XPP model

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

# Rate-based model of coupled neuron populations to 
# perform discrimination using integral feedback control.
# Discrete attractor version, so r2 is determined by 
# the sum of 20 units, r2a to r2t.
par w1_2=0.065 w2_1=-0.7 tau=0.005 di=0.001 i2l=0
par tstim=1 t1=4.0 t2=10.0 tauapp=0.005 dtapp=0.001
par rsp=20 tauNMDA=0.03
par f1=20 f2=24 

init r1=0.0 r2=0.0 
init r2a=0.0 r2b=0.0 r2c=0.0 r2d=0.0 r2e=0.0 
init r2f=0.0 r2g=0.0 r2h=0.0 r2i=0.0 r2j=0.0 
init r2k=0.0 r2l=0.0 r2m=0.0 r2n=0.0 r2o=0.0 
init r2p=0.0 r2q=0.0 r2r=0.0 r2s=0.0 r2t=0.0 
# init sapp1=0.0 sapp2=0.0 
init s1=0.0 s2=0.0

sapp1=f1/((1+exp(-2*(t-t1)/dtapp))*(1+exp(-2*(t1+tstim-t)/dtapp)))
sapp2=f2/((1+exp(-2*(t-t2)/dtapp))*(1+exp(-2*(t2+tstim-t)/dtapp)))

ds1/dt=(sapp1-s1)/tauapp
ds2/dt=(sapp2-s2)/tauapp

i2=w1_2*r1*heav(r1)+r2a+r2b+r2c+r2d+r2e+r2f+r2g+r2h+r2i+r2j+r2k+r2l+r2m+r2n+r2o+r2p+r2q+r2r+r2s+r2t-i2l
dr2/dt=(-r2+i2*heav(i2))/tauNMDA
i1=rsp+w2_1*r2+s1+s2
dr1/dt=(-r1+i1)/tau
dr2a/dt=(-r2a+2*heav(r2-1))/tau
dr2b/dt=(-r2b+3*heav(r2-4))/tau
dr2c/dt=(-r2c+3*heav(r2-7))/tau
dr2d/dt=(-r2d+3*heav(r2-10))/tau
dr2e/dt=(-r2e+3*heav(r2-13))/tau
dr2f/dt=(-r2f+3*heav(r2-16))/tau
dr2g/dt=(-r2g+3*heav(r2-19))/tau
dr2h/dt=(-r2h+3*heav(r2-22))/tau
dr2i/dt=(-r2i+3*heav(r2-25))/tau
dr2j/dt=(-r2j+3*heav(r2-28))/tau
dr2k/dt=(-r2k+3*heav(r2-31))/tau
dr2l/dt=(-r2l+3*heav(r2-34))/tau
dr2m/dt=(-r2m+3*heav(r2-37))/tau
dr2n/dt=(-r2n+3*heav(r2-40))/tau
dr2o/dt=(-r2o+3*heav(r2-43))/tau
dr2p/dt=(-r2p+3*heav(r2-46))/tau
dr2q/dt=(-r2q+3*heav(r2-49))/tau
dr2r/dt=(-r2r+3*heav(r2-52))/tau
dr2s/dt=(-r2s+3*heav(r2-55))/tau
dr2t/dt=(-r2t+3*heav(r2-58))/tau

# dsapp1/dt=(s1-sapp1)/tauapp
# dsapp2/dt=(s2-sapp2)/tauapp
# ds1/dt=0.0
# ds2/dt=0.0
aux i2out=i2
aux di2=-r2+i2
# global 1 {t-t1} {s1=f1}
# global 2 {t-t1-tstim} {s1=0.0}
# global 3 {t-t2} {s2=f2}
# global 4 {t-t2-tstim} {s2=0}

@total=12,bound=100,dt=.001,dtmin=1e-5,dtmax=10,atoler=1e-4
@toler=1e-5,xhi=12,yhi=50,ylo=0 njmp=50,bell=0
@bell=off,nout=50                                                             
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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
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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.


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Access SBML model  L3V1

FunctionDefinitions [4] 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

Parameters [45] name constant value unit derived unit sbo cvterm
w1_2 w1_2 = 0.065 0.065 None
w2_1 w2_1 = -0.7 -0.7 None
tau tau = 0.005 0.005 None
di di = 0.001 0.001 None
i2l i2l = 0 0.0 None
tstim tstim = 1 1.0 None
t1 t1 = 4.0 4.0 None
t2 t2 = 10.0 10.0 None
tauapp tauapp = 0.005 0.005 None
dtapp dtapp = 0.001 0.001 None
rsp rsp = 20 20.0 None
taunmda taunmda = 0.03 0.03 None
f1 f1 = 20 20.0 None
f2 f2 = 24 24.0 None
r1 r1 = 0.0 0.0 None
r2 r2 = 0.0 0.0 None
r2a r2a = 0.0 0.0 None
r2b r2b = 0.0 0.0 None
r2c r2c = 0.0 0.0 None
r2d r2d = 0.0 0.0 None
r2e r2e = 0.0 0.0 None
r2f r2f = 0.0 0.0 None
r2g r2g = 0.0 0.0 None
r2h r2h = 0.0 0.0 None
r2i r2i = 0.0 0.0 None
r2j r2j = 0.0 0.0 None
r2k r2k = 0.0 0.0 None
r2l r2l = 0.0 0.0 None
r2m r2m = 0.0 0.0 None
r2n r2n = 0.0 0.0 None
r2o r2o = 0.0 0.0 None
r2p r2p = 0.0 0.0 None
r2q r2q = 0.0 0.0 None
r2r r2r = 0.0 0.0 None
r2s r2s = 0.0 0.0 None
r2t r2t = 0.0 0.0 None
s1 s1 = 0.0 0.0 None
s2 s2 = 0.0 0.0 None
sapp1 0.0 dimensionless None
sapp2 0.0 dimensionless None
i2 0.0 dimensionless None
i1 0.0 dimensionless None
i2out 0.0 dimensionless None
di2 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [31]   assignment name derived units sbo cvterm
d s1/dt = sapp1 s1 tauapp None
d s2/dt = sapp2 s2 tauapp None
d r2/dt = r2 i2 heav i2 taunmda None
d r1/dt = r1 i1 tau None
d r2a/dt = r2a 2 heav r2 1 tau None
d r2b/dt = r2b 3 heav r2 4 tau None
d r2c/dt = r2c 3 heav r2 7 tau None
d r2d/dt = r2d 3 heav r2 10 tau None
d r2e/dt = r2e 3 heav r2 13 tau None
d r2f/dt = r2f 3 heav r2 16 tau None
d r2g/dt = r2g 3 heav r2 19 tau None
d r2h/dt = r2h 3 heav r2 22 tau None
d r2i/dt = r2i 3 heav r2 25 tau None
d r2j/dt = r2j 3 heav r2 28 tau None
d r2k/dt = r2k 3 heav r2 31 tau None
d r2l/dt = r2l 3 heav r2 34 tau None
d r2m/dt = r2m 3 heav r2 37 tau None
d r2n/dt = r2n 3 heav r2 40 tau None
d r2o/dt = r2o 3 heav r2 43 tau None
d r2p/dt = r2p 3 heav r2 46 tau None
d r2q/dt = r2q 3 heav r2 49 tau None
d r2r/dt = r2r 3 heav r2 52 tau None
d r2s/dt = r2s 3 heav r2 55 tau None
d r2t/dt = r2t 3 heav r2 58 tau None
sapp1 = f1 1 2 t t1 dtapp 1 2 t1 tstim t dtapp None
sapp2 = f2 1 2 t t2 dtapp 1 2 t2 tstim t dtapp None
i2 = w1_2 r1 heav r1 r2a r2b r2c r2d r2e r2f r2g r2h r2i r2j r2k r2l r2m r2n r2o r2p r2q r2r r2s r2t i2l None
i1 = rsp w2_1 r2 s1 s2 None
i2out = i2 None
di2 = r2 i2 None
t = time None