To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le NovĂ¨re N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. */ // unit definitions import nsrunit; unit conversion off; // SBML property definitions property sbmlRole=string; property sbmlName=string; property sbmlCompartment=string; // SBML reactions // rM: EmptySet <=> M // rTL: EmptySet <=> P0 // rP01: P0 <=> P1 // rP10: P1 <=> P0 // rP12: P1 <=> P2 // rP21: P2 <=> P1 // rP2n: P2 <=> Pn // rPn2: Pn <=> P2 // rmRNAd: M <=> EmptySet // rVd: P2 <=> EmptySet math main { realDomain time second; time.min=0; extern time.max; extern time.delta; // variable definitions real default = 1E-15 L; real CYTOPLASM = 1E-15 L; real compartment_0000004 = 1E-15 L; real EmptySet = 0 uM; /* boundaryCondition changed from default (i.e. false) to true, because EmptySet acts as a reactant. Nicolas Le Novere */ real M(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ real P0(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ real P1(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ real P2(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ real Pn(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ real Pt(time) uM; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro initial concentration for Pt is not used becuase Pt is determined by an Assigment Rule , Conversion to number of molecules removed to give result in micromoles. Pn added to formula for consistency with reference. Bruce Shapiro */ real rM(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real Vs = .76; real KI = 1; real n = 4; real rTL(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real ks = .38; real rP01(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real V1 = 3.2; real K1 = 2; real rP10(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real V2 = 1.58; real K2 = 2; real rP12(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real V3 = 5; real K3 = 2; real rP21(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real V4 = 2.5; real K4 = 2; real rP2n(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real k1 = 1.9; real rPn2(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real k2 = 1.3; real rmRNAd(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real Km = .5; real Vm = .65; real rVd(time) umol/hr; /* Formula modified to give units of substance/time Bruce Shapiro */ real Vd = .95; real Kd = .2; // equations when (time=time.min) M = .1; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ (M*CYTOPLASM):time = rM + -1*rmRNAd; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ when (time=time.min) P0 = .25; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ (P0*CYTOPLASM):time = rTL + -1*rP01 + rP10; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ when (time=time.min) P1 = .25; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ (P1*CYTOPLASM):time = rP01 + -1*rP10 + -1*rP12 + rP21; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ when (time=time.min) P2 = .25; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ (P2*CYTOPLASM):time = rP12 + -1*rP21 + -1*rP2n + rPn2 + -1*rVd; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ when (time=time.min) Pn = .25; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ (Pn*compartment_0000004):time = rP2n + -1*rPn2; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro */ Pt = P0+P1+P2+Pn; /* Initial condition changed from amount to concentration as per article. Bruce Shapiro initial concentration for Pt is not used becuase Pt is determined by an Assigment Rule , Conversion to number of molecules removed to give result in micromoles. Pn added to formula for consistency with reference. Bruce Shapiro */ rM = default*Vs*KI^n/(KI^n+Pn^n); /* Formula modified to give units of substance/time Bruce Shapiro */ rTL = ks*M*default; /* Formula modified to give units of substance/time Bruce Shapiro */ rP01 = CYTOPLASM*V1*P0/(K1+P0); /* Formula modified to give units of substance/time Bruce Shapiro */ rP10 = CYTOPLASM*V2*P1/(K2+P1); /* Formula modified to give units of substance/time Bruce Shapiro */ rP12 = CYTOPLASM*V3*P1/(K3+P1); /* Formula modified to give units of substance/time Bruce Shapiro */ rP21 = CYTOPLASM*V4*P2/(K4+P2); /* Formula modified to give units of substance/time Bruce Shapiro */ rP2n = k1*P2*CYTOPLASM; /* Formula modified to give units of substance/time Bruce Shapiro */ rPn2 = k2*Pn*compartment_0000004; /* Formula modified to give units of substance/time Bruce Shapiro */ rmRNAd = Vm*M*CYTOPLASM/(Km+M); /* Formula modified to give units of substance/time Bruce Shapiro */ rVd = CYTOPLASM*Vd*P2/(Kd+P2); /* Formula modified to give units of substance/time Bruce Shapiro */ // variable properties default.sbmlRole="compartment"; CYTOPLASM.sbmlRole="compartment"; compartment_0000004.sbmlRole="compartment"; EmptySet.sbmlRole="species"; EmptySet.sbmlCompartment="default"; M.sbmlRole="species"; M.sbmlCompartment="CYTOPLASM"; P0.sbmlRole="species"; P0.sbmlCompartment="CYTOPLASM"; P1.sbmlRole="species"; P1.sbmlCompartment="CYTOPLASM"; P2.sbmlRole="species"; P2.sbmlCompartment="CYTOPLASM"; Pn.sbmlRole="species"; Pn.sbmlCompartment="compartment_0000004"; Pt.sbmlRole="species"; Pt.sbmlCompartment="CYTOPLASM"; rM.sbmlRole="rate"; Vs.sbmlRole="parameter"; KI.sbmlRole="parameter"; n.sbmlRole="parameter"; rTL.sbmlRole="rate"; ks.sbmlRole="parameter"; rP01.sbmlRole="rate"; V1.sbmlRole="parameter"; K1.sbmlRole="parameter"; rP10.sbmlRole="rate"; V2.sbmlRole="parameter"; K2.sbmlRole="parameter"; rP12.sbmlRole="rate"; V3.sbmlRole="parameter"; K3.sbmlRole="parameter"; rP21.sbmlRole="rate"; V4.sbmlRole="parameter"; K4.sbmlRole="parameter"; rP2n.sbmlRole="rate"; k1.sbmlRole="parameter"; rPn2.sbmlRole="rate"; k2.sbmlRole="parameter"; rmRNAd.sbmlRole="rate"; Km.sbmlRole="parameter"; Vm.sbmlRole="parameter"; rVd.sbmlRole="rate"; Vd.sbmlRole="parameter"; Kd.sbmlRole="parameter"; }