XPP model

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

# Neuron_OXC.ode
# 
# Huang et al., Int J Neuropsychopharmacol 2008;11:597-610
# 
# initial conditions
init Vs=-60 Vd=-60

# Parameter values
par ip0=0.75
par gLs=0.1  gLd=0.1   gCa=1  gKahp=0.8

# Parameter values: simulate OXC effect final_gNa=16.5  final_gKdr=14,
par gKC=20
par init_gNa=18  final_gNa=16.5
par init_gKdr=15, final_gKdr=14
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=1.0e4 n=500
par gkatp=0.0236*(4^0.24)
par iatp=0.1
par natp=50
gNa=if(t<tstim)then(init_gNa)else(final_gNa)
gKdr=if(t<tstim)then(init_gKdr)else(final_gKdr)

# 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 ikca = gKC*cd*chid*(Vd-VK)
aux ina = gNa*(Minfs(Vs)^2)*hs*(Vs-VNa)
aux ikdr=gKdr*ns*(Vs-VK)
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

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 [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
gca gca = 1 1.0 None
gkahp gkahp = 0.8 0.8 None
gkc gkc = 20 20.0 None
init_gna init_gna = 18 18.0 None
final_gna final_gna = 16.5 16.5 None
init_gkdr init_gkdr = 15 15.0 None
final_gkdr final_gkdr = 14 14.0 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 = 1.0e4 10000.0 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
gna 0.0 dimensionless None
gkdr 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
ikca 0.0 dimensionless None
ina 0.0 dimensionless None
ikdr 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
gna = init_gna t tstim final_gna None
gkdr = init_gkdr t tstim final_gkdr 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
ikca = gkc cd chid vd vk None
ina = gna minfs vs 2 hs vs vna None
ikdr = gkdr ns vs vk None
ikatp = gkatp natp poatp vs vk None
t = time None