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)
Isyn(v,y)=gsyn*y*(v-Esyn)

#diff. equ.

v1'=(i-(ina(v1,m1,ha)+ikdr(v1,n1)+il(v1)+p0*Isyn(v1,y2))+eps*(ua1-v1)/dx)/C
v2'=(i-(ina(v2,m2,hb)+ikdr(v2,n2)+il(v2)+p0*Isyn(v2,y1))+eps*(ub1-v2)/dx)/C
m1'=am(v1)*(1-m1)-bm(v1)*m1
m2'=am(v2)*(1-m2)-bm(v2)*m2
n1'=an(v1)*(1-n1)-bn(v1)*n1
n2'=an(v2)*(1-n2)-bn(v2)*n2
ha'=ah(v1)*(1-ha)-bh(v1)*ha
hb'=ah(v2)*(1-hb)-bh(v2)*hb

## synapse
parameter taur=1,taud=3,thresh=-30
x1'=(-x1+.5*(1+tanh((v1-thresh)/3.0)))/taur
x2'=(-x2+.5*(1+tanh((v2-thresh)/3.0)))/taur
y1'=(-y1+x1)/taud
y2'=(-y2+x2)/taud
init x1=.001, y1=.001,x2=.001, y2=.001
p gsyn=.1, Esyn=0

p Vp=-50, Vsp=9, gnad=0.02, gld=.1, taupna=10

# !!!! the cable is passive if gnad=0 !!!!


pinfd(V)=1/(1+exp(-(V-Vp)/Vsp))
Ih(V,y)=gnad*y*(V-Ena)/gld
Ild(V)=V-El

ha[1..50]'=(pinfd(ua[j])-ha[j])/taupna
hb[1..50]'=(pinfd(ub[j])-hb[j])/taupna
# NOT TO CONFUSE WITH h GATE IN SOMA!!

# cable equation


ua1'=((lambda/dx)^2*(ua2-2*ua1+v1)-Ild(ua1)-Ih(ua1,ha1)-p1*Isyn(ua1,y2)/gld)/tau
ua[2..50]'= ((lambda/dx)^2*(ua[j+1]-2*ua[j]+ua[j-1])-Ild(ua[j])-Ih(ua[j],ha[j]) -p[j]*Isyn(ua[j],y2)/gld )/tau 
ua51=(c1+b1*ua50/dx)/(a1+b1/dx)

ub1'=((lambda/dx)^2*(ub2-2*ub1+v2)-Ild(ub1)-Ih(ub1,hb1)-p1*Isyn(ub1,y1)/gld)/tau
ub[2..50]'= ((lambda/dx)^2*(ub[j+1]-2*ub[j]+ub[j-1])-Ild(ub[j])-Ih(ub[j],hb[j])-p[j]*Isyn(ub[j],y1)/gld )/tau
ub51=(c1+b1*ub50/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

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 [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
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
isyn v y esyn gsyn gsyn y v esyn
pinfd v vp vsp 1 1 v vp vsp
ih v y ena gld gnad gnad y v ena gld
ild v el v el

Parameters [71] 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
x1 x1 = .001 0.001 None
y1 y1 = .001 0.001 None
x2 x2 = .001 0.001 None
y2 y2 = .001 0.001 None
gsyn gsyn = .1 0.1 None
esyn esyn = 0 0.0 None
vp vp = -50 -50.0 None
vsp vsp = 9 9.0 None
gnad gnad = 0.02 0.02 None
gld gld = .1 0.1 None
taupna taupna = 10 10.0 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 = .05 0.05 None
t0 t0 = 14.45 14.45 None
p[0..50] = 0 0.0 None
v1 0.0 dimensionless None
v2 0.0 dimensionless None
m1 0.0 dimensionless None
m2 0.0 dimensionless None
n1 0.0 dimensionless None
n2 0.0 dimensionless None
ha 0.0 dimensionless None
hb 0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
ua1 0.0 dimensionless None
0.0 dimensionless None
ub1 0.0 dimensionless None
0.0 dimensionless None
ua51 0.0 dimensionless None
ub51 0.0 dimensionless None
prc 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [22]   assignment name derived units sbo cvterm
d v1/dt = i ina v1 m1 ha ena gna ikdr v1 n1 ek gkdr il v1 el gl p0 isyn v1 y2 esyn gsyn eps ua1 v1 dx c None
d v2/dt = i ina v2 m2 hb ena gna ikdr v2 n2 ek gkdr il v2 el gl p0 isyn v2 y1 esyn gsyn eps ub1 v2 dx c None
d m1/dt = am v1 amhalf amphi amwidth 1 m1 bm v1 bmhalf bmphi bmwidth m1 None
d m2/dt = am v2 amhalf amphi amwidth 1 m2 bm v2 bmhalf bmphi bmwidth m2 None
d n1/dt = an v1 anhalf anphi anwidth 1 n1 bn v1 bnhalf bnphi bnwidth n1 None
d n2/dt = an v2 anhalf anphi anwidth 1 n2 bn v2 bnhalf bnphi bnwidth n2 None
d ha/dt = ah v1 ahhalf ahphi ahwidth 1 ha bh v1 bhhalf bhphi bhwidth ha None
d hb/dt = ah v2 ahhalf ahphi ahwidth 1 hb bh v2 bhhalf bhphi bhwidth hb None
d x1/dt = x1 0.5 1 v1 thresh 3 taur None
d x2/dt = x2 0.5 1 v2 thresh 3 taur None
d y1/dt = y1 x1 taud None
d y2/dt = y2 x2 taud None
= None None
= None None
d ua1/dt = lambda dx 2 ua2 2 ua1 v1 ild ua1 el ih ua1 ha1 ena gld gnad p1 isyn ua1 y2 esyn gsyn gld tau None
= None None
d ub1/dt = lambda dx 2 ub2 2 ub1 v2 ild ub1 el ih ub1 hb1 ena gld gnad p1 isyn ub1 y1 esyn gsyn gld tau None
= None None
ua51 = c1 b1 ua50 dx a1 b1 dx None
ub51 = c1 b1 ub50 dx a1 b1 dx None
prc = t0 t None
t = time None