// Created by libAntimony v2.8.0
model *Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF()
// Compartments and Species:
compartment cytosol;
species N in cytosol, Na in cytosol, Nan_ in cytosol, MF in cytosol, F in cytosol;
species Bp in cytosol, BN in cytosol, A in cytosol, K in cytosol, B in cytosol;
species MAx in cytosol, Rasa in cytosol, ERKa in cytosol, Xa in cytosol;
species MDusp in cytosol, Dusp in cytosol, $Rasi in cytosol, Rast in cytosol;
species $ERKi in cytosol, ERKt in cytosol, $Xi in cytosol, Xt in cytosol;
species D in cytosol, $AK in cytosol, $Kt in cytosol, $Fgf in cytosol;
// Assignment Rules:
Rasi := Rast - Rasa;
ERKi := ERKt - ERKa;
Xi := Xt - Xa;
AK := Kt - K;
vsFK := vsF*(KIG1/(KIG1 + K));
// Reactions:
n_synth: => N; cytosol*epsilon*vsN;
N_degradation: N => ; (epsilon*cytosol*vdN*N)/(KdN + N);
N_activation: N => Na; (epsilon*cytosol*kc*N*KIF^j)/(KIF^j + F^j);
Na_degradation: Na => ; (epsilon*cytosol*VdNa*Na)/(KdNa + Na);
Na_transport: Na -> Nan_; epsilon*cytosol*(kt1*Na - kt2*Nan_);
Nan_degradation: Nan_ => ; (epsilon*cytosol*VdNan*Nan_)/(KdNan + Nan_);
MF_transkription: => MF; (epsilon*cytosol*vsFK*Nan_^p)/(KA^p + Nan_^p);
MF_degradation: MF => ; (epsilon*cytosol*vmF*MF)/(KdMF + MF);
F_translation: => F; epsilon*cytosol*ksF*MF;
F_degradation: F => ; (epsilon*cytosol*vdF*F)/(KdF + F);
AK_dissoc: $AK -> A + K; theta*cytosol*(d1*AK - a1*A*K);
B_synth: => B; theta*cytosol*vsB;
B_degradation: B => ; theta*cytosol*kd1*B;
B_phosphorylation: B => Bp; (((theta*cytosol*VMK*KID)/(KID + D)*B)/(K1 + B)*AK)/Kt;
BP_dephosphorylation: Bp => B; (theta*cytosol*VMP*Bp)/(K2 + Bp);
B_shuttling: BN -> B; theta*cytosol*(kt4*BN - kt3*B);
Bp_degradation: Bp => ; theta*cytosol*kd2*Bp;
MAx_trans_basal: => MAx; theta*cytosol*v0;
MAx_trans_BN: => MAx; theta*cytosol*((vMB*BN^n)/(KaB^n + BN^n));
MAx_trans_Xa: => MAx; theta*cytosol*((vMXa*Xa^m)/(KaXa^m + Xa^m));
MAx_degradation: MAx => ; (theta*cytosol*vmd*MAx)/(Kmd + MAx);
A_translation: => A; theta*cytosol*ksAx*MAx;
A_degradation: A => ; (theta*cytosol*vdAx*A)/(KdAx + A);
Ras_activation: => Rasa; ((eta*cytosol*VMaRas*Fgf^r)/(KaFgf^r + Fgf^r)*Rasi)/(KaRas + Rasi);
Ras_inactivation: Rasa => ; (eta*cytosol*VMdRas*Rasa)/(KdRas + Rasa);
Erk_activation: => ERKa; ((eta*cytosol*VMaErk*Rasa)/Rast*ERKi)/(KaErk + ERKi);
Erk_inactivation: ERKa => ; (eta*cytosol*kcDusp*Dusp*ERKa)/(KdErk + ERKa);
X_activation: => Xa; ((eta*cytosol*VMaX*ERKa)/ERKt*Xi)/(KaX + Xi);
X_inactivation: Xa => ; (eta*cytosol*VMdX*Xa)/(KdX + Xa);
MDusp_transkription: => MDusp; (eta*cytosol*VMsMDusp*Xa^q)/(KaMDusp^q + Xa^q);
MDusp_degradation: MDusp => ; (eta*cytosol*VMdMDusp*MDusp)/(KdMDusp + MDusp);
Dusp_translation: => Dusp; eta*cytosol*ksDusp*MDusp;
Dusp_degradation: Dusp => ; (eta*cytosol*vdDusp*Dusp)/(KdDusp + Dusp);
// Species initializations:
N = 0.5;
Na = 0.2;
Nan_ = 0;
MF = 0.1;
F = 0.001;
Bp = 0.1;
BN = 0.001;
A = 0.1;
K = 3;
B = 0.1;
MAx = 0.1;
Rasa = 0.5;
ERKa = 0.2;
Xa = 0.1;
MDusp = 0.1;
Dusp = 0.1;
Rast = 2;
ERKt = 2;
Xt = 2;
D = 2;
Kt = 3;
Fgf = 1;
// Compartment initializations:
cytosol = 1;
cytosol has litre;
// Variable initializations:
KdN = 1.4;
KdN has nanomolar;
vsN = 0.23;
vsN has flux;
vdN = 2.82;
vdN has flux;
KdNa = 0.001;
KdNa has nanomolar;
VdNa = 0.01;
VdNa has flux;
kt1 = 0.1;
kt1 has first_order_rate_constant;
kt2 = 0.1;
kt2 has first_order_rate_constant;
KdNan = 0.001;
KdNan has nanomolar;
VdNan = 0.1;
VdNan has flux;
KdMF = 0.768;
KdMF has nanomolar;
KIG1 = 2.5;
KIG1 has nanomolar;
vsFK has flux;
vsF = 3;
vsF has flux;
vmF = 1.92;
vmF has flux;
KA = 0.05;
KA has nanomolar;
KdF = 0.37;
KdF has nanomolar;
vdF = 0.39;
vdF has flux;
ksF = 0.3;
ksF has first_order_rate_constant;
kd1 = 0;
kd1 has first_order_rate_constant;
vsB = 0.087;
vsB has flux;
kd2 = 7.062;
kd2 has first_order_rate_constant;
v0 = 0.06;
v0 has flux;
vMB = 1.64;
vMB has flux;
vmd = 0.8;
vmd has flux;
KaB = 0.7;
KaB has nanomolar;
KaXa = 0.05;
KaXa has nanomolar;
Kmd = 0.48;
Kmd has nanomolar;
n = 2;
n has dimensionless;
m = 2;
m has dimensionless;
vMXa = 0.5;
vMXa has flux;
ksAx = 0.02;
ksAx has first_order_rate_constant;
vdAx = 0.6;
vdAx has flux;
KdAx = 0.63;
KdAx has nanomolar;
d1 = 0.1;
d1 has first_order_rate_constant;
a1 = 1.8;
a1 has second_order_rate_constant;
K1 = 0.28;
K1 has nanomolar;
K2 = 0.03;
K2 has nanomolar;
kt3 = 0.7;
kt3 has first_order_rate_constant;
kt4 = 1.5;
kt4 has first_order_rate_constant;
ksDusp = 0.5;
ksDusp has first_order_rate_constant;
vdDusp = 2;
vdDusp has flux;
KdDusp = 0.5;
KdDusp has nanomolar;
kcDusp = 1.35;
kcDusp has first_order_rate_constant;
KaFgf = 0.5;
KaFgf has nanomolar;
KaRas = 0.103;
KaRas has nanomolar;
KdRas = 0.1;
KdRas has nanomolar;
KdErk = 0.05;
KdErk has nanomolar;
KaErk = 0.05;
KaErk has nanomolar;
KaX = 0.05;
KaX has nanomolar;
KIF = 0.5;
KIF has nanomolar;
KID = 0.5;
KID has nanomolar;
KdX = 0.05;
KdX has nanomolar;
KaMDusp = 0.5;
KaMDusp has nanomolar;
KdMDusp = 0.5;
KdMDusp has nanomolar;
q = 2;
q has dimensionless;
r = 2;
r has dimensionless;
kc = 3.45;
kc has first_order_rate_constant;
j = 2;
j has dimensionless;
p = 2;
p has dimensionless;
epsilon = 0.3;
epsilon has dimensionless;
theta = 1.5;
theta has dimensionless;
eta = 0.3;
eta has dimensionless;
VMsMDusp = 0.9;
VMsMDusp has flux;
VMdMDusp = 0.5;
VMdMDusp has flux;
VMK = 5.08;
VMK has flux;
VMP = 1;
VMP has flux;
VMaRas = 4.968;
VMaRas has flux;
VMdRas = 0.41;
VMdRas has flux;
VMaErk = 3.3;
VMaErk has flux;
VMaX = 1.6;
VMaX has flux;
VMdX = 0.5;
VMdX has flux;
// Other declarations:
var vsFK;
const cytosol, KdN, vsN, vdN, KdNa, VdNa, kt1, kt2, KdNan, VdNan, KdMF;
const KIG1, vsF, vmF, KA, KdF, vdF, ksF, kd1, vsB, kd2, v0, vMB, vmd, KaB;
const KaXa, Kmd, n, m, vMXa, ksAx, vdAx, KdAx, d1, a1, K1, K2, kt3, kt4;
const ksDusp, vdDusp, KdDusp, kcDusp, KaFgf, KaRas, KdRas, KdErk, KaErk;
const KaX, KIF, KID, KdX, KaMDusp, KdMDusp, q, r, kc, j, p, epsilon, theta;
const eta, VMsMDusp, VMdMDusp, VMK, VMP, VMaRas, VMdRas, VMaErk, VMaX, VMdX;
// Unit definitions:
unit substance = 1e-9 mole;
unit time_unit = 60 second;
unit first_order_rate_constant = 1 / 60 second;
unit second_order_rate_constant = litre / (1e-9 mole * 60 second);
unit flux = 1e-9 mole / (litre * 60 second);
unit nanomolar = 1e-9 mole / litre;
// Display Names:
substance is "nanomole";
time_unit is "minute";
N is "Notch protein";
Na is "cytosolic NicD";
Nan_ is "nuclear NicD";
MF is "Lunatic fringe mRNA";
F is "Lunatic Fringe protein";
Bp is "phosph. beta-catenin";
BN is "nuclear beta-catenin";
A is "Axin2 protein";
K is "Gsk3";
B is "beta-catenin";
MAx is "Axin2 mRNA";
Rasa is "active Ras";
ERKa is "active ERK";
Xa is "active TF X";
MDusp is "Dusp6 mRNA";
Dusp is "Dusp6 protein";
Rasi is "inactive Ras";
Rast is "Ras total";
ERKi is "inactive ERK";
ERKt is "ERK total";
Xi is "inactive TF X";
Xt is "X total";
D is "Dsh protein";
AK is "Axin2/Gsk3 destruction complex";
n_synth is "Notch_synthesis";
N_activation is "Notch_activation";
end