XPP model
This model was converted from XPP ode format to SBML using sbmlutils-0.1.5a6
.
# $Id: booth_bose.ode,v 1.29 2004/02/09 21:41:46 billl Exp $
# Edited by Luke Yuri Prince on 14/1/15
## booth_bose.ode
## Pinsky-Rinzel pyramidal cell
## |||#|||
# parameter values
par Isom0=-0.5
par Iden0=0
par gLs=0.1 gLd=0.1 gNa=30 gKdr=15 gCa=10 gKahp=0.8 gKC=15
par VNa=55
par VCa=80 VK=-75 VL=-60 Vsyn=0
par gc=1.425
par pp=0.5 Cm=3
par alphac=2 betac=0.1
par gnmda=1.75
# output cols are t, ODEs, AUXs in order, here:
# t vs vd cad hs ns sd cd qd gqk gkc
Vs'=(-gLs*(Vs-VL)-gNa*(Minfs(Vs)^2)*hs*(Vs-VNa)-gKdr*ns*(Vs-VK)+(gc/pp)*(Vd-Vs)+Isom0/pp)/Cm
Vd'=(-gLd*(Vd-VL)-ICad-gKahp*qd*(Vd-VK)-gKC*cd*chid*(Vd-VK)+(gc*(Vs-Vd))/(1.0-pp)-Inmda/(1-pp)+Iden0/(1-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'=(cinf(Vd)-cd)/tauc(Vd)
qd'=(qinf(Cad)-qd)/tauq(Cad)
# pyramidal cell functions
ICad= gCa*sd*sd*(Vd-VCa)
Inmda=gnmda*(Vd-0)/(1+0.28*exp(-0.062*(Vd-0)))
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)= 0.125*exp((-43.0-v)/18.0)
betahs(v)= 4/(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)
qinf(Ca)= (0.7894*exp(0.0002726*Ca))-(0.7292*exp(-0.01672*Ca))
tauq(Ca)= (657.9*exp(-0.02023*Ca))+(301.8*exp(-0.002381*Ca))
cinf(v)=(1.0/(1.0+exp((-10.1-v)/0.1016)))^0.00925
tauc(v)=3.627*exp(0.03704*v)
chid=1.073*sin(0.003453*Cad+0.08095)+0.08408*sin(0.01634*Cad-2.34)+0.01811*sin(0.0348*Cad-0.9918)
#chid=-1+2/(1+exp((-Cad)/96.82))
# auxiliary eqns
# aux sdc = (gc/pp)*(Vd-Vs)
# aux ICa = ICad
aux gkq = gKahp*qd
aux gkc = gKC*cd*chid
# initial conditions
init Vs=-62.89223689
init Vd=-62.98248752
init Cad=0.21664282
init hs=0.99806345
init ns=0.00068604
init sd=0.01086703
init qd=0.0811213
init cd=0.00809387
# integrator params
@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1.5e3,ylo=-100,yhi=30
@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3
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 [17]
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
0.125
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
qinf
ca
0.7894
0.0002726
ca
0.7292
0.01672
ca
FunctionDefinition
tauq
ca
657.9
0.02023
ca
301.8
0.002381
ca
FunctionDefinition
cinf
v
1
1
10.1
v
0.1016
0.00925
FunctionDefinition
tauc
v
3.627
0.03704
v
type
Parameters [33]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
isom0
isom0 = -0.5
F
-0.5
None
Parameter
iden0
iden0 = 0
F
0.0
None
Parameter
gls
gls = 0.1
F
0.1
None
Parameter
gld
gld = 0.1
F
0.1
None
Parameter
gna
gna = 30
F
30.0
None
Parameter
gkdr
gkdr = 15
F
15.0
None
Parameter
gca
gca = 10
F
10.0
None
Parameter
gkahp
gkahp = 0.8
F
0.8
None
Parameter
gkc
gkc = 15
F
15.0
None
Parameter
vna
vna = 55
F
55.0
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 = 1.425
F
1.425
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
gnmda
gnmda = 1.75
F
1.75
None
Parameter
vs
vs = -62.89223689
F
-62.89223689
None
Parameter
vd
vd = -62.98248752
F
-62.98248752
None
Parameter
cad
cad = 0.21664282
F
0.21664282
None
Parameter
hs
hs = 0.99806345
F
0.99806345
None
Parameter
ns
ns = 0.00068604
F
0.00068604
None
Parameter
sd
sd = 0.01086703
F
0.01086703
None
Parameter
qd
qd = 0.0811213
F
0.0811213
None
Parameter
cd
cd = 0.00809387
F
0.00809387
None
Parameter
icad
F
0.0
dimensionless
None
Parameter
inmda
F
0.0
dimensionless
None
Parameter
chid
F
0.0
dimensionless
None
Parameter
gkq
F
0.0
dimensionless
None
Parameter
t
model time
F
0.0
dimensionless
None
type
Rules [14]
assignment
name
derived units
sbo
cvterm
Rule
d vs/dt
=
gls
vs
vl
gna
minfs
vs
2
hs
vs
vna
gkdr
ns
vs
vk
gc
pp
vd
vs
isom0
pp
cm
None
Rule
d vd/dt
=
gld
vd
vl
icad
gkahp
qd
vd
vk
gkc
cd
chid
vd
vk
gc
vs
vd
1
pp
inmda
1
pp
iden0
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
=
cinf
vd
cd
tauc
vd
None
Rule
d qd/dt
=
qinf
cad
qd
tauq
cad
None
Rule
icad
=
gca
sd
sd
vd
vca
None
Rule
inmda
=
gnmda
vd
0
1
0.28
0.062
vd
0
None
Rule
chid
=
1.073
0.003453
cad
0.08095
0.08408
0.01634
cad
2.34
0.01811
0.0348
cad
0.9918
None
Rule
gkq
=
gkahp
qd
None
Rule
gkc
=
gkc
cd
chid
None
Rule
t
=
time
None