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
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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 [17] 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 0.125 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
qinf ca 0.7894 0.0002726 ca 0.7292 0.01672 ca
tauq ca 657.9 0.02023 ca 301.8 0.002381 ca
cinf v 1 1 10.1 v 0.1016 0.00925
tauc v 3.627 0.03704 v

Parameters [33] name constant value unit derived unit sbo cvterm
isom0 isom0 = -0.5 -0.5 None
iden0 iden0 = 0 0.0 None
gls gls = 0.1 0.1 None
gld gld = 0.1 0.1 None
gna gna = 30 30.0 None
gkdr gkdr = 15 15.0 None
gca gca = 10 10.0 None
gkahp gkahp = 0.8 0.8 None
gkc gkc = 15 15.0 None
vna vna = 55 55.0 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 = 1.425 1.425 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
gnmda gnmda = 1.75 1.75 None
vs vs = -62.89223689 -62.89223689 None
vd vd = -62.98248752 -62.98248752 None
cad cad = 0.21664282 0.21664282 None
hs hs = 0.99806345 0.99806345 None
ns ns = 0.00068604 0.00068604 None
sd sd = 0.01086703 0.01086703 None
qd qd = 0.0811213 0.0811213 None
cd cd = 0.00809387 0.00809387 None
icad 0.0 dimensionless None
inmda 0.0 dimensionless None
chid 0.0 dimensionless None
gkq 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [14]   assignment name derived units sbo cvterm
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
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
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 = cinf vd cd tauc vd None
d qd/dt = qinf cad qd tauq cad None
icad = gca sd sd vd vca None
inmda = gnmda vd 0 1 0.28 0.062 vd 0 None
chid = 1.073 0.003453 cad 0.08095 0.08408 0.01634 cad 2.34 0.01811 0.0348 cad 0.9918 None
gkq = gkahp qd None
gkc = gkc cd chid None
t = time None