XPP model

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

# RESPIRATORY RHYTHM MODEL
# J. Rubin, N. Shevtsova, B. Ermentrout, J. Smith, I. Rybak
# J. Neurophysiol. 101:2146-2165, 2009

# parameters/initial conditions set to give 3-phase rhythm

# general parameters
p C=20
p gL=2.8
p Eleak=-60
p gsynE=10
p EsynE=0
p gsynI=60
p EsynI=-75
p EK=-85
p ENa=50

# parameters of NaP and Kdr currents 
p V12n=-29,kn=-4,gKdr=5,V12mp=-40,kmp=-6
p V12hp=-48,khp=6,tauhp=6000,gNaP=5

# parameters of adaptive neurons
p gAD=10,Tad2=2000,Tad3=1000,Tad4=2000
p Kad2=0.9,Kad3=1.3,Kad4=0.9

# parameters of output function
p V12outpute=-30,Koutpute=-8
p V12outputi=-30,Koutputi=-4

foute(v)=1./(1+exp((v-V12outpute)/Koutpute))
fouti(v)=1./(1+exp((v-V12outputi)/Koutputi))

# between neurons
p a12=0.4,b23=0.25,b24=0.35,b31=0.3,b32=0.05,b34=0.35
p b41=0.2,b42=0.35,b43=0.1
p Drive1=1,Drive2=1,Drive3=1
p c11=0.115,c12=0.3,c13=0.63,c14=0.33
p c21=0.07,c22=0.3,c24=0.4,c31=0.025
p nf=1
p sdum1=0,sdum2=0,sdum3=0,sdum4=0,edum=0

init v1=-60,v2=-60,v3=-60,v4=-60
init h=0.35,m2=0,m3=0,m4=0

# functions
ninf(v)=1./(1+exp((v-V12n)/kn))
mpinf(v)=1./(1+exp((v-V12mp)/kmp))
hpinf(v)=1./(1+exp((v-V12hp)/khp))
tauinf(v)=tauhp/cosh((v-V12hp)/(2*khp))

# currents
Inap(v,h)=gNaP*mpinf(v)*h*(v-ENa)
Ikdr(v)=gKdr*ninf(v)^4*(v-EK)
Iad(v,m)=gAD*m*(v-EK)
Il(v)=gL*(v-Eleak)

# ODEs
v1'=(-Inap(v1,h)-Ikdr(v1)-Il(v1)-gsynI*(b31*fouti(v3)+b41*fouti(v4)+sdum1)*(v1-EsynI)-gsynE*(c11*Drive1+c21*Drive2+c31*Drive3)*(v1-EsynE))/C
v2'=(-Iad(v2,m2)-Il(v2)-gsynI*(b32*fouti(v3)+b42*fouti(v4)+sdum2)*(v2-EsynI)-gsynE*(a12*foute(v1)+c22*Drive2+c12*Drive1+edum)*(v2-EsynE))/C
v3'=(-Iad(v3,m3)-Il(v3)-gsynI*(b23*fouti(v2)+b43*fouti(v4)+sdum3)*(v3-EsynI)-gsynE*(c13*Drive1)*(v3-EsynE))/C
v4'=(-Iad(v4,m4)-Il(v4)-gsynI*(b24*fouti(v2)+b34*fouti(v3)+sdum4)*(v4-EsynI)-gsynE*(c14*Drive1+c24*Drive2)*(v4-EsynE))/C
h'=(hpinf(v1)-h)/tauinf(v1)
m2'=(-m2+Kad2*fouti(v2))/Tad2
m3'=(-m3+Kad3*fouti(v3))/Tad3
m4'=(-m4+Kad4*fouti(v4))/Tad4

aux inh1=b31*fouti(v3)+b41*fouti(v4)
aux inh2=b32*fouti(v3)+b42*fouti(v4)
aux inh3=b23*fouti(v2)+b43*fouti(v4)
aux inh4=b24*fouti(v2)+b34*fouti(v3)

aux exc2=a12*foute(v1)

@ dt=0.1,total=10000,meth=qualrk,xp=t,yp=v1,xlow=0,xhi=1000,ylo=-80,yhi=20.,bound=5000,maxstor=10000001

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.


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Access SBML model  L3V1

FunctionDefinitions [14] 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
foute v koutpute v12outpute 1 1 v v12outpute koutpute
fouti v koutputi v12outputi 1 1 v v12outputi koutputi
ninf v kn v12n 1 1 v v12n kn
mpinf v kmp v12mp 1 1 v v12mp kmp
hpinf v khp v12hp 1 1 v v12hp khp
tauinf v khp tauhp v12hp tauhp v v12hp 2 khp
inap v h ena gnap kmp v12mp gnap mpinf v kmp v12mp h v ena
ikdr v ek gkdr kn v12n gkdr ninf v v12n kn 4 v ek
iad v m ek gad gad m v ek
il v eleak gl gl v eleak

Parameters [69] name constant value unit derived unit sbo cvterm
c c = 20 20.0 None
gl gl = 2.8 2.8 None
eleak eleak = -60 -60.0 None
gsyne gsyne = 10 10.0 None
esyne esyne = 0 0.0 None
gsyni gsyni = 60 60.0 None
esyni esyni = -75 -75.0 None
ek ek = -85 -85.0 None
ena ena = 50 50.0 None
v12n v12n = -29 -29.0 None
kn kn = -4 -4.0 None
gkdr gkdr = 5 5.0 None
v12mp v12mp = -40 -40.0 None
kmp kmp = -6 -6.0 None
v12hp v12hp = -48 -48.0 None
khp khp = 6 6.0 None
tauhp tauhp = 6000 6000.0 None
gnap gnap = 5 5.0 None
gad gad = 10 10.0 None
tad2 tad2 = 2000 2000.0 None
tad3 tad3 = 1000 1000.0 None
tad4 tad4 = 2000 2000.0 None
kad2 kad2 = 0.9 0.9 None
kad3 kad3 = 1.3 1.3 None
kad4 kad4 = 0.9 0.9 None
v12outpute v12outpute = -30 -30.0 None
koutpute koutpute = -8 -8.0 None
v12outputi v12outputi = -30 -30.0 None
koutputi koutputi = -4 -4.0 None
a12 a12 = 0.4 0.4 None
b23 b23 = 0.25 0.25 None
b24 b24 = 0.35 0.35 None
b31 b31 = 0.3 0.3 None
b32 b32 = 0.05 0.05 None
b34 b34 = 0.35 0.35 None
b41 b41 = 0.2 0.2 None
b42 b42 = 0.35 0.35 None
b43 b43 = 0.1 0.1 None
drive1 drive1 = 1 1.0 None
drive2 drive2 = 1 1.0 None
drive3 drive3 = 1 1.0 None
c11 c11 = 0.115 0.115 None
c12 c12 = 0.3 0.3 None
c13 c13 = 0.63 0.63 None
c14 c14 = 0.33 0.33 None
c21 c21 = 0.07 0.07 None
c22 c22 = 0.3 0.3 None
c24 c24 = 0.4 0.4 None
c31 c31 = 0.025 0.025 None
nf nf = 1 1.0 None
sdum1 sdum1 = 0 0.0 None
sdum2 sdum2 = 0 0.0 None
sdum3 sdum3 = 0 0.0 None
sdum4 sdum4 = 0 0.0 None
edum edum = 0 0.0 None
v1 v1 = -60 -60.0 None
v2 v2 = -60 -60.0 None
v3 v3 = -60 -60.0 None
v4 v4 = -60 -60.0 None
h h = 0.35 0.35 None
m2 m2 = 0 0.0 None
m3 m3 = 0 0.0 None
m4 m4 = 0 0.0 None
inh1 0.0 dimensionless None
inh2 0.0 dimensionless None
inh3 0.0 dimensionless None
inh4 0.0 dimensionless None
exc2 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [14]   assignment name derived units sbo cvterm
d v1/dt = inap v1 h ena gnap kmp v12mp ikdr v1 ek gkdr kn v12n il v1 eleak gl gsyni b31 fouti v3 koutputi v12outputi b41 fouti v4 koutputi v12outputi sdum1 v1 esyni gsyne c11 drive1 c21 drive2 c31 drive3 v1 esyne c None
d v2/dt = iad v2 m2 ek gad il v2 eleak gl gsyni b32 fouti v3 koutputi v12outputi b42 fouti v4 koutputi v12outputi sdum2 v2 esyni gsyne a12 foute v1 koutpute v12outpute c22 drive2 c12 drive1 edum v2 esyne c None
d v3/dt = iad v3 m3 ek gad il v3 eleak gl gsyni b23 fouti v2 koutputi v12outputi b43 fouti v4 koutputi v12outputi sdum3 v3 esyni gsyne c13 drive1 v3 esyne c None
d v4/dt = iad v4 m4 ek gad il v4 eleak gl gsyni b24 fouti v2 koutputi v12outputi b34 fouti v3 koutputi v12outputi sdum4 v4 esyni gsyne c14 drive1 c24 drive2 v4 esyne c None
d h/dt = hpinf v1 khp v12hp h tauinf v1 khp tauhp v12hp None
d m2/dt = m2 kad2 fouti v2 koutputi v12outputi tad2 None
d m3/dt = m3 kad3 fouti v3 koutputi v12outputi tad3 None
d m4/dt = m4 kad4 fouti v4 koutputi v12outputi tad4 None
inh1 = b31 fouti v3 koutputi v12outputi b41 fouti v4 koutputi v12outputi None
inh2 = b32 fouti v3 koutputi v12outputi b42 fouti v4 koutputi v12outputi None
inh3 = b23 fouti v2 koutputi v12outputi b43 fouti v4 koutputi v12outputi None
inh4 = b24 fouti v2 koutputi v12outputi b34 fouti v3 koutputi v12outputi None
exc2 = a12 foute v1 koutpute v12outpute None
t = time None