XPP model

This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6.

# NG108_Acon.ode
# 
# IK(erg) was incorporated into the model.
# Ref: Lin et al., Neuropharmacology 2008;
# 

# Initial values of the variables
initial V=-63, A_na=0.2, inhibitedA=1.0, D=0.1, inhibitedD=0.2, m1=0.0, m=0.0, h=0.0, n1=0.0, h1=0.0, n=0.0
init nIR=0.003, rIR=0.282, h2=0.9

# Values of the model parameters: kio=k-1; koi=k+1 shown in the article
param  g_Na=60.0, g_Ca_L=1.1, g_Ca_T=0.94, g_K_dr=20.0, g_M=4.0,  g_ir=1.71, g_d=0.0277
param kio=0.00132, koi=0.00111
param ACO=0.001
param V_K=-75
number  V_Na=60.0, V_Ca=100.0, Vh=-40.0
number k1=0.3, k1_=0.03, k3=0.001, k3_=0.01
param  tau_h=22.0, tau_h1=1000.0, Cm=14.0
param girbar=50

# Kinetic equations
alpha= (10.0 / (1.0 + exp( - (0.1 * (6.0 + V)))))
beta= (10.0 / (1.0 + exp((0.2173913043478261 * (54.4 + V)))))
m_inf= (1.0 / (1.0 + exp( - (0.1 * (-56.1 + V)))))
m_inf1= (1.0 / (1.0 + exp( - (0.08333333333333333 * (V - Vh)))))
h_inf= (1.0 / (1.0 + exp((0.2127659574468085 * (86.4 + V)))))
n_inf= (1.0 / (1.0 + exp( - (0.25 * (37.0 + V)))))
n_inf1= (0.2 + (0.8 / (1.0 + exp((0.08333333333333333 * (80.0 + V))))))
n_inf2= (1.0 / (1.0 + exp( - (0.06666666666666667 * (25.0 + V)))))
h_inf1= (0.3 + (0.7 / (1.0 + exp( - (0.1 * (35.0 + V))))))
alphaIRn = 0.09/(1+exp(0.11*(V+50)))
betaIRn = 0.00035*exp(0.07*(V+25))
nIRinf = 1/(1+alphaIRn/betaIRn)
tauIRn = 1/(alphaIRn + betaIRn)
alphaIRr = 30/(1+exp(0.04*(V+245)))
betaIRr = 0.15/(1+exp(-0.05*(V+120)))
rIRinf = 1/(1+betaIRr/alphaIRr)
tauIRr = 1/(alphaIRr + betaIRr)
tau_n= (80.0 / (exp((0.06666666666666667 * (30.0 + V))) + exp( - (0.06666666666666667 * (30.0 + V)))))
tau_m= (0.8 + (7.0 / (exp((0.1111111111111111 * (50.0 + V))) + exp( - (0.1111111111111111 * (50.0 + V))))))
tau_n1= (1.0 + (15.0 / (exp((0.06666666666666667 * (30.0 + V))) + exp( - (0.06666666666666667 * (30.0 + V))))))
tau_m1= (5.0 / (exp((0.04 * (15.0 + V))) + exp( - (0.04 * (15.0 + V)))))
a= (k1 * k3_ / (k1_ * k3))^0.5
O= A_na^3

i_Na= (g_Na * O * (V - V_Na))
i_Ca_L= (g_Ca_L * m1^2 * (V - V_Ca))
i_Ca_T= (g_Ca_T * m^2 * h * (V - V_Ca))
i_K_dr= (g_K_dr * n1^4 * h1 * h2 * (V - V_K))
i_M= (g_M * n * (V - V_K))
iir=(g_ir)*n_inf1*(V-V_K)
i_d= (g_d * (V - V_Ca))
iKir=girbar*nIR*rIR*(V - V_K)

# Differential equations
V'=(-(i_Na + i_Ca_L + i_Ca_T + i_K_dr + i_M + iir + i_d + iKir) / Cm)
A_na'= D*alpha+inhibitedA*k1_-A_na*(beta+k1)
inhibitedA'=A_na*k1+inhibitedD*alpha*a-inhibitedA*(k1_+beta*a)
inhibitedD'=inhibitedA*beta*a+D*k3-inhibitedD*(alpha*a+k3_)
D'=A_na*beta+inhibitedD*k3_-D*(alpha+k3)
m1'=((m_inf1 - m1) / tau_m1)
m'=((m_inf - m) / tau_m)
h'=((h_inf - h) / tau_h)
n1'=((n_inf2 - n1) / tau_n1)
h1'=((h_inf1 - h1) / tau_h1)
n'=((n_inf - n) / tau_n)
nIR' = (nIRinf - nIR)/tauIRn
rIR' = (rIRinf - rIR)/tauIRr
h2'= kio*(1-h2)-koi*ACO*n^4*h2

aux ina=i_Na
aux iKdr=i_K_dr

# Numerical and plotting parameters for xpp
@ maxstor=800000, total=10000, bound=100000, dt=0.1
@ xlo=0, xhi=10000, ylo=-80, yhi=45
@ method=cvode, atol=0.0001, toler=0.0001

done
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Copyright © 2017 Matthias Koenig

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

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This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Model :

id
name
time
substance
extent
volume
area
length
Access SBML model  L3V1

FunctionDefinitions [4] name math sbo cvterm
max minimum x y x x y y
min maximum x y x x y y
heav heavyside x 0 x 0 0.5 x 0 1 x 0 0
mod modulo x y x y x y x 0 y 0 x y x y

Parameters [70] name constant value unit derived unit sbo cvterm
v v = -63 -63.0 None
a_na a_na = 0.2 0.2 None
inhibiteda inhibiteda = 1.0 1.0 None
d d = 0.1 0.1 None
inhibitedd inhibitedd = 0.2 0.2 None
m1 m1 = 0.0 0.0 None
m m = 0.0 0.0 None
h h = 0.0 0.0 None
n1 n1 = 0.0 0.0 None
h1 h1 = 0.0 0.0 None
n n = 0.0 0.0 None
nir nir = 0.003 0.003 None
rir rir = 0.282 0.282 None
h2 h2 = 0.9 0.9 None
g_na g_na = 60.0 60.0 None
g_ca_l g_ca_l = 1.1 1.1 None
g_ca_t g_ca_t = 0.94 0.94 None
g_k_dr g_k_dr = 20.0 20.0 None
g_m g_m = 4.0 4.0 None
g_ir g_ir = 1.71 1.71 None
g_d g_d = 0.0277 0.0277 None
kio kio = 0.00132 0.00132 None
koi koi = 0.00111 0.00111 None
aco aco = 0.001 0.001 None
v_k v_k = -75 -75.0 None
v_na v_na = 60.0 60.0 None
v_ca v_ca = 100.0 100.0 None
vh vh = -40.0 -40.0 None
k1 k1 = 0.3 0.3 None
k1_ k1_ = 0.03 0.03 None
k3 k3 = 0.001 0.001 None
k3_ k3_ = 0.01 0.01 None
tau_h tau_h = 22.0 22.0 None
tau_h1 tau_h1 = 1000.0 1000.0 None
cm cm = 14.0 14.0 None
girbar girbar = 50 50.0 None
alpha 0.0 dimensionless None
beta 0.0 dimensionless None
m_inf 0.0 dimensionless None
m_inf1 0.0 dimensionless None
h_inf 0.0 dimensionless None
n_inf 0.0 dimensionless None
n_inf1 0.0 dimensionless None
n_inf2 0.0 dimensionless None
h_inf1 0.0 dimensionless None
alphairn 0.0 dimensionless None
betairn 0.0 dimensionless None
nirinf 0.0 dimensionless None
tauirn 0.0 dimensionless None
alphairr 0.0 dimensionless None
betairr 0.0 dimensionless None
ririnf 0.0 dimensionless None
tauirr 0.0 dimensionless None
tau_n 0.0 dimensionless None
tau_m 0.0 dimensionless None
tau_n1 0.0 dimensionless None
tau_m1 0.0 dimensionless None
a 0.0 dimensionless None
o 0.0 dimensionless None
i_na 0.0 dimensionless None
i_ca_l 0.0 dimensionless None
i_ca_t 0.0 dimensionless None
i_k_dr 0.0 dimensionless None
i_m 0.0 dimensionless None
iir 0.0 dimensionless None
i_d 0.0 dimensionless None
ikir 0.0 dimensionless None
ina 0.0 dimensionless None
ikdr 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [48]   assignment name derived units sbo cvterm
d v/dt = i_na i_ca_l i_ca_t i_k_dr i_m iir i_d ikir cm None
d a_na/dt = d alpha inhibiteda k1_ a_na beta k1 None
d inhibiteda/dt = a_na k1 inhibitedd alpha a inhibiteda k1_ beta a None
d inhibitedd/dt = inhibiteda beta a d k3 inhibitedd alpha a k3_ None
d d/dt = a_na beta inhibitedd k3_ d alpha k3 None
d m1/dt = m_inf1 m1 tau_m1 None
d m/dt = m_inf m tau_m None
d h/dt = h_inf h tau_h None
d n1/dt = n_inf2 n1 tau_n1 None
d h1/dt = h_inf1 h1 tau_h1 None
d n/dt = n_inf n tau_n None
d nir/dt = nirinf nir tauirn None
d rir/dt = ririnf rir tauirr None
d h2/dt = kio 1 h2 koi aco n 4 h2 None
alpha = 10 1 0.1 6 v None
beta = 10 1 0.217391304347826 54.4 v None
m_inf = 1 1 0.1 56.1 v None
m_inf1 = 1 1 0.0833333333333333 v vh None
h_inf = 1 1 0.212765957446809 86.4 v None
n_inf = 1 1 0.25 37 v None
n_inf1 = 0.2 0.8 1 0.0833333333333333 80 v None
n_inf2 = 1 1 0.0666666666666667 25 v None
h_inf1 = 0.3 0.7 1 0.1 35 v None
alphairn = 0.09 1 0.11 v 50 None
betairn = 0.00035 0.07 v 25 None
nirinf = 1 1 alphairn betairn None
tauirn = 1 alphairn betairn None
alphairr = 30 1 0.04 v 245 None
betairr = 0.15 1 0.05 v 120 None
ririnf = 1 1 betairr alphairr None
tauirr = 1 alphairr betairr None
tau_n = 80 0.0666666666666667 30 v 0.0666666666666667 30 v None
tau_m = 0.8 7 0.111111111111111 50 v 0.111111111111111 50 v None
tau_n1 = 1 15 0.0666666666666667 30 v 0.0666666666666667 30 v None
tau_m1 = 5 0.04 15 v 0.04 15 v None
a = k1 k3_ k1_ k3 0.5 None
o = a_na 3 None
i_na = g_na o v v_na None
i_ca_l = g_ca_l m1 2 v v_ca None
i_ca_t = g_ca_t m 2 h v v_ca None
i_k_dr = g_k_dr n1 4 h1 h2 v v_k None
i_m = g_m n v v_k None
iir = g_ir n_inf1 v v_k None
i_d = g_d v v_ca None
ikir = girbar nir rir v v_k None
ina = i_na None
ikdr = i_k_dr None
t = time None