XPP model

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

#this is the two compartment model with a brief NMDA activation

alphan(V)=-0.0032*tk*(V+5.)/(exp(-(V+5.)/10.) - 1.)
betan(V)=0.05*tk*exp(-((V+10.)/16.))

alpham(V)=-0.32*(V+31.)/(exp(-(V+31.)/4.) - 1.)
betam(V)=0.28*(V+4.)/(exp((V+4.)/5.) - 1.)
minf(v)=alpham(v)/(alpham(v)+betam(v))
alphah(V)=0.2*th*exp(-((V+47.)/18.))
betah(V)=25.*th/(1.+(exp(-(V+24.)/5.)))

gNa1(v,h)=gbarNa1*(minf(v)**3)*h
gK2(n)=gbarK2*(n**4)
gK1(x)=gbarK1/(1. + exp(-(x-vHk)/vSk))


v1'=i1+gCa1(v1)*(ECa-v1)+(gKCa1(u1)+gk1(v1)+gK2(n1))*(EK-v1)+gL1*(EL1-v1)+gNa1(v1,h1)*(ENa-v1)+nd*gc*(v2-v1)*r1*r2*r2/(r1*r1+r2*r2)
u1'= 2.*buf1*(gCa1(v1)*(ECa - v1)/H - u1/tC1)/r1
n1'= alphan(v1)*(1.-n1)-betan(v1)*n1
h1'= alphah(v1)*(1.-h1)-betah(v1)*h1

v2'=gCa1(v2)*(ECa-v2)+(gKCa1(u2)+gK1(v2)+gK2(n2))*(EK-v2)+gL1*(EL1-v2)+gNa1(v2,h2)*(ENa-v2)+gc*(v1-v2)*r1*r1*r2/(r1*r1+r2*r2)+gnmda(v2)*(eNMDA-v2)+gampa*tnmda*(eAMPA-v2)+gGABA*(eGABA-v2)
u2'= 2.*buf1*(gCa1(v2)*(ECa - v2)/H - u2/tC1)/r2
n2'= alphan(v2)*(1.-n2)-betan(v2)*n2
h2'= alphah(v2)*(1.-h2)-betah(v2)*h2

alphac1(V,tsc)=if (abs(V+50)>0.00001) then (-0.0032*tsc*(V+50.)/(exp(-(V+50.)/5.) - 1.)) else (0.016*tsc)
betac1(V,tsc)=0.05*tsc*exp(-(V+55.)/40.)
csinf(V)=alphac1(V,1)/(alphac1(V,1)+betac1(V,1))

# NMDA receptor activation
tnmda=heav(t-idel)-heav(t-idur-idel)
gnmda(v)=(tnmda*gbarNMDA+gbarNMDAc)/(1+0.28*Mg*exp(-me*v))
aux nmda=gnmda(v2)
aux ilong=(v1-v2)*gc

gCa1(V)=gbarCa1*(csinf(V)**4)
gKCa1(x)=gbarKCa1*(x**4)/((x**4) + (k1**4))

par idel=600, idur=500
par gL1=0.05, EL1=-50, buf1=0.05, gbarKCa1=0.3, k1=250., r1=10., r2=0.5,tC1=4
par gbarCa1=0.15,  gbarK2=4
par gbarK1=0.4,vHk=-10, vSk=7
par i1=0., gc=0.3
par ENa=55., ECa=100., EK=-90.
par H=.019298,tk=1
par gbarNMDA=0.4,  gbarNMDAc=0, Mg=0.5, me=0.08, eNMDA=0
par nd=10
par gbarNa1=150, th=0.05
par gGABA=0,eGABA=-50
par gAMPA=0,eAMPA=0


init v1=-54.4, u1=91.6, n1=0.17, h1=0.13, v2=-60, u2=149, n2=0.0025, h2=1

@ MAXSTOR=40000,TOTAL=2000,bell=off,XP=t,YP=v1
@ BOUND=10000,DT=0.1,METH=stiff,XHI=2000,YLO=-60,YHI=60

done
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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:

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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 :

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Access SBML model  L3V1

FunctionDefinitions [20] 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
alphan v tk 0.0032 tk v 5 v 5 10 1
betan v tk 0.05 tk v 10 16
alpham v 0.32 v 31 v 31 4 1
betam v 0.28 v 4 v 4 5 1
minf v alpham v alpham v betam v
alphah v th 0.2 th v 47 18
betah v th 25 th 1 v 24 5
gna1 v h gbarna1 gbarna1 minf v 3 h
gk2 n gbark2 gbark2 n 4
gk1 x gbark1 vhk vsk gbark1 1 x vhk vsk
alphac1 v tsc 0.0032 tsc v 50 v 50 5 1 v 50 1 -5 0.016 tsc
betac1 v tsc 0.05 tsc v 55 40
csinf v alphac1 v 1 alphac1 v 1 betac1 v 1
gnmda v gbarnmda gbarnmdac me mg tnmda tnmda gbarnmda gbarnmdac 1 0.28 mg me v
gca1 v gbarca1 gbarca1 csinf v 4
gkca1 x gbarkca1 k1 gbarkca1 x 4 x 4 k1 4

Parameters [46] name constant value unit derived unit sbo cvterm
idel idel = 600 600.0 None
idur idur = 500 500.0 None
gl1 gl1 = 0.05 0.05 None
el1 el1 = -50 -50.0 None
buf1 buf1 = 0.05 0.05 None
gbarkca1 gbarkca1 = 0.3 0.3 None
k1 k1 = 250. 250.0 None
r1 r1 = 10. 10.0 None
r2 r2 = 0.5 0.5 None
tc1 tc1 = 4 4.0 None
gbarca1 gbarca1 = 0.15 0.15 None
gbark2 gbark2 = 4 4.0 None
gbark1 gbark1 = 0.4 0.4 None
vhk vhk = -10 -10.0 None
vsk vsk = 7 7.0 None
i1 i1 = 0. 0.0 None
gc gc = 0.3 0.3 None
ena ena = 55. 55.0 None
eca eca = 100. 100.0 None
ek ek = -90. -90.0 None
h h = .019298 0.019298 None
tk tk = 1 1.0 None
gbarnmda gbarnmda = 0.4 0.4 None
gbarnmdac gbarnmdac = 0 0.0 None
mg mg = 0.5 0.5 None
me me = 0.08 0.08 None
enmda enmda = 0 0.0 None
nd nd = 10 10.0 None
gbarna1 gbarna1 = 150 150.0 None
th th = 0.05 0.05 None
ggaba ggaba = 0 0.0 None
egaba egaba = -50 -50.0 None
gampa gampa = 0 0.0 None
eampa eampa = 0 0.0 None
v1 v1 = -54.4 -54.4 None
u1 u1 = 91.6 91.6 None
n1 n1 = 0.17 0.17 None
h1 h1 = 0.13 0.13 None
v2 v2 = -60 -60.0 None
u2 u2 = 149 149.0 None
n2 n2 = 0.0025 0.0025 None
h2 h2 = 1 1.0 None
tnmda 0.0 dimensionless None
nmda 0.0 dimensionless None
ilong 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [12]   assignment name derived units sbo cvterm
d v1/dt = i1 gca1 v1 gbarca1 eca v1 gkca1 u1 gbarkca1 k1 gk1 v1 gbark1 vhk vsk gk2 n1 gbark2 ek v1 gl1 el1 v1 gna1 v1 h1 gbarna1 ena v1 nd gc v2 v1 r1 r2 r2 r1 r1 r2 r2 None
d u1/dt = 2 buf1 gca1 v1 gbarca1 eca v1 h u1 tc1 r1 None
d n1/dt = alphan v1 tk 1 n1 betan v1 tk n1 None
d h1/dt = alphah v1 th 1 h1 betah v1 th h1 None
d v2/dt = gca1 v2 gbarca1 eca v2 gkca1 u2 gbarkca1 k1 gk1 v2 gbark1 vhk vsk gk2 n2 gbark2 ek v2 gl1 el1 v2 gna1 v2 h2 gbarna1 ena v2 gc v1 v2 r1 r1 r2 r1 r1 r2 r2 gnmda v2 gbarnmda gbarnmdac me mg tnmda enmda v2 gampa tnmda eampa v2 ggaba egaba v2 None
d u2/dt = 2 buf1 gca1 v2 gbarca1 eca v2 h u2 tc1 r2 None
d n2/dt = alphan v2 tk 1 n2 betan v2 tk n2 None
d h2/dt = alphah v2 th 1 h2 betah v2 th h2 None
tnmda = heav t idel heav t idur idel None
nmda = gnmda v2 gbarnmda gbarnmdac me mg tnmda None
ilong = v1 v2 gc None
t = time None