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
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Copyright © 2017 Matthias Koenig

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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
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time
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Access SBML model  L3V1

FunctionDefinitions [15] 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
alphams v 0.32 46.9 v 46.9 v 4 1
betams v 0.28 v 19.9 v 19.9 5 1
minfs v alphams v alphams v betams v
alphans v 0.016 24.9 v 24.9 v 5 1
betans v 0.25 1 0.025 v
alphahs v 0.128 43 v 18
betahs v 4 1 20 v 5
alphasd v 1.6 1 0.072 v 5
betasd v 0.02 v 8.9 v 8.9 5 1
alphacd v 1 heav v 10 v 50 11 v 53.5 27 18.975 heav v 10 2 53.5 v 27
betacd v 1 heav v 10 2 53.5 v 27 alphacd v

Parameters [46] name constant value unit derived unit sbo cvterm
vs vs = -60 -60.0 None
vd vd = -60 -60.0 None
ip0 ip0 = 0.75 0.75 None
gls gls = 0.1 0.1 None
gld gld = 0.1 0.1 None
gkdr gkdr = 15 15.0 None
gca gca = 1 1.0 None
gkahp gkahp = 0.8 0.8 None
init_gkca init_gkca = 20 20.0 None
final_gkca final_gkca = 40 40.0 None
init_gna init_gna = 18 18.0 None
final_gna final_gna = 17 17.0 None
vna vna = 60 60.0 None
vca vca = 80 80.0 None
vk vk = -75 -75.0 None
vl vl = -60 -60.0 None
vsyn vsyn = 0 0.0 None
gc gc = 2.1 2.1 None
pp pp = 0.5 0.5 None
cm cm = 3 3.0 None
alphac alphac = 2 2.0 None
betac betac = 0.1 0.1 None
tstim tstim = 8.0e3 8000.0 None
n n = 500 500.0 None
gkatp gkatp 0.0 None
iatp iatp = 0.1 0.1 None
natp natp = 50 50.0 None
cad 0.0 dimensionless None
hs 0.0 dimensionless None
ns 0.0 dimensionless None
sd 0.0 dimensionless None
cd 0.0 dimensionless None
qd 0.0 dimensionless None
gkc 0.0 dimensionless None
gna 0.0 dimensionless None
icad 0.0 dimensionless None
alphaqd 0.0 dimensionless None
betaqd 0.0 dimensionless None
chid 0.0 dimensionless None
poatp 0.0 dimensionless None
ica 0.0 dimensionless None
gkq 0.0 dimensionless None
ikca 0.0 dimensionless None
ina 0.0 dimensionless None
ikatp 0.0 dimensionless None
t model time 0.0 dimensionless None

InitialAssignments [1] name assignment derived units sbo cvterm
gkatp = 0.0236 4 0.24 None

Rules [21]   assignment name derived units sbo cvterm
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
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
d cad/dt = 0.13 icad 0.075 cad None
d hs/dt = alphahs vs alphahs vs betahs vs hs None
d ns/dt = alphans vs alphans vs betans vs ns None
d sd/dt = alphasd vd alphasd vd betasd vd sd None
d cd/dt = alphacd vd alphacd vd betacd vd cd None
d qd/dt = alphaqd alphaqd betaqd qd None
gkc = init_gkca t tstim final_gkca None
gna = init_gna t tstim final_gna None
icad = gca sd sd vd vca None
alphaqd = min 2 -5 cad 0.01 None
betaqd = 0.001 None
chid = min cad 250 1 None
poatp = 0.8 1 iatp 0.023 2 None
ica = icad None
gkq = gkahp qd None
ikca = gkc cd chid vd vk None
ina = gna minfs vs 2 hs vs vna None
ikatp = gkatp natp poatp vs vk None
t = time None