- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-04-13 11:20:35+12:00
- Desc:
- With adjusted A_geo in matlab code, and new parameters fitting Kernik cell
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/823/rawfile/ca80ea3bb1f5e21fbf2b123193f5917598ce817c/parameter_finder/output/TEMP.cellml.txt
def model individual_K as
def import using "units_and_constants/units_BG.cellml" for
unit mM using unit mM;
unit fmol using unit fmol;
unit per_fmol using unit per_fmol;
unit J_per_mol using unit J_per_mol;
unit fmol_per_sec using unit fmol_per_sec;
unit C_per_mol using unit C_per_mol;
unit J_per_C using unit J_per_C;
unit microm3 using unit microm3;
unit fF using unit fF;
unit fC using unit fC;
unit fA using unit fA;
unit per_second using unit per_second;
unit millivolt using unit millivolt;
unit per_sec using unit per_sec;
unit J_per_K_per_mol using unit J_per_K_per_mol;
unit fmol_per_L using unit fmol_per_L;
unit fmol_per_L_per_sec using unit fmol_per_L_per_sec;
unit per_sec_per_fmol_per_L using unit per_sec_per_fmol_per_L;
unit uM using unit uM;
unit mM_per_sec using unit mM_per_sec;
unit uM_per_sec using unit uM_per_sec;
unit pL using unit pL;
unit m_to_u using unit m_to_u;
enddef;
def import using "units_and_constants/constants_BG.cellml" for
comp constants using comp constants;
enddef;
def comp environment as
var time: second {pub: out};
// initial values
var q_K_i: fmol {init: 1e-888, pub: out};
var q_K_o: fmol {init: 1e-888, pub: out};
var q_S00_K: fmol {init: 1e-888, pub: out};
var q_S10_K: fmol {init: 1e-888, pub: out};
var q_S20_K: fmol {init: 1e-888, pub: out};
var q_S01_K: fmol {init: 1e-888, pub: out};
var q_S11_K: fmol {init: 1e-888, pub: out};
var q_S21_K: fmol {init: 1e-888, pub: out};
// From submodule
var v_K: fmol_per_sec {pub: in};
var v_X00_K: fmol_per_sec {pub: in};
var v_X10_K: fmol_per_sec {pub: in};
var v_X01_K: fmol_per_sec {pub: in};
var v_X11_K: fmol_per_sec {pub: in};
var v_i00_K: fmol_per_sec {pub: in};
var v_i10_K: fmol_per_sec {pub: in};
var v_i20_K: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_S00_K, time) = vvv;
ode(q_S10_K, time) = vvv;
ode(q_S20_K, time) = vvv;
ode(q_S01_K, time) = vvv;
ode(q_S11_K, time) = vvv;
ode(q_S21_K, time) = vvv;
enddef;
def comp K_parameters as
var kappa_K: fmol_per_sec {init: 60.7677, pub: out};
var kappa_X00_K: fmol_per_sec {init: 0.0575544, pub: out};
var kappa_X10_K: fmol_per_sec {init: 0.223387, pub: out};
var kappa_X01_K: fmol_per_sec {init: 0.332081, pub: out};
var kappa_X11_K: fmol_per_sec {init: 1.28891, pub: out};
var kappa_i00_K: fmol_per_sec {init: 12.8417, pub: out};
var kappa_i10_K: fmol_per_sec {init: 99.6854, pub: out};
var kappa_i20_K: fmol_per_sec {init: 193.456, pub: out};
var K_K_i: per_fmol {init: 5.86652, pub: out};
var K_K_o: per_fmol {init: 43.0211, pub: out};
var K_S00_K: per_fmol {init: 77.5516, pub: out};
var K_S10_K: per_fmol {init: 9.99036, pub: out};
var K_S20_K: per_fmol {init: 5.14792, pub: out};
var K_S01_K: per_fmol {init: 13.4408, pub: out};
var K_S11_K: per_fmol {init: 1.73147, pub: out};
var K_S21_K: per_fmol {init: 0.892208, pub: out};
enddef;
def comp K as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_K: fmol_per_sec {pub: in};
var kappa_X00_K: fmol_per_sec {pub: in};
var kappa_X10_K: fmol_per_sec {pub: in};
var kappa_X01_K: fmol_per_sec {pub: in};
var kappa_X11_K: fmol_per_sec {pub: in};
var kappa_i00_K: fmol_per_sec {pub: in};
var kappa_i10_K: fmol_per_sec {pub: in};
var kappa_i20_K: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_S00_K: per_fmol {pub: in};
var K_S10_K: per_fmol {pub: in};
var K_S20_K: per_fmol {pub: in};
var K_S01_K: per_fmol {pub: in};
var K_S11_K: per_fmol {pub: in};
var K_S21_K: per_fmol {pub: in};
// Input from global environment
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_S00_K: fmol {pub: in};
var q_S10_K: fmol {pub: in};
var q_S20_K: fmol {pub: in};
var q_S01_K: fmol {pub: in};
var q_S11_K: fmol {pub: in};
var q_S21_K: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_S00_K: J_per_mol;
var mu_S10_K: J_per_mol;
var mu_S20_K: J_per_mol;
var mu_S01_K: J_per_mol;
var mu_S11_K: J_per_mol;
var mu_S21_K: J_per_mol;
var v_K: fmol_per_sec {pub: out};
var v_X00_K: fmol_per_sec {pub: out};
var v_X10_K: fmol_per_sec {pub: out};
var v_X01_K: fmol_per_sec {pub: out};
var v_X11_K: fmol_per_sec {pub: out};
var v_i00_K: fmol_per_sec {pub: out};
var v_i10_K: fmol_per_sec {pub: out};
var v_i20_K: fmol_per_sec {pub: out};
mu_K_i = R*T*ln(K_K_i*q_K_i);
mu_K_o = R*T*ln(K_K_o*q_K_o);
mu_S00_K = R*T*ln(K_S00_K*q_S00_K);
mu_S10_K = R*T*ln(K_S10_K*q_S10_K);
mu_S20_K = R*T*ln(K_S20_K*q_S20_K);
mu_S01_K = R*T*ln(K_S01_K*q_S01_K);
mu_S11_K = R*T*ln(K_S11_K*q_S11_K);
mu_S21_K = R*T*ln(K_S21_K*q_S21_K);
v_K = ppp;
v_X00_K = ppp;
v_X10_K = ppp;
v_X01_K = ppp;
v_X11_K = ppp;
v_i00_K = ppp;
v_i10_K = ppp;
v_i20_K = ppp;
enddef;
def map between environment and K for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_S00_K and q_S00_K;
vars q_S10_K and q_S10_K;
vars q_S20_K and q_S20_K;
vars q_S01_K and q_S01_K;
vars q_S11_K and q_S11_K;
vars q_S21_K and q_S21_K;
vars v_K and v_K;
vars v_X00_K and v_X00_K;
vars v_X10_K and v_X10_K;
vars v_X01_K and v_X01_K;
vars v_X11_K and v_X11_K;
vars v_i00_K and v_i00_K;
vars v_i10_K and v_i10_K;
vars v_i20_K and v_i20_K;
enddef;
def map between K and K_parameters for
vars kappa_K and kappa_K;
vars kappa_X00_K and kappa_X00_K;
vars kappa_X10_K and kappa_X10_K;
vars kappa_X01_K and kappa_X01_K;
vars kappa_X11_K and kappa_X11_K;
vars kappa_i00_K and kappa_i00_K;
vars kappa_i10_K and kappa_i10_K;
vars kappa_i20_K and kappa_i20_K;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_S00_K and K_S00_K;
vars K_S10_K and K_S10_K;
vars K_S20_K and K_S20_K;
vars K_S01_K and K_S01_K;
vars K_S11_K and K_S11_K;
vars K_S21_K and K_S21_K;
enddef;
def map between constants and K for
vars R and R;
vars T and T;
enddef;
enddef;
