// This model generated automatically from SBML
// WARNING: Renamed variable _space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine to xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine due to JSim namespace restrictions
// WARNING: Renamed variable _space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole to xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole due to JSim namespace restrictions
// WARNING: Renamed variable _space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine to xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine due to JSim namespace restrictions
// WARNING: Renamed variable _space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate to xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate due to JSim namespace restrictions

// unit definitions
import nsrunit;
unit conversion off;

// SBML property definitions
property sbmlRole=string;
property sbmlName=string;
property sbmlCompartment=string;

// SBML reactions
// R00615: Thiamin_space_monophosphate <=> Thiamin_space_diphosphate 
// R00617: Thiamin_space_monophosphate <=> Thiamin_space_diphosphate 
// R00619: Thiamin <=> Thiamin_space_diphosphate 
// R03223: _space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate _space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole <=> Thiamin_space_monophosphate 
// R04509: _space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine <=> _space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate 
// R03471: _space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine <=> _space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine 
// R00616: Thiamin_space_triphosphate <=> Thiamin_space_diphosphate 

math main {
  realDomain time second;
  time.min=0;
  extern time.max;
  extern time.delta;

  // variable definitions
  real default = 1 L;
  real uVol = 1 L;
  real E2_space_7_space_1_space_49 = 0 M;
  real E2_space_7_space_4_space_7 = 0 M;
  real E2_space_5_space_1_space_3 = 0 M;
  real E2_space_7_space_4_space_16 = 0 M;
  real E3_space_6_space_1_space_15 = 0 M;
  real E2_space_7_space_6_space_2 = 0 M;
  real xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine(time) M;
  real xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole(time) M;
  real xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine(time) M;
  real xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate(time) M;
  real Thiamin_space_monophosphate(time) M;
  real Thiamin(time) M;
  real Thiamin_space_diphosphate(time) M;
  real Thiamin_space_triphosphate(time) M;
  real R00615(time) katal;
  extern real R00615.kf;
  extern real R00615.kb;
  real R00617(time) katal;
  extern real R00617.kf;
  extern real R00617.kb;
  real R00619(time) katal;
  extern real R00619.kf;
  extern real R00619.kb;
  real R03223(time) katal;
  extern real R03223.kf;
  extern real R03223.kb;
  real R04509(time) katal;
  extern real R04509.kf;
  extern real R04509.kb;
  real R03471(time) katal;
  extern real R03471.kf;
  extern real R03471.kb;
  real R00616(time) katal;
  extern real R00616.kf;
  extern real R00616.kb;

  // equations
  when (time=time.min) xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine = 0;
  (xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine*uVol):time = -1*R03471;
  when (time=time.min) xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole = 0;
  (xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole*uVol):time = -1*R03223;
  when (time=time.min) xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine = 0;
  (xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine*uVol):time = -1*R04509 + R03471;
  when (time=time.min) xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate = 0;
  (xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate*uVol):time = -1*R03223 + R04509;
  when (time=time.min) Thiamin_space_monophosphate = 0;
  (Thiamin_space_monophosphate*uVol):time = -1*R00615 + -1*R00617 + R03223;
  when (time=time.min) Thiamin = 0;
  (Thiamin*uVol):time = -1*R00619;
  when (time=time.min) Thiamin_space_diphosphate = 0;
  (Thiamin_space_diphosphate*uVol):time = R00615 + R00617 + R00619 + R00616;
  when (time=time.min) Thiamin_space_triphosphate = 0;
  (Thiamin_space_triphosphate*uVol):time = -1*R00616;
  R00615 = R00615.kf*Thiamin_space_monophosphate - R00615.kb*Thiamin_space_diphosphate;
  R00617 = R00617.kf*Thiamin_space_monophosphate - R00617.kb*Thiamin_space_diphosphate;
  R00619 = R00619.kf*Thiamin - R00619.kb*Thiamin_space_diphosphate;
  R03223 = R03223.kf*_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate*_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole - R03223.kb*Thiamin_space_monophosphate;
  R04509 = R04509.kf*_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine - R04509.kb*_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate;
  R03471 = R03471.kf*_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine - R03471.kb*_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine;
  R00616 = R00616.kf*Thiamin_space_triphosphate - R00616.kb*Thiamin_space_diphosphate;

  // variable properties
  default.sbmlRole="compartment";
  uVol.sbmlRole="compartment";
  E2_space_7_space_1_space_49.sbmlRole="species";
  E2_space_7_space_1_space_49.sbmlCompartment="uVol";
  E2_space_7_space_4_space_7.sbmlRole="species";
  E2_space_7_space_4_space_7.sbmlCompartment="uVol";
  E2_space_5_space_1_space_3.sbmlRole="species";
  E2_space_5_space_1_space_3.sbmlCompartment="uVol";
  E2_space_7_space_4_space_16.sbmlRole="species";
  E2_space_7_space_4_space_16.sbmlCompartment="uVol";
  E3_space_6_space_1_space_15.sbmlRole="species";
  E3_space_6_space_1_space_15.sbmlCompartment="uVol";
  E2_space_7_space_6_space_2.sbmlRole="species";
  E2_space_7_space_6_space_2.sbmlCompartment="uVol";
  xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine.sbmlRole="species";
  xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine.sbmlName="_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine";
  xxx_space_4_minus_Amino_minus_5_minus_hydroxymethyl_minus_2_minus_methylpyrimidine.sbmlCompartment="uVol";
  xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole.sbmlRole="species";
  xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole.sbmlName="_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole";
  xxx_space_4_minus_Methyl_minus_5_minus__space_2_minus_phosphoethyl_space__minus_thiazole.sbmlCompartment="uVol";
  xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine.sbmlRole="species";
  xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine.sbmlName="_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine";
  xxx_space_4_minus_Amino_minus_2_minus_methyl_minus_5_minus_phosphomethylpyrimidine.sbmlCompartment="uVol";
  xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate.sbmlRole="species";
  xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate.sbmlName="_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate";
  xxx_space_2_minus_Methyl_minus_4_minus_amino_minus_5_minus_hydroxymethylpyrimidine_space_diphosphate.sbmlCompartment="uVol";
  Thiamin_space_monophosphate.sbmlRole="species";
  Thiamin_space_monophosphate.sbmlCompartment="uVol";
  Thiamin.sbmlRole="species";
  Thiamin.sbmlCompartment="uVol";
  Thiamin_space_diphosphate.sbmlRole="species";
  Thiamin_space_diphosphate.sbmlCompartment="uVol";
  Thiamin_space_triphosphate.sbmlRole="species";
  Thiamin_space_triphosphate.sbmlCompartment="uVol";
  R00615.sbmlRole="rate";
  R00615.kf.sbmlRole="rate";
  R00615.kb.sbmlRole="rate";
  R00617.sbmlRole="rate";
  R00617.kf.sbmlRole="rate";
  R00617.kb.sbmlRole="rate";
  R00619.sbmlRole="rate";
  R00619.kf.sbmlRole="rate";
  R00619.kb.sbmlRole="rate";
  R03223.sbmlRole="rate";
  R03223.kf.sbmlRole="rate";
  R03223.kb.sbmlRole="rate";
  R04509.sbmlRole="rate";
  R04509.kf.sbmlRole="rate";
  R04509.kb.sbmlRole="rate";
  R03471.sbmlRole="rate";
  R03471.kf.sbmlRole="rate";
  R03471.kb.sbmlRole="rate";
  R00616.sbmlRole="rate";
  R00616.kf.sbmlRole="rate";
  R00616.kb.sbmlRole="rate";
}