XPP model

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

# 2 Compartment Spinal Cord Injury Motoneuron Model
# Basic SCI motoneuron model without synaptic inputs
# Applied current can be a ramp, pulse or a single value
# Change parameter values to get different motoneuron behavior

#-------------------------------------------------------------
#   Current Balance
#-------------------------------------------------------------
dvs/dt=(-INa-IKdr-IsCaN-IsKCa-Isleak+Is+gc*(vd-vs)/p)/c
dvd/dt=(-ICaP-INap-IdKCa-Idleak+Id+gc*(vs-vd)/(1-p))/c

#-------------------------------------------------------------
#   Currents: Soma
#-------------------------------------------------------------
INa=gna*mna^3*hna*(vs-ena)
IKdr=gkdr*n^4*(vs-ek)
IsCaN=gscan*mscan^2*hscan*(vs-eca)
IsKCa=gskca*(cas/(cas+0.2))*(vs-ek)
Isleak=gl*(vs-el)

Is=Iramp+Ipulse+Iappls
Id=Iappld

#-------------------------------------------------------------
#   Currents: Dendrites
#-------------------------------------------------------------
IdKCa=gdkca*(cad/(cad+0.2))*(vd-ek)
ICaP=gcap*mcap*(vd-eca)
Idleak=gl*(vd-el)
INap=gnap*mnap*(vd-ena)

#-------------------------------------------------------------
#   Variables: Soma
#-------------------------------------------------------------
mna=1/(1+exp((vs-thetamna)/kmna))
dhna/dt=(hnainf-hna)/tauhna
hnainf=1/(1+exp((vs-thetahna)/khna))
tauhna=120/(exp((vs+50)/15)+exp(-(vs+50)/16))

dn/dt=(ninf-n)/taun
ninf=1/(1+exp((vs-thetan)/kn))
taun=28/(exp((vs+40)/40)+exp(-(vs+40)/50))

dmscan/dt=(mscaninf-mscan)/taumscan
mscaninf=1/(1+exp((vs-thetamsca)/kmscan))
dhscan/dt=(hscaninf-hscan)/tauhscan
hscaninf=1/(1+exp((vs-thetahsca)/khscan))

dcas/dt=f*(-alpha1*IsCaN-kca*cas)

#-------------------------------------------------------------
#   Variables:  Dendrites
#-------------------------------------------------------------
dmcap/dt=(mcapinf-mcap)/taumcap
mcapinf=1/(1+exp((vd-thetamcap)/kmcap))

dmnap/dt=(mnapinf-mnap)/taumnap
mnapinf=1/(1+exp((vd-thetamnap)/kmnap))

dcad/dt=f*(-alpha2*ICaP-kca*cad)

#-------------------------------------------------------------
# Applied Current
#-------------------------------------------------------------
# Applied
par Iappls=0
par Iappld=0

# Ramp
Iramp=offsetr+scaler*(t-tonr)*(heav(t-tonr)*heav(toffr-t))\
+2*scaler*(tswitchr-t)*(heav(t-tswitchr)*heav(toffr-t))
par offsetr=0
#par scaler=0
par scaler=0.01
par tonr=0
par toffr=10000
par tswitchr=2500

# Pulse
Ipulse=offsetp+scalep1*(heav(t-tonp1)*heav(toffp1-t))\
+scalep2*(heav(t-tonp2)*heav(toffp2-t))
par offsetp=0
par scalep1=0
#par scalep1=20 for pulse figures
par tonp1=2000
par toffp1=4000
par scalep2=0
par tonp2=4000
par toffp2=10000

#-------------------------------------------------------------
#  Parameters
#-------------------------------------------------------------
par gc=0.1
par p=0.1
par c=1

par gna=120
par ena=55
par thetamna=-35
par kmna=-7.8
par thetahna=-55
par khna=7

par gkdr=100
par ek=-80
par thetan=-28
par kn=-15

par gscan=14
par eca=80
par thetamsca=-30
par kmscan=-5
par taumscan=16
par thetahsca=-45
par khscan=5
par tauhscan=160

par gskca=3.136
par gdkca=0.69

par gl=0.51
par el=-60

par f=0.01
par alpha1=0.009
par alpha2=0.009
par kca=2

par gcap=.33
par thetamcap=-40
par kmcap=-7
par taumcap=40

par gnap=.2
par thetamnap=-25
par kmnap=-4
par taumnap=40

# ------------------------------------------------------------
#   Auxiliary Variables
# ------------------------------------------------------------
aux Na=INa
aux Kdr=IKdr
aux Ca1=IsCaN
aux CaCs=cas
aux CaCd=cad
aux sKCa=IsKCa
aux dKCa=IdKCa
aux sLeak=Isleak
aux dLeak=Idleak
aux CaP=ICaP
#aux Cap=ICap
aux Nap=INap
aux I1=Is
aux I2=Id

# --------------------------------------------------------
#   Initial Conditions
# --------------------------------------------------------

init vs=-53.97266
init vd=-52.66585
init hna=0.463375
init n=0.1503945
init mscan=0.008206959
init hscan=0.857482
init cas=0.0004874682
init mcap=0.1407098
init mnap=0.0009903489
init cad=0.02772107


# ------------------------------------------------------------
#   Settings
# ------------------------------------------------------------	
@ bounds=1000000
@ TOTAL=10000
@ DT=.05
@ xlo=0
@ xhi=10000
@ ylo=-100
@ yhi=80
@ nplot=2
@ yp2=I1
@ METH=qualrk
@ maxstor=1000000

d
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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 [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 [97] name constant value unit derived unit sbo cvterm
iappls iappls = 0 0.0 None
iappld iappld = 0 0.0 None
offsetr offsetr = 0 0.0 None
scaler scaler = 0.01 0.01 None
tonr tonr = 0 0.0 None
toffr toffr = 10000 10000.0 None
tswitchr tswitchr = 2500 2500.0 None
offsetp offsetp = 0 0.0 None
scalep1 scalep1 = 0 0.0 None
tonp1 tonp1 = 2000 2000.0 None
toffp1 toffp1 = 4000 4000.0 None
scalep2 scalep2 = 0 0.0 None
tonp2 tonp2 = 4000 4000.0 None
toffp2 toffp2 = 10000 10000.0 None
gc gc = 0.1 0.1 None
p p = 0.1 0.1 None
c c = 1 1.0 None
gna gna = 120 120.0 None
ena ena = 55 55.0 None
thetamna thetamna = -35 -35.0 None
kmna kmna = -7.8 -7.8 None
thetahna thetahna = -55 -55.0 None
khna khna = 7 7.0 None
gkdr gkdr = 100 100.0 None
ek ek = -80 -80.0 None
thetan thetan = -28 -28.0 None
kn kn = -15 -15.0 None
gscan gscan = 14 14.0 None
eca eca = 80 80.0 None
thetamsca thetamsca = -30 -30.0 None
kmscan kmscan = -5 -5.0 None
taumscan taumscan = 16 16.0 None
thetahsca thetahsca = -45 -45.0 None
khscan khscan = 5 5.0 None
tauhscan tauhscan = 160 160.0 None
gskca gskca = 3.136 3.136 None
gdkca gdkca = 0.69 0.69 None
gl gl = 0.51 0.51 None
el el = -60 -60.0 None
f f = 0.01 0.01 None
alpha1 alpha1 = 0.009 0.009 None
alpha2 alpha2 = 0.009 0.009 None
kca kca = 2 2.0 None
gcap gcap = .33 0.33 None
thetamcap thetamcap = -40 -40.0 None
kmcap kmcap = -7 -7.0 None
taumcap taumcap = 40 40.0 None
gnap gnap = .2 0.2 None
thetamnap thetamnap = -25 -25.0 None
kmnap kmnap = -4 -4.0 None
taumnap taumnap = 40 40.0 None
vs vs = -53.97266 -53.97266 None
vd vd = -52.66585 -52.66585 None
hna hna = 0.463375 0.463375 None
n n = 0.1503945 0.1503945 None
mscan mscan = 0.008206959 0.008206959 None
hscan hscan = 0.857482 0.857482 None
cas cas = 0.0004874682 0.0004874682 None
mcap mcap = 0.1407098 0.1407098 None
mnap mnap = 0.0009903489 0.0009903489 None
cad cad = 0.02772107 0.02772107 None
ina 0.0 dimensionless None
ikdr 0.0 dimensionless None
iscan 0.0 dimensionless None
iskca 0.0 dimensionless None
isleak 0.0 dimensionless None
is 0.0 dimensionless None
id 0.0 dimensionless None
idkca 0.0 dimensionless None
icap 0.0 dimensionless None
idleak 0.0 dimensionless None
inap 0.0 dimensionless None
mna 0.0 dimensionless None
hnainf 0.0 dimensionless None
tauhna 0.0 dimensionless None
ninf 0.0 dimensionless None
taun 0.0 dimensionless None
mscaninf 0.0 dimensionless None
hscaninf 0.0 dimensionless None
mcapinf 0.0 dimensionless None
mnapinf 0.0 dimensionless None
iramp 0.0 dimensionless None
ipulse 0.0 dimensionless None
na 0.0 dimensionless None
kdr 0.0 dimensionless None
ca1 0.0 dimensionless None
cacs 0.0 dimensionless None
cacd 0.0 dimensionless None
skca 0.0 dimensionless None
dkca 0.0 dimensionless None
sleak 0.0 dimensionless None
dleak 0.0 dimensionless None
cap 0.0 dimensionless None
nap 0.0 dimensionless None
i1 0.0 dimensionless None
i2 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [46]   assignment name derived units sbo cvterm
d vs/dt = ina ikdr iscan iskca isleak is gc vd vs p c None
d vd/dt = icap inap idkca idleak id gc vs vd 1 p c None
d hna/dt = hnainf hna tauhna None
d n/dt = ninf n taun None
d mscan/dt = mscaninf mscan taumscan None
d hscan/dt = hscaninf hscan tauhscan None
d cas/dt = f alpha1 iscan kca cas None
d mcap/dt = mcapinf mcap taumcap None
d mnap/dt = mnapinf mnap taumnap None
d cad/dt = f alpha2 icap kca cad None
ina = gna mna 3 hna vs ena None
ikdr = gkdr n 4 vs ek None
iscan = gscan mscan 2 hscan vs eca None
iskca = gskca cas cas 0.2 vs ek None
isleak = gl vs el None
is = iramp ipulse iappls None
id = iappld None
idkca = gdkca cad cad 0.2 vd ek None
icap = gcap mcap vd eca None
idleak = gl vd el None
inap = gnap mnap vd ena None
mna = 1 1 vs thetamna kmna None
hnainf = 1 1 vs thetahna khna None
tauhna = 120 vs 50 15 vs 50 16 None
ninf = 1 1 vs thetan kn None
taun = 28 vs 40 40 vs 40 50 None
mscaninf = 1 1 vs thetamsca kmscan None
hscaninf = 1 1 vs thetahsca khscan None
mcapinf = 1 1 vd thetamcap kmcap None
mnapinf = 1 1 vd thetamnap kmnap None
iramp = offsetr scaler t tonr heav t tonr heav toffr t 2 scaler tswitchr t heav t tswitchr heav toffr t None
ipulse = offsetp scalep1 heav t tonp1 heav toffp1 t scalep2 heav t tonp2 heav toffp2 t None
na = ina None
kdr = ikdr None
ca1 = iscan None
cacs = cas None
cacd = cad None
skca = iskca None
dkca = idkca None
sleak = isleak None
dleak = idleak None
cap = icap None
nap = inap None
i1 = is None
i2 = id None
t = time None