XPP model

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

# Kuznetsova and Deth, JCN, 2007
# 4-cell network, all-to-all connections: E cells (V1, V2) and I cells (V3, V4) 
init V1=-0.75  R1=0.26  CA1=0.1 H1=0.1
init V2=-0.71  R2=0.26  CA2=0.1 H2=0.1
init V3=-0.75  R3=0.26  CA3=0.1
init V4=-0.71  R4=0.26  CA4=0.1

init F1=0.0  S1=0.0  F2=0.0  S2=0.0 F3=0.0  S3=0.0  F4=0.0  S4=0.0
init F5=0.0  S5=0.0  F6=0.0  S6=0.0 F7=0.0  S7=0.0  F8=0.0  S8=0.0
init F9=0.0  S9=0.0  F10=0.0  S10=0.0 F11=0.0  S11=0.0  F12=0.0  S12=0.0

par Ie1=0.6, Ie2=0.6
#continuos input in both E cells

par GCA=0.1, GH=4.
par TR1=2.2, TR2=2.2
par GSYNee=6, GSYNei=6, TSYN=2, W=-0.1
#GSYNee=6 or 11

par GCAi=0.25
par TR3=1.5, TR4=1.5
par GSYNi=3, TSYNi=8
 
V1'=-MB(V1)*(V1-0.5)-26.*R1*(V1+0.95)-GCA*CA1*(V1-1.2)-GH*H1*(V1+0.95)-GSYNee*S1*(V1+0.0)-GSYNi*(V1+0.75)*(S2+S3)+Ie1  
R1'=(1./TR1)*(-R1+RB(V1))
CA1'=(1./14.)*(-CA1+CAB(V1))
H1'=(1./45.)*(-H1+3.*CA1)
F1'=(1./TSYN)*(-F1+heav(V2-W))
S1'=(1./TSYN)*(-S1+F1)
F2'=(1./TSYNi)*(-F2+heav(V3-W))
S2'=(1./TSYNi)*(-S2+F2)
F3'=(1./TSYNi)*(-F3+heav(V4-W))
S3'=(1./TSYNi)*(-S3+F3)

V2'=-MB(V2)*(V2-0.5)-26.*R2*(V2+0.95)-GCA*CA2*(V2-1.2)-GH*H2*(V2+0.95)-GSYNee*S4*(V2+0.0)-GSYNi*(V2+0.75)*(S5+S6)+Ie2
R2'=(1./TR2)*(-R2+RB(V2))
CA2'=(1./14.)*(-CA2+CAB(V2))
H2'=(1./45.)*(-H2+3.*CA2)
F4'=(1./TSYN)*(-F4+heav(V1-W))
S4'=(1./TSYN)*(-S4+F4)
F5'=(1./TSYNi)*(-F5+heav(V3-W))
S5'=(1./TSYNi)*(-S5+F5)
F6'=(1./TSYNi)*(-F6+heav(V4-W))
S6'=(1./TSYNi)*(-S6+F6)

V3'=-MB(V3)*(V3-0.5)-26.*R3*(V3+0.95)-GCAi*CA3*(V3-1.2)-GSYNi*S7*(V3+0.75)-GSYNei*(V3+0.0)*(S8+S9)
R3'=(1./TR3)*(-R3+RB(V3))
CA3'=(1./14.)*(-CA3+CAB(V3))
F7'=(1./TSYNi)*(-F7+heav(V4-W))
S7'=(1./TSYNi)*(-S7+F7)
F8'=(1./TSYN)*(-F8+heav(V1-W))
S8'=(1./TSYN)*(-S8+F8)
F9'=(1./TSYN)*(-F9+heav(V2-W))
S9'=(1./TSYN)*(-S9+F9)

V4'=-MB(V4)*(V4-0.5)-26.*R4*(V4+0.95)-GCAi*CA4*(V4-1.2)-GSYNi*S10*(V4+0.75)-GSYNei*(V4+0.0)*(S11+S12)
R4'=(1./TR4)*(-R4+RB(V4))
CA4'=(1./14.)*(-CA4+CAB(V4))
F10'=(1./TSYNi)*(-F10+heav(V4-W))
S10'=(1./TSYNi)*(-S10+F10)
F11'=(1./TSYN)*(-F11+heav(V1-W))
S11'=(1./TSYN)*(-S11+F11)
F12'=(1./TSYN)*(-F12+heav(V2-W))
S12'=(1./TSYN)*(-S12+F12)


CAB(V)=8.*(V+0.725)^2
MB(V)=17.8+47.6*V+33.8*V*V
RB(V)=1.24+3.7*V+3.2*V*V

um(Ve1,Ve2)=(Ve1+Ve2)/2

@ METHOD=stiff, TOLERANCE=.00001 BELL=0
@ dt=.01, total=600, xplot=t,yplot=CA1
@ xmin=0.0,xmax=600,ymin=-1.0,ymax=0.4
@ xlo=0.0,ylo=0.0,xhi=600,yhi=0.4,bound=30000,MAXSTOR=400000

aux n=um(V1,V2)

done
This file has been produced by sbmlutils.

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 :

id
name
time
substance
extent
volume
area
length
Access SBML model  L3V1

FunctionDefinitions [8] 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
cab v 8 v 0.725 2
mb v 17.8 47.6 v 33.8 v v
rb v 1.24 3.7 v 3.2 v v
um ve1 ve2 ve1 ve2 2

Parameters [55] name constant value unit derived unit sbo cvterm
v1 v1 = -0.75 -0.75 None
r1 r1 = 0.26 0.26 None
ca1 ca1 = 0.1 0.1 None
h1 h1 = 0.1 0.1 None
v2 v2 = -0.71 -0.71 None
r2 r2 = 0.26 0.26 None
ca2 ca2 = 0.1 0.1 None
h2 h2 = 0.1 0.1 None
v3 v3 = -0.75 -0.75 None
r3 r3 = 0.26 0.26 None
ca3 ca3 = 0.1 0.1 None
v4 v4 = -0.71 -0.71 None
r4 r4 = 0.26 0.26 None
ca4 ca4 = 0.1 0.1 None
f1 f1 = 0.0 0.0 None
s1 s1 = 0.0 0.0 None
f2 f2 = 0.0 0.0 None
s2 s2 = 0.0 0.0 None
f3 f3 = 0.0 0.0 None
s3 s3 = 0.0 0.0 None
f4 f4 = 0.0 0.0 None
s4 s4 = 0.0 0.0 None
f5 f5 = 0.0 0.0 None
s5 s5 = 0.0 0.0 None
f6 f6 = 0.0 0.0 None
s6 s6 = 0.0 0.0 None
f7 f7 = 0.0 0.0 None
s7 s7 = 0.0 0.0 None
f8 f8 = 0.0 0.0 None
s8 s8 = 0.0 0.0 None
f9 f9 = 0.0 0.0 None
s9 s9 = 0.0 0.0 None
f10 f10 = 0.0 0.0 None
s10 s10 = 0.0 0.0 None
f11 f11 = 0.0 0.0 None
s11 s11 = 0.0 0.0 None
f12 f12 = 0.0 0.0 None
s12 s12 = 0.0 0.0 None
ie1 ie1 = 0.6 0.6 None
ie2 ie2 = 0.6 0.6 None
gca gca = 0.1 0.1 None
gh gh = 4. 4.0 None
tr1 tr1 = 2.2 2.2 None
tr2 tr2 = 2.2 2.2 None
gsynee gsynee = 6 6.0 None
gsynei gsynei = 6 6.0 None
tsyn tsyn = 2 2.0 None
w w = -0.1 -0.1 None
gcai gcai = 0.25 0.25 None
tr3 tr3 = 1.5 1.5 None
tr4 tr4 = 1.5 1.5 None
gsyni gsyni = 3 3.0 None
tsyni tsyni = 8 8.0 None
n 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [40]   assignment name derived units sbo cvterm
d v1/dt = mb v1 v1 0.5 26 r1 v1 0.95 gca ca1 v1 1.2 gh h1 v1 0.95 gsynee s1 v1 0 gsyni v1 0.75 s2 s3 ie1 None
d r1/dt = 1 tr1 r1 rb v1 None
d ca1/dt = 1 14 ca1 cab v1 None
d h1/dt = 1 45 h1 3 ca1 None
d f1/dt = 1 tsyn f1 heav v2 w None
d s1/dt = 1 tsyn s1 f1 None
d f2/dt = 1 tsyni f2 heav v3 w None
d s2/dt = 1 tsyni s2 f2 None
d f3/dt = 1 tsyni f3 heav v4 w None
d s3/dt = 1 tsyni s3 f3 None
d v2/dt = mb v2 v2 0.5 26 r2 v2 0.95 gca ca2 v2 1.2 gh h2 v2 0.95 gsynee s4 v2 0 gsyni v2 0.75 s5 s6 ie2 None
d r2/dt = 1 tr2 r2 rb v2 None
d ca2/dt = 1 14 ca2 cab v2 None
d h2/dt = 1 45 h2 3 ca2 None
d f4/dt = 1 tsyn f4 heav v1 w None
d s4/dt = 1 tsyn s4 f4 None
d f5/dt = 1 tsyni f5 heav v3 w None
d s5/dt = 1 tsyni s5 f5 None
d f6/dt = 1 tsyni f6 heav v4 w None
d s6/dt = 1 tsyni s6 f6 None
d v3/dt = mb v3 v3 0.5 26 r3 v3 0.95 gcai ca3 v3 1.2 gsyni s7 v3 0.75 gsynei v3 0 s8 s9 None
d r3/dt = 1 tr3 r3 rb v3 None
d ca3/dt = 1 14 ca3 cab v3 None
d f7/dt = 1 tsyni f7 heav v4 w None
d s7/dt = 1 tsyni s7 f7 None
d f8/dt = 1 tsyn f8 heav v1 w None
d s8/dt = 1 tsyn s8 f8 None
d f9/dt = 1 tsyn f9 heav v2 w None
d s9/dt = 1 tsyn s9 f9 None
d v4/dt = mb v4 v4 0.5 26 r4 v4 0.95 gcai ca4 v4 1.2 gsyni s10 v4 0.75 gsynei v4 0 s11 s12 None
d r4/dt = 1 tr4 r4 rb v4 None
d ca4/dt = 1 14 ca4 cab v4 None
d f10/dt = 1 tsyni f10 heav v4 w None
d s10/dt = 1 tsyni s10 f10 None
d f11/dt = 1 tsyn f11 heav v1 w None
d s11/dt = 1 tsyn s11 f11 None
d f12/dt = 1 tsyn f12 heav v2 w None
d s12/dt = 1 tsyn s12 f12 None
n = um v1 v2 None
t = time None