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
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:
Redistributions of this SBML file must retain the above copyright notice, this list of conditions
and the following disclaimer.
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
L3V1
type
FunctionDefinitions [11]
name
math
sbo
cvterm
FunctionDefinition
max
minimum
x
y
x
x
y
y
FunctionDefinition
min
maximum
x
y
x
x
y
y
FunctionDefinition
heav
heavyside
x
0
x
0
0.5
x
0
1
x
0
0
FunctionDefinition
mod
modulo
x
y
x
y
x
y
x
0
y
0
x
y
x
y
FunctionDefinition
n_inf
c
d_5
c
c
d_5
FunctionDefinition
h_inf
c
q_2
q_2
q_2
c
FunctionDefinition
tau_h
c
a_2
q_2
1
a_2
q_2
c
FunctionDefinition
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
FunctionDefinition
j_leak
c
c_t
gamma
v_leak
v_leak
c_t
c
gamma
c
FunctionDefinition
j_serca
c
k_serca
v_serca
v_serca
c
1.75
c
1.75
k_serca
1.75
FunctionDefinition
j_soc
c
c_t
gamma
k_soc
v_soc
v_soc
k_soc
4
k_soc
4
c_t
c
gamma
4
type
Parameters [28]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
c
c = 0.0865415
F
0.0865415
None
Parameter
h
h = 0.6255124
F
0.6255124
None
Parameter
c_t
c_t = 36.49084
F
36.49084
None
Parameter
ip
ip = 0
F
0.0
None
Parameter
gamma
gamma = 5.4054
F
5.4054
None
Parameter
v_leak
v_leak = 0.002
F
0.002
None
Parameter
v_in
v_in = 0.05
F
0.05
None
Parameter
k_out
k_out = 1.2
F
1.2
None
Parameter
v_ip3r
v_ip3r = 0.222
F
0.222
None
Parameter
d_1
d_1 = .13
F
0.13
None
Parameter
d_2
d_2 = 1.049
F
1.049
None
Parameter
d_3
d_3 = .9434
F
0.9434
None
Parameter
d_5
d_5 = .08234
F
0.08234
None
Parameter
a_2
a_2 = 0.04
F
0.04
None
Parameter
v_pmca
v_pmca = 10
F
10.0
None
Parameter
k_pmca
k_pmca = 2.5
F
2.5
None
Parameter
v_soc
v_soc = 1.57
F
1.57
None
Parameter
k_soc
k_soc = 90
F
90.0
None
Parameter
v_serca
v_serca = 0.9
F
0.9
None
Parameter
k_serca
k_serca = 0.1
F
0.1
None
Parameter
delta
delta = 0.2
F
0.2
None
Parameter
ca_er
F
0.0
dimensionless
None
Parameter
m_inf
F
0.0
dimensionless
None
Parameter
q_2
F
0.0
dimensionless
None
Parameter
j_in
F
0.0
dimensionless
None
Parameter
j_out
F
0.0
dimensionless
None
Parameter
j_pmca
F
0.0
dimensionless
None
Parameter
t
model time
F
0.0
dimensionless
None
type
Rules [10]
assignment
name
derived units
sbo
cvterm
Rule
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
Rule
d c_t/dt
=
j_in
j_out
j_pmca
j_soc
c
c_t
gamma
k_soc
v_soc
delta
None
Rule
d h/dt
=
h_inf
c
q_2
h
tau_h
c
a_2
q_2
None
Rule
ca_er
=
c_t
c
gamma
None
Rule
m_inf
=
ip
ip
d_1
None
Rule
q_2
=
d_2
ip
d_1
ip
d_3
None
Rule
j_in
=
v_in
None
Rule
j_out
=
k_out
c
None
Rule
j_pmca
=
v_pmca
c
2
k_pmca
2
c
2
None
Rule
t
=
time
None