XPP model

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

###########################################################################
# This model has a delayed rectifier, a leak and
# a sodium current based on the famous Traub and Miles model but with changes put in
# by Bard Ermerntrout in linearization of F-I curves by adaptation, Neural computation, 
# 10:1721-9, 1998
# 
# Input Currents are in nA, maximal conductances in mS/cm2, membrane potential 
# in mV time in ms,and capacitance in uF/cm2
############################################################################

#adjust defaults for xpp internal variables
@ MAXSTOR=40000
@ YP=v
@ TOTAL=1000
@ DT=0.05
@ BOUND=100000
@ XHI=1000
@ YLO=-100
@ YHI=50
#@ METH=gear
@ BACKGROUND=white

# parameters


par gbarNa=80

par gbarK=80

par gleak=0.2
par C=1., i=0.61

v' = (i-(gleak*(v-Vl)+gK*(v-vk)+gNa*(v-vna))+eps*(u1-v)/dx)/C+p0*pulse(t-taup)

aux longcur=eps*(u1-v)/dx
#****************************************************
gNa=gbarNa*(m**3)*h

alpham=if (v+54) then (0.32*(V+54)/(1-exp(-(V+54)/4))) else (0.32)
betam=if (V+27) then (0.28*(V+27)/(exp((V+27)/5)-1)) else (0.28)

alphah=0.128*exp(-(V+50)/18)
betah=4/(1+exp(-(V+27)/5))

dm/dt=alpham*(1-m)-betam*m
dh/dt=alphah*(1-h)-betah*h

#**********************************************************

gK=gbarK*(n**4)

alphan=if (V+52) then (0.032*(V+52)/(1-exp(-(V+52)/5))) else (0.032)
betan=0.5*exp(-(V+57)/40)

dn/dt=alphan*(1-n)-betan*n



# auxiliary variables
# sod is sodium current
aux sod=gbarNa*(m**3)*h*(v-vna)
# pot is potassium current
aux pot=gbarK*(n**4)*(v-vk)

#initial conditions
init v=-70
init h=1-.000001,m=.000001,n=.000001

par Vna=50,Vk=-100,Vl=-67
par gld=0.1
p Vp=-50, Vsp=9, gnad=0.02, taupna=10



pinfd(V)=1/(1+exp(-(V-Vp)/Vsp))
Inap(V,y)=gnad*y*(V-Vna)/gld

pn[1..50]'=(pinfd(u[j])-pn[j])/taupna



Ild(V)=V-Vl

# cable equation


p p[0..50]=0


u1'=((lambda/dx)^2*(u2-2*u1+v)-Ild(u1)-Inap(u1,pn1))/tau +p1*pulse(t-taup)
u[2..50]'= ((lambda/dx)^2*(u[j+1]-2*u[j]+u[j-1])-Ild(u[j])-Inap(u[j],pn[j]))/tau +p[j]*pulse(t-taup)
u51=(c1+b1*u50/dx)/(a1+b1/dx)

par lambda=1,tau=10,dx=.1,c1=0,a1=0,b1=1,c0=0,a0=0,b0=1,eps=.025

pulse(t)=heav(t)*heav(sigma-t)
par sigma=.2
par t0=241.3
aux prc=t0-t
taup'=0

i u[1..50]=-60
i pn[1..50]=.1

par taur=1,taud=3,thresh=-30,gsyn=.1,Esyn=0
x1'=(-x1+.5*(1+tanh((v-thresh)/3.0)))/taur
y1'=(-y1+x1)/taud
init x1=0,y1=0

d
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 [8] 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
pinfd v vp vsp 1 1 v vp vsp
inap v y gld gnad vna gnad y v vna gld
ild v vl v vl
pulse t sigma heav t heav sigma t

Parameters [57] name constant value unit derived unit sbo cvterm
gbarna gbarna = 80 80.0 None
gbark gbark = 80 80.0 None
gleak gleak = 0.2 0.2 None
c c = 1. 1.0 None
i i = 0.61 0.61 None
v v = -70 -70.0 None
h h 0.0 None
m m = .000001 1e-06 None
n n = .000001 1e-06 None
vna vna = 50 50.0 None
vk vk = -100 -100.0 None
vl vl = -67 -67.0 None
gld gld = 0.1 0.1 None
vp vp = -50 -50.0 None
vsp vsp = 9 9.0 None
gnad gnad = 0.02 0.02 None
taupna taupna = 10 10.0 None
p[0..50] = 0 0.0 None
lambda lambda = 1 1.0 None
tau tau = 10 10.0 None
dx dx = .1 0.1 None
c1 c1 = 0 0.0 None
a1 a1 = 0 0.0 None
b1 b1 = 1 1.0 None
c0 c0 = 0 0.0 None
a0 a0 = 0 0.0 None
b0 b0 = 1 1.0 None
eps eps = .025 0.025 None
sigma sigma = .2 0.2 None
t0 t0 = 241.3 241.3 None
u[1..50] = -60 -60.0 None
pn[1..50] = .1 0.1 None
taur taur = 1 1.0 None
taud taud = 3 3.0 None
thresh thresh = -30 -30.0 None
gsyn gsyn = .1 0.1 None
esyn esyn = 0 0.0 None
x1 x1 = 0 0.0 None
y1 y1 = 0 0.0 None
0.0 dimensionless None
u1 0.0 dimensionless None
0.0 dimensionless None
taup 0.0 dimensionless None
longcur 0.0 dimensionless None
gna 0.0 dimensionless None
alpham 0.0 dimensionless None
betam 0.0 dimensionless None
alphah 0.0 dimensionless None
betah 0.0 dimensionless None
gk 0.0 dimensionless None
alphan 0.0 dimensionless None
betan 0.0 dimensionless None
sod 0.0 dimensionless None
pot 0.0 dimensionless None
u51 0.0 dimensionless None
prc 0.0 dimensionless None
t model time 0.0 dimensionless None

InitialAssignments [1] name assignment derived units sbo cvterm
h = 1 1 -6 None

Rules [24]   assignment name derived units sbo cvterm
d v/dt = i gleak v vl gk v vk gna v vna eps u1 v dx c p0 pulse t taup sigma None
d m/dt = alpham 1 m betam m None
d h/dt = alphah 1 h betah h None
d n/dt = alphan 1 n betan n None
= None None
d u1/dt = lambda dx 2 u2 2 u1 v ild u1 vl inap u1 pn1 gld gnad vna tau p1 pulse t taup sigma None
= None None
d taup/dt = 0 None
d x1/dt = x1 0.5 1 v thresh 3 taur None
d y1/dt = y1 x1 taud None
longcur = eps u1 v dx None
gna = gbarna m 3 h None
alpham = 0.32 v 54 1 v 54 4 v 54 0.32 None
betam = 0.28 v 27 v 27 5 1 v 27 0.28 None
alphah = 0.128 v 50 18 None
betah = 4 1 v 27 5 None
gk = gbark n 4 None
alphan = 0.032 v 52 1 v 52 5 v 52 0.032 None
betan = 0.5 v 57 40 None
sod = gbarna m 3 h v vna None
pot = gbark n 4 v vk None
u51 = c1 b1 u50 dx a1 b1 dx None
prc = t0 t None
t = time None