XPP model

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

# 200 e and 50 I HH equations
# random applied current, random conductances
# to get it started, just set the excitatory synapses
# to some random values between 0 and 1
# you will get persistent activity.
# here are the HH functions
am(v)=phi*.1*(v+40)/(1-exp(-(v+40)/10))
bm(v)=phi*4*exp(-(v+65)/18)
ah(v)=phi*.07*exp(-(v+65)/20)
bh(v)=phi*1/(1+exp(-(v+35)/10))
an(v)=phi*.01*(v+55)/(1-exp(-(v+55)/10))
bn(v)=phi*.125*exp(-(v+65)/80)
par phi=1
# this is the current for each cell
ihh(v,m,h,n)=gna*h*(v-vna)*m^3+gk*(v-vk)*n^4+gl*(v-vl)
# synaptic onset parameters
# s' = a(vpre)(1-s)-s/tau
ae(x)=ae0/(1+exp(-x/5))
ai(x)=ai0/(1+exp(-x/5))
par ae0=4,ai0=1
# dont recompute the random tables every time a parameter is changed
@ autoeval=0
# random synapses - 20 % connectivity
table wee % 40000 0 39999 ran(1)<.02
table wei % 10000 0 9999 ran(1)<.02
table wie % 10000 0 9999 ran(1)<.02
table wii % 2500 0 2499  ran(1)<.02
# multiply synapses by weights
special see=mmult(200,200,wee,se0)
special sei=mmult(200,50,wei,se0)
special sie=mmult(50,200,wie,si0)
special sii=mmult(50,50,wii,si0)
# random currents applied to each cell
table r_e % 200 0 199  ran(1)-.5
table r_i % 50 0 49 ran(1)-.5
# parameters
par taue=4,taui=10
par vna=50  vk=-77  vl=-54.4  gna=120  gk=36  gl=0.3
par ie0=10,ie1=0
par ii0=10,ii1=0
par gee=0,gie=0,gii=0,gei=0
par eex=0,ein=-75
# finally the ODEs
ve[0..199]'=ie0+ie1*r_e([j])-ihh(ve[j],me[j],he[j],ne[j])-gee*see([j])*(ve[j]-eex)-gie*sie([j])*(ve[j]-ein)
vi[0..49]'=ii0+ii1*r_i([j])-ihh(vi[j],mi[j],hi[j],ni[j])-gei*sei([j])*(vi[j]-eex)-gii*sii([j])*(vi[j]-ein)
# synapses...
se[0..199]'=-se[j]/taue+ae(ve[j])*(1-se[j])
si[0..49]'=-si[j]/taui+ai(vi[j])*(1-si[j])
# gating variables
me[0..199]'=am(ve[j])*(1-me[j])-bm(ve[j])*me[j]
he[0..199]'=ah(ve[j])*(1-he[j])-bh(ve[j])*he[j]
ne[0..199]'=an(ve[j])*(1-ne[j])-bn(ve[j])*ne[j]
mi[0..49]'=am(vi[j])*(1-mi[j])-bm(vi[j])*mi[j]
hi[0..49]'=ah(vi[j])*(1-hi[j])-bh(vi[j])*hi[j]
ni[0..49]'=an(vi[j])*(1-ni[j])-bn(vi[j])*ni[j]
# initial data
init ve[0..199]=-65
init vi[0..49]=-65
# some numerical settings
@ total=200,meth=euler,nout=10,dt=.01
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 :

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Access SBML model  L3V1

FunctionDefinitions [13] 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 phi phi 0.1 v 40 1 v 40 10
bm v phi phi 4 v 65 18
ah v phi phi 0.07 v 65 20
bh v phi phi 1 1 v 35 10
an v phi phi 0.01 v 55 1 v 55 10
bn v phi phi 0.125 v 65 80
ihh v m h n gk gl gna vk vl vna gna h v vna m 3 gk v vk n 4 gl v vl
ae x ae0 ae0 1 x 5
ai x ai0 ai0 1 x 5

Parameters [34] name constant value unit derived unit sbo cvterm
phi phi = 1 1.0 None
ae0 ae0 = 4 4.0 None
ai0 ai0 = 1 1.0 None
taue taue = 4 4.0 None
taui taui = 10 10.0 None
vna vna = 50 50.0 None
vk vk = -77 -77.0 None
vl vl = -54.4 -54.4 None
gna gna = 120 120.0 None
gk gk = 36 36.0 None
gl gl = 0.3 0.3 None
ie0 ie0 = 10 10.0 None
ie1 ie1 = 0 0.0 None
ii0 ii0 = 10 10.0 None
ii1 ii1 = 0 0.0 None
gee gee = 0 0.0 None
gie gie = 0 0.0 None
gii gii = 0 0.0 None
gei gei = 0 0.0 None
eex eex = 0 0.0 None
ein ein = -75 -75.0 None
ve[0..199] = -65 -65.0 None
vi[0..49] = -65 -65.0 None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [11]   assignment name derived units sbo cvterm
= None None
= None None
= None None
= None None
= None None
= None None
= None None
= None None
= None None
= None None
t = time None