XPP model

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

# Neuron_EUG01.ode
# 
# gNani - noninactivating sodium conductace
# initial conditions
init Vs=-59, Vd=-59
init cad=0.056, hs=0.995, ma_ni=0.00583, ns=0.00148, sd=0.0153, cd=0.01169, qd=0.00125

# Parameter values
par ip0=0.75
par gLs=0.0,  gLd=0.0,   gCa=1,  gKahp=2.5

" Parameter values: simulate EUG (1 uM) effect final_gNa=17.1  final_gNani=0.3
par gKC=20
par gNa=18, gNani=0.5
par gKdr=24
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

# 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)-gNani*ma_ni^3*(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
ma_ni'=(1/(1+exp((-23-Vs)/7.0))-ma_ni)*(alphams(Vs)+betams(Vs))
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

# 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)
aux ina_ni=gNani*ma_ni^3*(Vs-VNa)

# Numerical and plotting parameters for xpp
@ maxstor=1600000,total=5000,bound=10000,xlo=0,xhi=5000,ylo=-90,yhi=40
@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.05
set EUG {gNa=17.1, gNani=0.3}

done
This file has been produced by sbmlutils.

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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. 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
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 [41] name constant value unit derived unit sbo cvterm
vs vs = -59 -59.0 None
vd vd = -59 -59.0 None
cad cad = 0.056 0.056 None
hs hs = 0.995 0.995 None
ma_ni ma_ni = 0.00583 0.00583 None
ns ns = 0.00148 0.00148 None
sd sd = 0.0153 0.0153 None
cd cd = 0.01169 0.01169 None
qd qd = 0.00125 0.00125 None
ip0 ip0 = 0.75 0.75 None
gls gls = 0.0 0.0 None
gld gld = 0.0 0.0 None
gca gca = 1 1.0 None
gkahp gkahp = 2.5 2.5 None
gkc gkc = 20 20.0 None
gna gna = 18 18.0 None
gnani gnani = 0.5 0.5 None
gkdr gkdr = 24 24.0 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
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
ina 0.0 dimensionless None
ina_ni 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 [17]   assignment name derived units sbo cvterm
d vs/dt = gls vs vl gna minfs vs 2 hs vs vna gnani ma_ni 3 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 ma_ni/dt = 1 1 23 vs 7 ma_ni alphams vs betams vs 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
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
ina = gna minfs vs 2 hs vs vna None
ina_ni = gnani ma_ni 3 vs vna None
t = time None