XPP model

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

# XPP code to recreate bifurcation diagrams
# Copyright: Marsa Taheri and Gregory Handy, 2016

# ODEs
c' = (j_ip3r(c)-j_serca(c)+j_leak(c)+(j_in-j_out-j_pmca+j_soc(c,c_t))*delta)
c_t' = ((j_in-j_out-j_pmca+j_soc(c,c_t))*delta)
h'=((h_inf(c)-h)/tau_h(c))

aux ca_er=(c_t-c)*gamma

# Terms on ER
m_inf = ip/(ip+d_1)
n_inf(c) = c/(c+d_5)
h_inf(c) = q_2/(q_2+c)

q_2 = d_2 *(ip+d_1)/(ip+d_3)
tau_h(c) = 1/(a_2*(q_2+c))

j_ip3r(c) = v_ip3r*m_inf^3*n_inf(c)^3*h^3*((c_t-c)*gamma-c)

j_leak(c) = v_leak*((c_t-c)*gamma-c)

j_serca(c) = v_serca*c^1.75/(c^1.75+k_serca^1.75)

# Terms on plasma membrane
j_in = v_in
j_out = k_out*c

j_pmca=v_pmca*c^2/(k_pmca^2 + c^2)

j_soc(c,c_t) = v_soc*k_soc^4/(k_soc^4+((c_t-c)*gamma)^4)

# Initial Conditions
init c=0.0865415,h=0.6255124
init c_t=36.49084

param ip=0

param gamma=5.4054

# Leak for ER
param v_leak=0.002

# Leak across plasma membrane
param v_in=0.05, k_out=1.2

# IP3R Parameters
param v_ip3r=0.222
param d_1=.13,d_2=1.049,d_3=.9434,d_5=.08234
param a_2=0.04

# PMCA Terms
param v_pmca=10,k_pmca=2.5

# SOC Terms
param v_soc=1.57,k_soc=90

# SERCA Terms
param v_serca=0.9, k_serca=0.1

# Sneyd Parameter
param delta=0.2

@ ylo=0,ds=0.005,dsmin=0.001,dsmax=0.01,nmax=700,npr=700
@ autoymin=0,autoymax=.708,parmax=100,autoxmin=0,autoxmax=.5
@ total=1000,xhi=100,ylo=0,yhi=1.5,nmesh=100

@ bounds=1000

done
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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:

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  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 [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
n_inf c d_5 c c d_5
h_inf c q_2 q_2 q_2 c
tau_h c a_2 q_2 1 a_2 q_2 c
j_ip3r c c_t d_5 gamma h m_inf v_ip3r v_ip3r m_inf 3 n_inf c d_5 3 h 3 c_t c gamma c
j_leak c c_t gamma v_leak v_leak c_t c gamma c
j_serca c k_serca v_serca v_serca c 1.75 c 1.75 k_serca 1.75
j_soc c c_t gamma k_soc v_soc v_soc k_soc 4 k_soc 4 c_t c gamma 4

Parameters [28] name constant value unit derived unit sbo cvterm
c c = 0.0865415 0.0865415 None
h h = 0.6255124 0.6255124 None
c_t c_t = 36.49084 36.49084 None
ip ip = 0 0.0 None
gamma gamma = 5.4054 5.4054 None
v_leak v_leak = 0.002 0.002 None
v_in v_in = 0.05 0.05 None
k_out k_out = 1.2 1.2 None
v_ip3r v_ip3r = 0.222 0.222 None
d_1 d_1 = .13 0.13 None
d_2 d_2 = 1.049 1.049 None
d_3 d_3 = .9434 0.9434 None
d_5 d_5 = .08234 0.08234 None
a_2 a_2 = 0.04 0.04 None
v_pmca v_pmca = 10 10.0 None
k_pmca k_pmca = 2.5 2.5 None
v_soc v_soc = 1.57 1.57 None
k_soc k_soc = 90 90.0 None
v_serca v_serca = 0.9 0.9 None
k_serca k_serca = 0.1 0.1 None
delta delta = 0.2 0.2 None
ca_er 0.0 dimensionless None
m_inf 0.0 dimensionless None
q_2 0.0 dimensionless None
j_in 0.0 dimensionless None
j_out 0.0 dimensionless None
j_pmca 0.0 dimensionless None
t model time 0.0 dimensionless None

Rules [10]   assignment name derived units sbo cvterm
d c/dt = j_ip3r c c_t d_5 gamma h m_inf v_ip3r j_serca c k_serca v_serca j_leak c c_t gamma v_leak j_in j_out j_pmca j_soc c c_t gamma k_soc v_soc delta None
d c_t/dt = j_in j_out j_pmca j_soc c c_t gamma k_soc v_soc delta None
d h/dt = h_inf c q_2 h tau_h c a_2 q_2 None
ca_er = c_t c gamma None
m_inf = ip ip d_1 None
q_2 = d_2 ip d_1 ip d_3 None
j_in = v_in None
j_out = k_out c None
j_pmca = v_pmca c 2 k_pmca 2 c 2 None
t = time None