XPP model

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

# from Rho and Prescott, PLoS Comput Biol 2012
# to be run in XPP
# code for 3-D "ungrouped" model; see Fig 7 from paper


# DIFFERENTIAL EQUATIONS

dv/dt = (Istim-gna*minf(V)*(V-Vna)-gk*w*(V-VK)-gl*(V-Vl)-gsubNa*yNa*(V-Vna)-gsubK*yK*(V-Vk))/cap
dw/dt = phi_w*(winf(V)-w)/tauw(V)
dyNa/dt = phi_yna*(yna_inf(V)-yNa)/tauyna(V)
dyK/dt = phi_yk*(yk_inf(V)-yK)/tauyk(V)

# FUNCTIONS AND PARAMETERS

minf(v)=.5*(1+tanh((v-beta_m)/gamma_m))
winf(v)=.5*(1+tanh((v-beta_w)/gamma_w))
yna_inf(v)=.5*(1+tanh((v-beta_y)/gamma_y))
yk_inf(v)=.5*(1+tanh((v-beta_y)/gamma_y))

tauw(v)=1/cosh((v-beta_w)/(2*gamma_w))
tauyna(v)=1/cosh((v-beta_y)/(2*gamma_y))
tauyk(v)=1/cosh((v-beta_y)/(2*gamma_y))

param Istim=0 
param vna=50,vk=-100,vl=-70
param gk=20,gl=2,gna=20
param beta_m=-1.2,gamma_m=18
param beta_w=-13,gamma_w=10
# for some simulations, beta_w was -21
param phi_w=.15

# This code is designed to implement either a subthreshold Na or K current by setting the corresponding gsub to >0
# Leave the other gsub at 0 
param gsubNa=0,gsubK=0
param beta_y=-23,gamma_y=9,
param phi_yna=0.3,phi_yk=0.15
param cap=2

# INITIAL CONDITIONS
yNa(0)=0
yK(0)=0
V(0)=-70
w(0)=0.000025

# ALWAYS USE EULER! - Actually this is only true for noise
@ total=10000,dt=.05,xlo=-100,xhi=60,ylo=-.125,yhi=.6,xp=v,yp=w
@ meth=euler
@ MAXSTOR=1000000,bounds=10000

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 [11] 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
minf v beta_m gamma_m 0.5 1 v beta_m gamma_m
winf v beta_w gamma_w 0.5 1 v beta_w gamma_w
yna_inf v beta_y gamma_y 0.5 1 v beta_y gamma_y
yk_inf v beta_y gamma_y 0.5 1 v beta_y gamma_y
tauw v beta_w gamma_w 1 v beta_w 2 gamma_w
tauyna v beta_y gamma_y 1 v beta_y 2 gamma_y
tauyk v beta_y gamma_y 1 v beta_y 2 gamma_y

Parameters [24] name constant value unit derived unit sbo cvterm
istim istim = 0 0.0 None
vna vna = 50 50.0 None
vk vk = -100 -100.0 None
vl vl = -70 -70.0 None
gk gk = 20 20.0 None
gl gl = 2 2.0 None
gna gna = 20 20.0 None
beta_m beta_m = -1.2 -1.2 None
gamma_m gamma_m = 18 18.0 None
beta_w beta_w = -13 -13.0 None
gamma_w gamma_w = 10 10.0 None
phi_w phi_w = .15 0.15 None
gsubna gsubna = 0 0.0 None
gsubk gsubk = 0 0.0 None
beta_y beta_y = -23 -23.0 None
gamma_y gamma_y = 9 9.0 None
phi_yna phi_yna = 0.3 0.3 None
phi_yk phi_yk = 0.15 0.15 None
cap cap = 2 2.0 None
yna yna = 0 0.0 None
yk yk = 0 0.0 None
v v = -70 -70.0 None
w w = 0.000025 2.5e-05 None
t model time 0.0 dimensionless None

Rules [5]   assignment name derived units sbo cvterm
d v/dt = istim gna minf v beta_m gamma_m v vna gk w v vk gl v vl gsubna yna v vna gsubk yk v vk cap None
d w/dt = phi_w winf v beta_w gamma_w w tauw v beta_w gamma_w None
d yna/dt = phi_yna yna_inf v beta_y gamma_y yna tauyna v beta_y gamma_y None
d yk/dt = phi_yk yk_inf v beta_y gamma_y yk tauyk v beta_y gamma_y None
t = time None