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
# 3-D model with slow Na channel inactivation (see Fig 4); noise is also included here

# DIFFERENTIAL EQUATIONS

dv/dt = (Istim+sqrt(Qi)*ni-gna*minf(V)*h*(V-Vna)-gk*w*(V-VK)-gl*(V-Vl))/cap
dw/dt = phi_w*(winf(V)-w)/tauw(V)
dh/dt = (hinf(V)-h)/tauh

# TO IMPLEMENT NOISE
wiener ni
param Qi=1
# noise amplitude is adjusted by varying Qi. Remove noise by setting to 0

# FUNCTIONS AND PARAMETERS

minf(v)=.5*(1+tanh((v-beta_m)/gamma_m))
winf(v)=.5*(1+tanh((v-beta_w)/gamma_w))
hinf(v)= 1/(1+exp(-(v-beta_h)/gamma_h))

tauw(v)=1/cosh((v-beta_w)/(2*gamma_w))


param Istim=0 
param vna=50,vk=-100,vl=-70
param gk=20,gl=2,gna=20
param beta_m=-1.2,gamma_m=15
param beta_w=-13,gamma_w=10
# beta_w = -21 for transient spiking; beta_w = -13 for repetitive spiking
param phi_w=.15
param beta_h=-30,gamma_h=-5,tauh=2000
param cap=2

# INITIAL CONDITIONS
V(0)=-70
w(0)=0.000025
h(0)=1

# 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
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
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
hinf v beta_h gamma_h 1 1 v beta_h gamma_h
tauw v beta_w gamma_w 1 v beta_w 2 gamma_w

Parameters [22] name constant value unit derived unit sbo cvterm
ni 0.0 None
qi qi = 1 1.0 None
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 = 15 15.0 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
beta_h beta_h = -30 -30.0 None
gamma_h gamma_h = -5 -5.0 None
tauh tauh = 2000 2000.0 None
cap cap = 2 2.0 None
v v = -70 -70.0 None
w w = 0.000025 2.5e-05 None
h h = 1 1.0 None
t model time 0.0 dimensionless None

Rules [4]   assignment name derived units sbo cvterm
d v/dt = istim 2 qi ni gna minf v beta_m gamma_m h v vna gk w v vk gl v vl cap None
d w/dt = phi_w winf v beta_w gamma_w w tauw v beta_w gamma_w None
d h/dt = hinf v beta_h gamma_h h tauh None
t = time None