XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# Adoped from Pinsky-Rinzel CA3 pyramidal cell model
# Pinsky and Rinzel, J Comput Neurosci 1994;1:39-60.
# K(ATP) channel was inserted into the model.
# Parameters for K(ATP) channels are from Koyto model
# Matsuoka et al. Prog Biophys Mol Biol 2004;85:279-299.
# Simulation results were mimicked by the data from H19-7 cells.
# Simulation of zonisamide (ZNS) effect on CA3 pyramidal cells
# Implemented by Drs. Sheng-Nan Wu and Chin-Wei Huang
# initial conditions
init Vs=-60 Vd=-60
# Parameter values
par ip0=0.75
par gLs=0.1 gLd=0.1 gKdr=15 gCa=1 gKahp=0.8
# Parameter values: simulate ZNS effect final_gNa=17 final_gKCa=40,
par init_gKCa=20 final_gKCa=40
par init_gNa=18 final_gNa=17
par VNa=60 VCa=80 VK=-75 VL=-60 Vsyn=0
par gc=2.1 pp=0.5 Cm=3
par alphac=2 betac=0.1
par tstim=8.0e3 n=500
par gkatp=0.0236*(4^0.24)
par iatp=0.1
par natp=50
gKC=if(t<tstim)then(init_gKCa)else(final_gKCa)
gNa=if(t<tstim)then(init_gNa)else(final_gNa)
# Output cols are t, ODEs, AUXs in order, here:
# t versus vd cad hs ns sd cd qd gqk gkc
Vs'=(-gLs*(Vs-VL)-gNa*(Minfs(Vs)^2)*hs*(Vs-VNa)-gKdr*ns*(Vs-VK)-gkatp*natp*poatp*(Vs-VK)+(gc/pp)*(Vd-Vs)+Ip0/pp)/Cm
Vd'=(-gLd*(Vd-VL)-ICad-gKahp*qd*(Vd-VK)-gKC*cd*chid*(Vd-VK)-gkatp*natp*poatp*(Vd-VK)+(gc*(Vs-Vd))/(1.0-pp))/Cm
Cad'= -0.13*ICad-0.075*Cad
hs'= alphahs(Vs)-(alphahs(Vs)+betahs(Vs))*hs
ns'= alphans(Vs)-(alphans(Vs)+betans(Vs))*ns
sd'= alphasd(Vd)-(alphasd(Vd)+betasd(Vd))*sd
cd'= alphacd(Vd)-(alphacd(Vd)+betacd(Vd))*cd
qd'= alphaqd-(alphaqd+betaqd)*qd
# Pyramidal cell functions
ICad = gCa*sd*sd*(Vd-VCa)
alphams(v) = 0.32*(-46.9-v)/(exp((-46.9-v)/4.0)-1.0)
betams(v) = 0.28*(v+19.9)/(exp((v+19.9)/5.0)-1.0)
Minfs(v) = alphams(v)/(alphams(v)+betams(v))
alphans(v) = 0.016*(-24.9-v)/(exp((-24.9-v)/5.0)-1.0)
betans(v) = 0.25*exp(-1.0-0.025*v)
alphahs(v) = 0.128*exp((-43.0-v)/18.0)
betahs(v) = 4.0/(1.0+exp((-20.0-v)/5.0))
alphasd(v) = 1.6/(1.0+exp(-0.072*(v-5.0)))
betasd(v) = 0.02*(v+8.9)/(exp((v+8.9)/5.0)-1.0)
alphacd(v) = (1.0-heav(v+10.0))*exp((v+50.0)/11-(v+53.5)/27)/18.975+heav(v+10.0)*2.0*exp((-53.5-v)/27.0)
betacd(v) = (1.0-heav(v+10.0))*(2.0*exp((-53.5-v)/27.0)-alphacd(v))
alphaqd = min(0.00002*Cad,0.01)
betaqd = 0.001
chid = min(Cad/250.0,1.0)
# Level of intracellular ATP concentration
poatp = 0.8/(1+(iatp/0.023)^2)
# auxiliary equationns
aux Ica=ICad
aux gkq = gKahp*qd
aux ikca = gKC*cd*chid*(Vd-VK)
aux ina = gNa*(Minfs(Vs)^2)*hs*(Vs-VNa)
aux ikatp = gkatp*natp*poatp*(Vs-VK)
# integrator params
@ maxstor=1600000,total=2.0e4,bound=10000,xlo=0,xhi=2.0e4,ylo=-90,yhi=40
@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.05
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 [15]
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
FunctionDefinition
alphams
v
0.32
46.9
v
46.9
v
4
1
FunctionDefinition
betams
v
0.28
v
19.9
v
19.9
5
1
FunctionDefinition
minfs
v
alphams
v
alphams
v
betams
v
FunctionDefinition
alphans
v
0.016
24.9
v
24.9
v
5
1
FunctionDefinition
betans
v
0.25
1
0.025
v
FunctionDefinition
alphahs
v
0.128
43
v
18
FunctionDefinition
betahs
v
4
1
20
v
5
FunctionDefinition
alphasd
v
1.6
1
0.072
v
5
FunctionDefinition
betasd
v
0.02
v
8.9
v
8.9
5
1
FunctionDefinition
alphacd
v
1
heav
v
10
v
50
11
v
53.5
27
18.975
heav
v
10
2
53.5
v
27
FunctionDefinition
betacd
v
1
heav
v
10
2
53.5
v
27
alphacd
v
type
Parameters [46]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
vs
vs = -60
F
-60.0
None
Parameter
vd
vd = -60
F
-60.0
None
Parameter
ip0
ip0 = 0.75
F
0.75
None
Parameter
gls
gls = 0.1
F
0.1
None
Parameter
gld
gld = 0.1
F
0.1
None
Parameter
gkdr
gkdr = 15
F
15.0
None
Parameter
gca
gca = 1
F
1.0
None
Parameter
gkahp
gkahp = 0.8
F
0.8
None
Parameter
init_gkca
init_gkca = 20
F
20.0
None
Parameter
final_gkca
final_gkca = 40
F
40.0
None
Parameter
init_gna
init_gna = 18
F
18.0
None
Parameter
final_gna
final_gna = 17
F
17.0
None
Parameter
vna
vna = 60
F
60.0
None
Parameter
vca
vca = 80
F
80.0
None
Parameter
vk
vk = -75
F
-75.0
None
Parameter
vl
vl = -60
F
-60.0
None
Parameter
vsyn
vsyn = 0
F
0.0
None
Parameter
gc
gc = 2.1
F
2.1
None
Parameter
pp
pp = 0.5
F
0.5
None
Parameter
cm
cm = 3
F
3.0
None
Parameter
alphac
alphac = 2
F
2.0
None
Parameter
betac
betac = 0.1
F
0.1
None
Parameter
tstim
tstim = 8.0e3
F
8000.0
None
Parameter
n
n = 500
F
500.0
None
Parameter
gkatp
gkatp
F
0.0
None
Parameter
iatp
iatp = 0.1
F
0.1
None
Parameter
natp
natp = 50
F
50.0
None
Parameter
cad
F
0.0
dimensionless
None
Parameter
hs
F
0.0
dimensionless
None
Parameter
ns
F
0.0
dimensionless
None
Parameter
sd
F
0.0
dimensionless
None
Parameter
cd
F
0.0
dimensionless
None
Parameter
qd
F
0.0
dimensionless
None
Parameter
gkc
F
0.0
dimensionless
None
Parameter
gna
F
0.0
dimensionless
None
Parameter
icad
F
0.0
dimensionless
None
Parameter
alphaqd
F
0.0
dimensionless
None
Parameter
betaqd
F
0.0
dimensionless
None
Parameter
chid
F
0.0
dimensionless
None
Parameter
poatp
F
0.0
dimensionless
None
Parameter
ica
F
0.0
dimensionless
None
Parameter
gkq
F
0.0
dimensionless
None
Parameter
ikca
F
0.0
dimensionless
None
Parameter
ina
F
0.0
dimensionless
None
Parameter
ikatp
F
0.0
dimensionless
None
Parameter
t
model time
F
0.0
dimensionless
None
type
InitialAssignments [1]
name
assignment
derived units
sbo
cvterm
InitialAssignment
gkatp
=
0.0236
4
0.24
None
type
Rules [21]
assignment
name
derived units
sbo
cvterm
Rule
d vs/dt
=
gls
vs
vl
gna
minfs
vs
2
hs
vs
vna
gkdr
ns
vs
vk
gkatp
natp
poatp
vs
vk
gc
pp
vd
vs
ip0
pp
cm
None
Rule
d vd/dt
=
gld
vd
vl
icad
gkahp
qd
vd
vk
gkc
cd
chid
vd
vk
gkatp
natp
poatp
vd
vk
gc
vs
vd
1
pp
cm
None
Rule
d cad/dt
=
0.13
icad
0.075
cad
None
Rule
d hs/dt
=
alphahs
vs
alphahs
vs
betahs
vs
hs
None
Rule
d ns/dt
=
alphans
vs
alphans
vs
betans
vs
ns
None
Rule
d sd/dt
=
alphasd
vd
alphasd
vd
betasd
vd
sd
None
Rule
d cd/dt
=
alphacd
vd
alphacd
vd
betacd
vd
cd
None
Rule
d qd/dt
=
alphaqd
alphaqd
betaqd
qd
None
Rule
gkc
=
init_gkca
t
tstim
final_gkca
None
Rule
gna
=
init_gna
t
tstim
final_gna
None
Rule
icad
=
gca
sd
sd
vd
vca
None
Rule
alphaqd
=
min
2 -5
cad
0.01
None
Rule
betaqd
=
0.001
None
Rule
chid
=
min
cad
250
1
None
Rule
poatp
=
0.8
1
iatp
0.023
2
None
Rule
ica
=
icad
None
Rule
gkq
=
gkahp
qd
None
Rule
ikca
=
gkc
cd
chid
vd
vk
None
Rule
ina
=
gna
minfs
vs
2
hs
vs
vna
None
Rule
ikatp
=
gkatp
natp
poatp
vs
vk
None
Rule
t
=
time
None