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
Terms of use
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:
Redistributions of this SBML file must retain the above copyright notice, this list of conditions
and the following disclaimer.
Redistributions in a different form must reproduce the above copyright notice, this list of
conditions and the following disclaimer in the documentation and/or other materials provided
with the distribution.
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
L3V1
type
FunctionDefinitions [4]
name
math
sbo
cvterm
FunctionDefinition
max
minimum
x
y
x
x
y
y
FunctionDefinition
min
maximum
x
y
x
x
y
y
FunctionDefinition
heav
heavyside
x
0
x
0
0.5
x
0
1
x
0
0
FunctionDefinition
mod
modulo
x
y
x
y
x
y
x
0
y
0
x
y
x
y
type
Parameters [70]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
v
v = -63
F
-63.0
None
Parameter
a_na
a_na = 0.2
F
0.2
None
Parameter
inhibiteda
inhibiteda = 1.0
F
1.0
None
Parameter
d
d = 0.1
F
0.1
None
Parameter
inhibitedd
inhibitedd = 0.2
F
0.2
None
Parameter
m1
m1 = 0.0
F
0.0
None
Parameter
m
m = 0.0
F
0.0
None
Parameter
h
h = 0.0
F
0.0
None
Parameter
n1
n1 = 0.0
F
0.0
None
Parameter
h1
h1 = 0.0
F
0.0
None
Parameter
n
n = 0.0
F
0.0
None
Parameter
nir
nir = 0.003
F
0.003
None
Parameter
rir
rir = 0.282
F
0.282
None
Parameter
h2
h2 = 0.9
F
0.9
None
Parameter
g_na
g_na = 60.0
F
60.0
None
Parameter
g_ca_l
g_ca_l = 1.1
F
1.1
None
Parameter
g_ca_t
g_ca_t = 0.94
F
0.94
None
Parameter
g_k_dr
g_k_dr = 20.0
F
20.0
None
Parameter
g_m
g_m = 4.0
F
4.0
None
Parameter
g_ir
g_ir = 1.71
F
1.71
None
Parameter
g_d
g_d = 0.0277
F
0.0277
None
Parameter
kio
kio = 0.00132
F
0.00132
None
Parameter
koi
koi = 0.00111
F
0.00111
None
Parameter
aco
aco = 0.001
F
0.001
None
Parameter
v_k
v_k = -75
F
-75.0
None
Parameter
v_na
v_na = 60.0
F
60.0
None
Parameter
v_ca
v_ca = 100.0
F
100.0
None
Parameter
vh
vh = -40.0
F
-40.0
None
Parameter
k1
k1 = 0.3
F
0.3
None
Parameter
k1_
k1_ = 0.03
F
0.03
None
Parameter
k3
k3 = 0.001
F
0.001
None
Parameter
k3_
k3_ = 0.01
F
0.01
None
Parameter
tau_h
tau_h = 22.0
F
22.0
None
Parameter
tau_h1
tau_h1 = 1000.0
F
1000.0
None
Parameter
cm
cm = 14.0
F
14.0
None
Parameter
girbar
girbar = 50
F
50.0
None
Parameter
alpha
F
0.0
dimensionless
None
Parameter
beta
F
0.0
dimensionless
None
Parameter
m_inf
F
0.0
dimensionless
None
Parameter
m_inf1
F
0.0
dimensionless
None
Parameter
h_inf
F
0.0
dimensionless
None
Parameter
n_inf
F
0.0
dimensionless
None
Parameter
n_inf1
F
0.0
dimensionless
None
Parameter
n_inf2
F
0.0
dimensionless
None
Parameter
h_inf1
F
0.0
dimensionless
None
Parameter
alphairn
F
0.0
dimensionless
None
Parameter
betairn
F
0.0
dimensionless
None
Parameter
nirinf
F
0.0
dimensionless
None
Parameter
tauirn
F
0.0
dimensionless
None
Parameter
alphairr
F
0.0
dimensionless
None
Parameter
betairr
F
0.0
dimensionless
None
Parameter
ririnf
F
0.0
dimensionless
None
Parameter
tauirr
F
0.0
dimensionless
None
Parameter
tau_n
F
0.0
dimensionless
None
Parameter
tau_m
F
0.0
dimensionless
None
Parameter
tau_n1
F
0.0
dimensionless
None
Parameter
tau_m1
F
0.0
dimensionless
None
Parameter
a
F
0.0
dimensionless
None
Parameter
o
F
0.0
dimensionless
None
Parameter
i_na
F
0.0
dimensionless
None
Parameter
i_ca_l
F
0.0
dimensionless
None
Parameter
i_ca_t
F
0.0
dimensionless
None
Parameter
i_k_dr
F
0.0
dimensionless
None
Parameter
i_m
F
0.0
dimensionless
None
Parameter
iir
F
0.0
dimensionless
None
Parameter
i_d
F
0.0
dimensionless
None
Parameter
ikir
F
0.0
dimensionless
None
Parameter
ina
F
0.0
dimensionless
None
Parameter
ikdr
F
0.0
dimensionless
None
Parameter
t
model time
F
0.0
dimensionless
None
type
Rules [48]
assignment
name
derived units
sbo
cvterm
Rule
d v/dt
=
i_na
i_ca_l
i_ca_t
i_k_dr
i_m
iir
i_d
ikir
cm
None
Rule
d a_na/dt
=
d
alpha
inhibiteda
k1_
a_na
beta
k1
None
Rule
d inhibiteda/dt
=
a_na
k1
inhibitedd
alpha
a
inhibiteda
k1_
beta
a
None
Rule
d inhibitedd/dt
=
inhibiteda
beta
a
d
k3
inhibitedd
alpha
a
k3_
None
Rule
d d/dt
=
a_na
beta
inhibitedd
k3_
d
alpha
k3
None
Rule
d m1/dt
=
m_inf1
m1
tau_m1
None
Rule
d m/dt
=
m_inf
m
tau_m
None
Rule
d h/dt
=
h_inf
h
tau_h
None
Rule
d n1/dt
=
n_inf2
n1
tau_n1
None
Rule
d h1/dt
=
h_inf1
h1
tau_h1
None
Rule
d n/dt
=
n_inf
n
tau_n
None
Rule
d nir/dt
=
nirinf
nir
tauirn
None
Rule
d rir/dt
=
ririnf
rir
tauirr
None
Rule
d h2/dt
=
kio
1
h2
koi
aco
n
4
h2
None
Rule
alpha
=
10
1
0.1
6
v
None
Rule
beta
=
10
1
0.217391304347826
54.4
v
None
Rule
m_inf
=
1
1
0.1
56.1
v
None
Rule
m_inf1
=
1
1
0.0833333333333333
v
vh
None
Rule
h_inf
=
1
1
0.212765957446809
86.4
v
None
Rule
n_inf
=
1
1
0.25
37
v
None
Rule
n_inf1
=
0.2
0.8
1
0.0833333333333333
80
v
None
Rule
n_inf2
=
1
1
0.0666666666666667
25
v
None
Rule
h_inf1
=
0.3
0.7
1
0.1
35
v
None
Rule
alphairn
=
0.09
1
0.11
v
50
None
Rule
betairn
=
0.00035
0.07
v
25
None
Rule
nirinf
=
1
1
alphairn
betairn
None
Rule
tauirn
=
1
alphairn
betairn
None
Rule
alphairr
=
30
1
0.04
v
245
None
Rule
betairr
=
0.15
1
0.05
v
120
None
Rule
ririnf
=
1
1
betairr
alphairr
None
Rule
tauirr
=
1
alphairr
betairr
None
Rule
tau_n
=
80
0.0666666666666667
30
v
0.0666666666666667
30
v
None
Rule
tau_m
=
0.8
7
0.111111111111111
50
v
0.111111111111111
50
v
None
Rule
tau_n1
=
1
15
0.0666666666666667
30
v
0.0666666666666667
30
v
None
Rule
tau_m1
=
5
0.04
15
v
0.04
15
v
None
Rule
a
=
k1
k3_
k1_
k3
0.5
None
Rule
o
=
a_na
3
None
Rule
i_na
=
g_na
o
v
v_na
None
Rule
i_ca_l
=
g_ca_l
m1
2
v
v_ca
None
Rule
i_ca_t
=
g_ca_t
m
2
h
v
v_ca
None
Rule
i_k_dr
=
g_k_dr
n1
4
h1
h2
v
v_k
None
Rule
i_m
=
g_m
n
v
v_k
None
Rule
iir
=
g_ir
n_inf1
v
v_k
None
Rule
i_d
=
g_d
v
v_ca
None
Rule
ikir
=
girbar
nir
rir
v
v_k
None
Rule
ina
=
i_na
None
Rule
ikdr
=
i_k_dr
None
Rule
t
=
time
None