_protein
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PhlF_protein : [0..PhlF_protein_MAX] init 70;
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// PhlF_protein : int init 70;
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// PhlF_degradation_interaction
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[PhlF_degradation_interaction] PhlF_protein > 0 -> (PhlF_protein'=PhlF_protein-1);
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// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0
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[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
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// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1
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[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] PhlF_protein <= PhlF_protein_MAX-10 -> (PhlF_protein'=PhlF_protein+10);
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endmodule
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// Species YFP_protein
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const int YFP_protein_MAX = MAX_AMOUNT;
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module YFP_protein
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YFP_protein : [0..YFP_protein_MAX] init 0;
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// YFP_protein : int init 0;
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// YFP_degradation_interaction
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[YFP_degradation_interaction] YFP_protein > 0 -> (YFP_protein'=YFP_protein-1);
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// topModel_YFPpart_module_sub__YFP_protein_interaction_0
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[topModel_YFPpart_module_sub__YFP_protein_interaction_0] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
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// topModel_YFPpart_module_sub__YFP_protein_interaction_1
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[topModel_YFPpart_module_sub__YFP_protein_interaction_1] YFP_protein <= YFP_protein_MAX-10 -> (YFP_protein'=YFP_protein+10);
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endmodule
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// Species Ara
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const int Ara_MAX = MAX_AMOUNT;
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module Ara
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Ara : [0..Ara_MAX] init 60;
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// Ara : int init 60;
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// Complex_Ara_AraC_protein
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[Complex_Ara_AraC_protein] Ara > 1 -> (Ara'=Ara-2);
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endmodule
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// Species topModel_AmtRpart_module_sub__pBAD
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const int topModel_AmtRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
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module topModel_AmtRpart_module_sub__pBAD
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topModel_AmtRpart_module_sub__pBAD : [0..topModel_AmtRpart_module_sub__pBAD_MAX] init 2;
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// topModel_AmtRpart_module_sub__pBAD : int init 2;
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endmodule
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// Species topModel_AmtRpart_module_sub__pHlyIIR
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const int topModel_AmtRpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
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module topModel_AmtRpart_module_sub__pHlyIIR
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topModel_AmtRpart_module_sub__pHlyIIR : [0..topModel_AmtRpart_module_sub__pHlyIIR_MAX] init 2;
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// topModel_AmtRpart_module_sub__pHlyIIR : int init 2;
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endmodule
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// Species topModel_YFPpart_module_sub__pPhlF
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const int topModel_YFPpart_module_sub__pPhlF_MAX = MAX_AMOUNT;
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module topModel_YFPpart_module_sub__pPhlF
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topModel_YFPpart_module_sub__pPhlF : [0..topModel_YFPpart_module_sub__pPhlF_MAX] init 2;
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// topModel_YFPpart_module_sub__pPhlF : int init 2;
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endmodule
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// Species topModel_YFPpart_module_sub__pBetI
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const int topModel_YFPpart_module_sub__pBetI_MAX = MAX_AMOUNT;
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module topModel_YFPpart_module_sub__pBetI
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topModel_YFPpart_module_sub__pBetI : [0..topModel_YFPpart_module_sub__pBetI_MAX] init 2;
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// topModel_YFPpart_module_sub__pBetI : int init 2;
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endmodule
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// Species topModel_BetIpart_module_sub__pHlyIIR
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const int topModel_BetIpart_module_sub__pHlyIIR_MAX = MAX_AMOUNT;
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module topModel_BetIpart_module_sub__pHlyIIR
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topModel_BetIpart_module_sub__pHlyIIR : [0..topModel_BetIpart_module_sub__pHlyIIR_MAX] init 2;
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// topModel_BetIpart_module_sub__pHlyIIR : int init 2;
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endmodule
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// Species topModel_BetIpart_module_sub__pTet
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const int topModel_BetIpart_module_sub__pTet_MAX = MAX_AMOUNT;
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module topModel_BetIpart_module_sub__pTet
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topModel_BetIpart_module_sub__pTet : [0..topModel_BetIpart_module_sub__pTet_MAX] init 2;
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// topModel_BetIpart_module_sub__pTet : int init 2;
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endmodule
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// Species topModel_PhlFpart_module_sub__pTac
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const int topModel_PhlFpart_module_sub__pTac_MAX = MAX_AMOUNT;
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module topModel_PhlFpart_module_sub__pTac
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topModel_PhlFpart_module_sub__pTac : [0..topModel_PhlFpart_module_sub__pTac_MAX] init 2;
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// topModel_PhlFpart_module_sub__pTac : int init 2;
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endmodule
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// Species topModel_PhlFpart_module_sub__pAmtR
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const int topModel_PhlFpart_module_sub__pAmtR_MAX = MAX_AMOUNT;
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module topModel_PhlFpart_module_sub__pAmtR
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topModel_PhlFpart_module_sub__pAmtR : [0..topModel_PhlFpart_module_sub__pAmtR_MAX] init 2;
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// topModel_PhlFpart_module_sub__pAmtR : int init 2;
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endmodule
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// Species topModel_HlyIIRpart_module_sub__pTet
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const int topModel_HlyIIRpart_module_sub__pTet_MAX = MAX_AMOUNT;
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module topModel_HlyIIRpart_module_sub__pTet
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topModel_HlyIIRpart_module_sub__pTet : [0..topModel_HlyIIRpart_module_sub__pTet_MAX] init 2;
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// topModel_HlyIIRpart_module_sub__pTet : int init 2;
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endmodule
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// Species topModel_HlyIIRpart_module_sub__pBAD
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const int topModel_HlyIIRpart_module_sub__pBAD_MAX = MAX_AMOUNT;
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module topModel_HlyIIRpart_module_sub__pBAD
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topModel_HlyIIRpart_module_sub__pBAD : [0..topModel_HlyIIRpart_module_sub__pBAD_MAX] init 2;
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// topModel_HlyIIRpart_module_sub__pBAD : 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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// AraC_degradation_interaction: ->
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[AraC_degradation_interaction] (kd * AraC_protein) > 0 -> ((kd * AraC_protein)) : true;
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// Complex_aTc_TetR_protein: -> aTc_TetR_protein
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[Complex_aTc_TetR_protein] (((kc_f * pow(TetR_protein , nc)) * pow(aTc , nc)) - (kc_r * aTc_TetR_protein)) > 0 -> ((((kc_f * pow(TetR_protein , nc)) * pow(aTc , nc)) - (kc_r * aTc_TetR_protein))) : true;
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// TetR_degradation_interaction: ->
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[TetR_degradation_interaction] (kd * TetR_protein) > 0 -> ((kd * TetR_protein)) : true;
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// Ara_AraC_protein_degradation_interaction: ->
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[Ara_AraC_protein_degradation_interaction] (kd * Ara_AraC_protein) > 0 -> ((kd * Ara_AraC_protein)) : true;
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// IPTG_LacI_protein_degradation_interaction: ->
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[IPTG_LacI_protein_degradation_interaction] (kd * IPTG_LacI_protein) > 0 -> ((kd * IPTG_LacI_protein)) : true;
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// PhlF_degradation_interaction: ->
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[PhlF_degradation_interaction] (kd * PhlF_protein) > 0 -> ((kd * PhlF_protein)) : true;
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// aTc_TetR_protein_degradation_interaction: ->
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[aTc_TetR_protein_degradation_interaction] (kd * aTc_TetR_protein) > 0 -> ((kd * aTc_TetR_protein)) : true;
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// Complex_IPTG_LacI_protein: -> IPTG_LacI_protein
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[Complex_IPTG_LacI_protein] (((kc_f * pow(IPTG , nc)) * pow(LacI_protein , nc)) - (kc_r * IPTG_LacI_protein)) > 0 -> ((((kc_f * pow(IPTG , nc)) * pow(LacI_protein , nc)) - (kc_r * IPTG_LacI_protein))) : true;
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// YFP_degradation_interaction: ->
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[YFP_degradation_interaction] (kd * YFP_protein) > 0 -> ((kd * YFP_protein)) : true;
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// LacI_degradation_interaction: ->
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[LacI_degradation_interaction] (kd * LacI_protein) > 0 -> ((kd * LacI_protein)) : true;
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// Complex_Ara_AraC_protein: -> Ara_AraC_protein
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[Complex_Ara_AraC_protein] (((kc_f * pow(AraC_protein , nc)) * pow(Ara , nc)) - (kc_r * Ara_AraC_protein)) > 0 -> ((((kc_f * pow(AraC_protein , nc)) * pow(Ara , nc)) - (kc_r * Ara_AraC_protein))) : true;
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// HlyIIR_degradation_interaction: ->
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[HlyIIR_degradation_interaction] (kd * HlyIIR_protein) > 0 -> ((kd * HlyIIR_protein)) : true;
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// BetI_degradation_interaction: ->
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[BetI_degradation_interaction] (kd * BetI_protein) > 0 -> ((kd * BetI_protein)) : true;
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// AmtR_degradation_interaction: ->
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[AmtR_degradation_interaction] (kd * AmtR_protein) > 0 -> ((kd * AmtR_protein)) : true;
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// topModel_AmtRpart_module_sub__AmtR_protein_interaction_0: -> AmtR_protein
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[topModel_AmtRpart_module_sub__AmtR_protein_interaction_0] ((topModel_AmtRpart_module_sub__pBAD * ((((topModel_AmtRpart_module_sub__kb * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) + ((((topModel_AmtRpart_module_sub__ka * topModel_AmtRpart_module_sub__kao_f) / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + (((topModel_AmtRpart_module_sub__kao_f / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) > 0 -> (((topModel_AmtRpart_module_sub__pBAD * ((((topModel_AmtRpart_module_sub__kb * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) + ((((topModel_AmtRpart_module_sub__ka * topModel_AmtRpart_module_sub__kao_f) / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc)))) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + (((topModel_AmtRpart_module_sub__kao_f / topModel_AmtRpart_module_sub__kao_r) * topModel_AmtRpart_module_sub__nr) * pow(((topModel_AmtRpart_module_sub__ka_f / topModel_AmtRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_AmtRpart_module_sub__nc))))) : true;
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// topModel_AmtRpart_module_sub__AmtR_protein_interaction_1: -> AmtR_protein
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[topModel_AmtRpart_module_sub__AmtR_protein_interaction_1] (((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc))) > 0 -> ((((((topModel_AmtRpart_module_sub__pHlyIIR * topModel_AmtRpart_module_sub__ko) * topModel_AmtRpart_module_sub__ko_f) / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr) / ((1 + ((topModel_AmtRpart_module_sub__ko_f / topModel_AmtRpart_module_sub__ko_r) * topModel_AmtRpart_module_sub__nr)) + pow(((topModel_AmtRpart_module_sub__kr_f / topModel_AmtRpart_module_sub__kr_r) * HlyIIR_protein) , topModel_AmtRpart_module_sub__nc)))) : true;
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// topModel_YFPpart_module_sub__YFP_protein_interaction_0: -> YFP_protein
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[topModel_YFPpart_module_sub__YFP_protein_interaction_0] (((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> ((((((topModel_YFPpart_module_sub__pPhlF * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * PhlF_protein) , topModel_YFPpart_module_sub__nc)))) : true;
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// topModel_YFPpart_module_sub__YFP_protein_interaction_1: -> YFP_protein
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[topModel_YFPpart_module_sub__YFP_protein_interaction_1] (((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc))) > 0 -> ((((((topModel_YFPpart_module_sub__pBetI * topModel_YFPpart_module_sub__ko) * topModel_YFPpart_module_sub__ko_f) / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr) / ((1 + ((topModel_YFPpart_module_sub__ko_f / topModel_YFPpart_module_sub__ko_r) * topModel_YFPpart_module_sub__nr)) + pow(((topModel_YFPpart_module_sub__kr_f / topModel_YFPpart_module_sub__kr_r) * BetI_protein) , topModel_YFPpart_module_sub__nc)))) : true;
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// topModel_BetIpart_module_sub__BetI_protein_interaction_0: -> BetI_protein
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[topModel_BetIpart_module_sub__BetI_protein_interaction_0] (((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> ((((((topModel_BetIpart_module_sub__pHlyIIR * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * HlyIIR_protein) , topModel_BetIpart_module_sub__nc)))) : true;
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// topModel_BetIpart_module_sub__BetI_protein_interaction_1: -> BetI_protein
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[topModel_BetIpart_module_sub__BetI_protein_interaction_1] (((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc))) > 0 -> ((((((topModel_BetIpart_module_sub__pTet * topModel_BetIpart_module_sub__ko) * topModel_BetIpart_module_sub__ko_f) / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr) / ((1 + ((topModel_BetIpart_module_sub__ko_f / topModel_BetIpart_module_sub__ko_r) * topModel_BetIpart_module_sub__nr)) + pow(((topModel_BetIpart_module_sub__kr_f / topModel_BetIpart_module_sub__kr_r) * TetR_protein) , topModel_BetIpart_module_sub__nc)))) : true;
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// topModel_PhlFpart_module_sub__PhlF_protein_interaction_0: -> PhlF_protein
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[topModel_PhlFpart_module_sub__PhlF_protein_interaction_0] (((((topModel_PhlFpart_module_sub__pTac * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * LacI_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> ((((((topModel_PhlFpart_module_sub__pTac * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * LacI_protein) , topModel_PhlFpart_module_sub__nc)))) : true;
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// topModel_PhlFpart_module_sub__PhlF_protein_interaction_1: -> PhlF_protein
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[topModel_PhlFpart_module_sub__PhlF_protein_interaction_1] (((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc))) > 0 -> ((((((topModel_PhlFpart_module_sub__pAmtR * topModel_PhlFpart_module_sub__ko) * topModel_PhlFpart_module_sub__ko_f) / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr) / ((1 + ((topModel_PhlFpart_module_sub__ko_f / topModel_PhlFpart_module_sub__ko_r) * topModel_PhlFpart_module_sub__nr)) + pow(((topModel_PhlFpart_module_sub__kr_f / topModel_PhlFpart_module_sub__kr_r) * AmtR_protein) , topModel_PhlFpart_module_sub__nc)))) : true;
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// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0: -> HlyIIR_protein
|
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[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_0] ((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) > 0 -> (((topModel_HlyIIRpart_module_sub__pTet * ((((topModel_HlyIIRpart_module_sub__kb * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) + ((((topModel_HlyIIRpart_module_sub__ka * topModel_HlyIIRpart_module_sub__kao_f) / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc)))) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + (((topModel_HlyIIRpart_module_sub__kao_f / topModel_HlyIIRpart_module_sub__kao_r) * topModel_HlyIIRpart_module_sub__nr) * pow(((topModel_HlyIIRpart_module_sub__ka_f / topModel_HlyIIRpart_module_sub__ka_r) * Ara_AraC_protein) , topModel_HlyIIRpart_module_sub__nc))))) : true;
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// topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1: -> HlyIIR_protein
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[topModel_HlyIIRpart_module_sub__HlyIIR_protein_interaction_1] (((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc))) > 0 -> ((((((topModel_HlyIIRpart_module_sub__pBAD * topModel_HlyIIRpart_module_sub__ko) * topModel_HlyIIRpart_module_sub__ko_f) / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr) / ((1 + ((topModel_HlyIIRpart_module_sub__ko_f / topModel_HlyIIRpart_module_sub__ko_r) * topModel_HlyIIRpart_module_sub__nr)) + pow(((topModel_HlyIIRpart_module_sub__kr_f / topModel_HlyIIRpart_module_sub__kr_r) * TetR_protein) , topModel_HlyIIRpart_module_sub__nc)))) : true;
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endmodule
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// Reward structures (one per species)
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// Reward 1: AmtR_protein
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|
rewards "AmtR_protein" true : AmtR_protein; endrewards
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// Reward 2: IPTG
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|
rewards "IPTG" true : IPTG; endrewards
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// Reward 3: Ara_AraC_protein
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rewards "Ara_AraC_protein" true : Ara_AraC_protein; endrewards
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// Reward 4: TetR_protein
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|
rewards "TetR_protein" true : TetR_protein; endrewards
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// Reward 5: LacI_protein
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|
rewards "LacI_protein" true : LacI_protein; endrewards
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// Reward 6: aTc_TetR_protein
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|
rewards "aTc_TetR_protein" true : aTc_TetR_protein; endrewards
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// Reward 7: AraC_protein
|
|
rewards "AraC_protein" true : AraC_protein; endrewards
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// Reward 8: IPTG_LacI_protein
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|
rewards "IPTG_LacI_protein" true : IPTG_LacI_protein; endrewards
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// Reward 9: aTc
|
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rewards "aTc" true : aTc; endrewards
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// Reward 10: BetI_protein
|
|
rewards "BetI_protein" true : BetI_protein; endrewards
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// Reward 11: HlyIIR_protein
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rewards "HlyIIR_protein" true : HlyIIR_protein; endrewards
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// Reward 12: PhlF_protein
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rewards "PhlF_protein" true : PhlF_protein; endrewards
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// Reward 13: YFP_protein
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|
rewards "YFP_protein" true : YFP_protein; endrewards
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// Reward 14: Ara
|
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rewards "Ara" true : Ara; endrewards
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// Reward 15: topModel_AmtRpart_module_sub__pBAD
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rewards "topModel_AmtRpart_module_sub__pBAD" true : topModel_AmtRpart_module_sub__pBAD; endrewards
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// Reward 16: topModel_AmtRpart_module_sub__pHlyIIR
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rewards "topModel_AmtRpart_module_sub__pHlyIIR" true : topModel_AmtRpart_module_sub__pHlyIIR; endrewards
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// Reward 17: topModel_YFPpart_module_sub__pPhlF
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rewards "topModel_YFPpart_module_sub__pPhlF" true : topModel_YFPpart_module_sub__pPhlF; endrewards
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// Reward 18: topModel_YFPpart_module_sub__pBetI
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rewards "topModel_YFPpart_module_sub__pBetI" true : topModel_YFPpart_module_sub__pBetI; endrewards
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// Reward 19: topModel_BetIpart_module_sub__pHlyIIR
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rewards "topModel_BetIpart_module_sub__pHlyIIR" true : topModel_BetIpart_module_sub__pHlyIIR; endrewards
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// Reward 20: topModel_BetIpart_module_sub__pTet
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rewards "topModel_BetIpart_module_sub__pTet" true : topModel_BetIpart_module_sub__pTet; endrewards
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// Reward 21: topModel_PhlFpart_module_sub__pTac
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rewards "topModel_PhlFpart_module_sub__pTac" true : topModel_PhlFpart_module_sub__pTac; endrewards
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// Reward 22: topModel_PhlFpart_module_sub__pAmtR
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rewards "topModel_PhlFpart_module_sub__pAmtR" true : topModel_PhlFpart_module_sub__pAmtR; endrewards
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// Reward 23: topModel_HlyIIRpart_module_sub__pTet
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rewards "topModel_HlyIIRpart_module_sub__pTet" true : topModel_HlyIIRpart_module_sub__pTet; endrewards
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// Reward 24: topModel_HlyIIRpart_module_sub__pBAD
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rewards "topModel_HlyIIRpart_module_sub__pBAD" true : topModel_HlyIIRpart_module_sub__pBAD; endrewards
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