XPP model

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

# default: gnap=2,gcan=0.7,I=1 (SD-Burst)

# AUGUST 2010
# cell is combination of  Nap and CaN burster (Can closed-cell model with ER in dendrtes) 
# NaP burster is from from Butera, 1999; setting gcan=0 reproduce Butera 1999 model
# Frequency of Ca oscillations controlled by either Catot or I (larger values - faster bursting)

# units: V = mV; Cm = pF; g = uS

minf=1/(1+exp((v-vm) /sm)) 
ninf=1/(1+exp((v-vn) /sn))
minfp=1/(1+exp((v-vmp)/smp))
hinf=1/(1+exp((v-vh) /sh))

taun=taunb/cosh((v-vn)/(2*sn))
tauh=tauhb/cosh((v-vh)/(2*sh))

I_na=gna*minf^3*(1-n)*(v-vna)
I_k=gk*n^4*(v-Vk)
I_nap=gnap*minfp*h*(v-vna)
I_l =gl*(v-vleaks)

# Equations for CaN current
caninf =1/(1+(Kcan/C)^ncan)
I_can=gcan*caninf*(v-vna)

#Fluxes in and out of ER
# l is fraction of open IP3 channels
J_ER_in=(LL + P*( (I*C*l)/( (I+Ki)*(C+Ka) ) )^3 )*(Ce - C)
J_ER_out=Ve*C^2/(Ke^2+C^2)
Ce = (Ct - C)/sigma

# Equations
v'= (-I_k - I_na-I_nap-I_l-I_aps-I_can)/Cms
n'= (ninf-n)/taun
h'= (hinf-h)/tauh
C' = fi*( J_ER_in- J_ER_out)
l' = A*( Kd - (C + Kd)*l )

# Auxilary variables
aux Ce=Ce
aux ican=I_can
aux inaps=I_nap

#Initial conditions

v(0)=-50
n(0)=0.004
h(0)=0.33
C(0)=0.03
l(0)=0.93

# Voltage parameters
par Cms=21, I_aps=0
num vna=50,vk=-85, vleaks=-58 
num vm=-34,vn=-29, vmp=-40, vh=-48
num sm=-5, sn=-4,  smp=-6,  sh=5
num taunb=10,  tauhb=10000, 
par gk=11.2, gna=28, gnap=2,gl=2.3

# Ca parameters
par Kcan=0.74, ncan=0.97,gcan=0.7
par I=1
par Ct=1.25
par fi=0.000025
num LL=0.37
par P=31000
par Ki=1.0
par Ka=0.4
par Ve=400
par Ke=0.2
par A=0.005 
par Kd=0.4
par sigma=0.185


@ dt=0.1,total=10000,meth=qualrk,xp=t,yp=v
@ xlo=0,xhi=10000,ylo=-60,yhi=10.,bound=500001,maxstor=5000001

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 :

id
name
time
substance
extent
volume
area
length
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 [57] name constant value unit derived unit sbo cvterm
v v = -50 -50.0 None
n n = 0.004 0.004 None
h h = 0.33 0.33 None
c c = 0.03 0.03 None
l l = 0.93 0.93 None
cms cms = 21 21.0 None
i_aps i_aps = 0 0.0 None
vna vna = 50 50.0 None
vk vk = -85 -85.0 None
vleaks vleaks = -58 -58.0 None
vm vm = -34 -34.0 None
vn vn = -29 -29.0 None
vmp vmp = -40 -40.0 None
vh vh = -48 -48.0 None
sm sm = -5 -5.0 None
sn sn = -4 -4.0 None
smp smp = -6 -6.0 None
sh sh = 5 5.0 None
taunb taunb = 10 10.0 None
tauhb tauhb = 10000 10000.0 None
gk gk = 11.2 11.2 None
gna gna = 28 28.0 None
gnap gnap = 2 2.0 None
gl gl = 2.3 2.3 None
kcan kcan = 0.74 0.74 None
ncan ncan = 0.97 0.97 None
gcan gcan = 0.7 0.7 None
i i = 1 1.0 None
ct ct = 1.25 1.25 None
fi fi = 0.000025 2.5e-05 None
ll ll = 0.37 0.37 None
p p = 31000 31000.0 None
ki ki = 1.0 1.0 None
ka ka = 0.4 0.4 None
ve ve = 400 400.0 None
ke ke = 0.2 0.2 None
a a = 0.005 0.005 None
kd kd = 0.4 0.4 None
sigma sigma = 0.185 0.185 None
minf 0.0 dimensionless None
ninf 0.0 dimensionless None
minfp 0.0 dimensionless None
hinf 0.0 dimensionless None
taun 0.0 dimensionless None
tauh 0.0 dimensionless None
i_na 0.0 dimensionless None
i_k 0.0 dimensionless None
i_nap 0.0 dimensionless None
i_l 0.0 dimensionless None
caninf 0.0 dimensionless None
i_can 0.0 dimensionless None
j_er_in 0.0 dimensionless None
j_er_out 0.0 dimensionless None
ce 0.0 dimensionless None
ican 0.0 dimensionless None
inaps 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [23]   assignment name derived units sbo cvterm
d v/dt = i_k i_na i_nap i_l i_aps i_can cms None
d n/dt = ninf n taun None
d h/dt = hinf h tauh None
d c/dt = fi j_er_in j_er_out None
d l/dt = a kd c kd l None
minf = 1 1 v vm sm None
ninf = 1 1 v vn sn None
minfp = 1 1 v vmp smp None
hinf = 1 1 v vh sh None
taun = taunb v vn 2 sn None
tauh = tauhb v vh 2 sh None
i_na = gna minf 3 1 n v vna None
i_k = gk n 4 v vk None
i_nap = gnap minfp h v vna None
i_l = gl v vleaks None
caninf = 1 1 kcan c ncan None
i_can = gcan caninf v vna None
j_er_in = ll p i c l i ki c ka 3 ce c None
j_er_out = ve c 2 ke 2 c 2 None
ce = ct c sigma None
ican = i_can None
inaps = i_nap None
t = time None