XPP model

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

# Soma is Hodgkin-Huxley
p Ek=-77,Ena=50, El=-54.4
p gl=.3,gkdr=36,gna=120
p i=11
p C=1.

p amphi=.1,amhalf=-40,amwidth=10
p bmphi=4,bmhalf=-65,bmwidth=18
p ahphi=0.07,ahhalf=-65,ahwidth=20
p bhphi=1,bhhalf=-35,bhwidth=10
p anphi=.01,anhalf=-55,anwidth=10
p bnphi=.125,bnhalf=-65,bnwidth=80


# functions
am(v)=amphi*(v-amhalf)/(1-exp(-(v-amhalf)/amwidth))
bm(v)=bmphi*exp(-(v-bmhalf)/bmwidth)
ah(v)=ahphi*exp(-(v-ahhalf)/ahwidth)
bh(v)=bhphi/(1+exp(-(v-bhhalf)/bhwidth))
an(v)=anphi*(v-anhalf)/(1-exp(-(v-anhalf)/anwidth))
bn(v)=bnphi*exp(-(v-bnhalf)/bnwidth)

#currents
ina(v,m,h)=gna*m^3*h*(v-Ena)
ikdr(v,n)=gkdr*n^4*(v-Ek)
il(v)=gl*(v-El)

#diff. equ.

v'=(i-(ina(v,m,h)+ikdr(v,n)+il(v))+p0*pulse(t-taup)+eps*(u1-v)/dx)/C
m'=am(v)*(1-m)-bm(v)*m
n'=an(v)*(1-n)-bn(v)*n
h'=ah(v)*(1-h)-bh(v)*h

## synapse
parameter taur=1,taud=3,thresh=-30
x'=(-x+.5*(1+tanh((v-thresh)/3.0)))/taur
y'=(-y+x)/taud
init x=.001, y=.001


Ild(V)=V-El


# cable equation

u1'=((lambda/dx)^2*(u2-2*u1+v)-Ild(u1))/tau+p1*pulse(t-taup)
u[2..50]'= ((lambda/dx)^2*(u[j+1]-2*u[j]+u[j-1])-Ild(u[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=.05
par t0=14.45
aux prc=t0-t
taup'=0

p p[0..50]=0

@ total=300,xlo=0,xhi=300,ylo=-100,yhi=60,dt=0.05,bounds=10000000

d
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Copyright © 2017 Matthias Koenig

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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
am v amhalf amphi amwidth amphi v amhalf 1 v amhalf amwidth
bm v bmhalf bmphi bmwidth bmphi v bmhalf bmwidth
ah v ahhalf ahphi ahwidth ahphi v ahhalf ahwidth
bh v bhhalf bhphi bhwidth bhphi 1 v bhhalf bhwidth
an v anhalf anphi anwidth anphi v anhalf 1 v anhalf anwidth
bn v bnhalf bnphi bnwidth bnphi v bnhalf bnwidth
ina v m h ena gna gna m 3 h v ena
ikdr v n ek gkdr gkdr n 4 v ek
il v el gl gl v el
ild v el v el
pulse t sigma heav t heav sigma t

Parameters [54] name constant value unit derived unit sbo cvterm
ek ek = -77 -77.0 None
ena ena = 50 50.0 None
el el = -54.4 -54.4 None
gl gl = .3 0.3 None
gkdr gkdr = 36 36.0 None
gna gna = 120 120.0 None
i i = 11 11.0 None
c c = 1. 1.0 None
amphi amphi = .1 0.1 None
amhalf amhalf = -40 -40.0 None
amwidth amwidth = 10 10.0 None
bmphi bmphi = 4 4.0 None
bmhalf bmhalf = -65 -65.0 None
bmwidth bmwidth = 18 18.0 None
ahphi ahphi = 0.07 0.07 None
ahhalf ahhalf = -65 -65.0 None
ahwidth ahwidth = 20 20.0 None
bhphi bhphi = 1 1.0 None
bhhalf bhhalf = -35 -35.0 None
bhwidth bhwidth = 10 10.0 None
anphi anphi = .01 0.01 None
anhalf anhalf = -55 -55.0 None
anwidth anwidth = 10 10.0 None
bnphi bnphi = .125 0.125 None
bnhalf bnhalf = -65 -65.0 None
bnwidth bnwidth = 80 80.0 None
taur taur = 1 1.0 None
taud taud = 3 3.0 None
thresh thresh = -30 -30.0 None
x x = .001 0.001 None
y y = .001 0.001 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 = .05 0.05 None
t0 t0 = 14.45 14.45 None
p[0..50] = 0 0.0 None
v 0.0 dimensionless None
m 0.0 dimensionless None
n 0.0 dimensionless None
h 0.0 dimensionless None
u1 0.0 dimensionless None
0.0 dimensionless None
taup 0.0 dimensionless None
u51 0.0 dimensionless None
prc 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [12]   assignment name derived units sbo cvterm
d v/dt = i ina v m h ena gna ikdr v n ek gkdr il v el gl p0 pulse t taup sigma eps u1 v dx c None
d m/dt = am v amhalf amphi amwidth 1 m bm v bmhalf bmphi bmwidth m None
d n/dt = an v anhalf anphi anwidth 1 n bn v bnhalf bnphi bnwidth n None
d h/dt = ah v ahhalf ahphi ahwidth 1 h bh v bhhalf bhphi bhwidth h None
d x/dt = x 0.5 1 v thresh 3 taur None
d y/dt = y x taud None
d u1/dt = lambda dx 2 u2 2 u1 v ild u1 el tau p1 pulse t taup sigma None
= None None
d taup/dt = 0 None
u51 = c1 b1 u50 dx a1 b1 dx None
prc = t0 t None
t = time None