Location: BG_RyR @ 1e765e41142f / parameter_finder / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-06-13 13:16:07+12:00
Desc:
Fixing stoich matrices to include Ca
Permanent Source URI:
https://models.physiomeproject.org/workspace/6e3/rawfile/1e765e41142f364dd32d4e54789f396b8d2c0362/parameter_finder/TEMP.cellml.txt
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def model individual_RyR 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_Ca_SR_init: fmol {init: 1e-888};
var q_Ca_di_init: fmol {init: 1e-888};
var q_C_RyR_init: fmol {init: 1e-888};
var q_CI_RyR_init: fmol {init: 1e-888};
var q_I_RyR_init: fmol {init: 1e-888};
var q_O_RyR_init: fmol {init: 1e-888};
// Global value
var q_Ca_SR: fmol {pub: out};
var q_Ca_di: fmol {pub: out};
var q_C_RyR: fmol {pub: out};
var q_CI_RyR: fmol {pub: out};
var q_I_RyR: fmol {pub: out};
var q_O_RyR: fmol {pub: out};
// From submodule
var q_Ca_SR_mRyR: fmol {pub: in};
var q_Ca_di_mRyR: fmol {pub: in};
var q_C_RyR_mRyR: fmol {pub: in};
var q_CI_RyR_mRyR: fmol {pub: in};
var q_I_RyR_mRyR: fmol {pub: in};
var q_O_RyR_mRyR: fmol {pub: in};
q_Ca_SR = q_Ca_SR_mRyR + q_Ca_SR_init;
q_Ca_di = q_Ca_di_mRyR + q_Ca_di_init;
q_C_RyR = q_C_RyR_mRyR + q_C_RyR_init;
q_CI_RyR = q_CI_RyR_mRyR + q_CI_RyR_init;
q_I_RyR = q_I_RyR_mRyR + q_I_RyR_init;
q_O_RyR = q_O_RyR_mRyR + q_O_RyR_init;
enddef;

def comp RyR_parameters as
var kappa_RyR: fmol_per_sec {init: 34574.2, pub: out};
var kappa_OC: fmol_per_sec {init: 8.83262, pub: out};
var kappa_CCI: fmol_per_sec {init: 0.12618, pub: out};
var kappa_CII: fmol_per_sec {init: 883.262, pub: out};
var kappa_IO: fmol_per_sec {init: 73.6052, pub: out};
var K_Ca_SR: per_fmol {init: 154.436, pub: out};
var K_Ca_di: per_fmol {init: 100.283, pub: out};
var K_C_RyR: per_fmol {init: 3962.58, pub: out};
var K_CI_RyR: per_fmol {init: 39.6258, pub: out};
var K_I_RyR: per_fmol {init: 0.06793, pub: out};
var K_O_RyR: per_fmol {init: 6.793, pub: out};
enddef;
def comp RyR as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_RyR: fmol_per_sec {pub: in};
var kappa_OC: fmol_per_sec {pub: in};
var kappa_CCI: fmol_per_sec {pub: in};
var kappa_CII: fmol_per_sec {pub: in};
var kappa_IO: fmol_per_sec {pub: in};
var K_Ca_SR: per_fmol {pub: in};
var K_Ca_di: per_fmol {pub: in};
var K_C_RyR: per_fmol {pub: in};
var K_CI_RyR: per_fmol {pub: in};
var K_I_RyR: per_fmol {pub: in};
var K_O_RyR: per_fmol {pub: in};
// Input from global environment
var q_Ca_SR_global: fmol {pub: in};
var q_Ca_di_global: fmol {pub: in};
var q_C_RyR_global: fmol {pub: in};
var q_CI_RyR_global: fmol {pub: in};
var q_I_RyR_global: fmol {pub: in};
var q_O_RyR_global: fmol {pub: in};
// Output to global environment
var q_Ca_SR: fmol {init: 1e-16, pub: out};
var q_Ca_di: fmol {init: 1e-16, pub: out};
var q_C_RyR: fmol {init: 1e-16, pub: out};
var q_CI_RyR: fmol {init: 1e-16, pub: out};
var q_I_RyR: fmol {init: 1e-16, pub: out};
var q_O_RyR: fmol {init: 1e-16, pub: out};
// Constitutive parameters
var mu_Ca_SR: J_per_mol;
var mu_Ca_di: J_per_mol;
var mu_C_RyR: J_per_mol;
var mu_CI_RyR: J_per_mol;
var mu_I_RyR: J_per_mol;
var mu_O_RyR: J_per_mol;
var v_RyR: fmol_per_sec;
var v_OC: fmol_per_sec;
var v_CCI: fmol_per_sec;
var v_CII: fmol_per_sec;
var v_IO: fmol_per_sec;
mu_Ca_SR = R*T*ln(K_Ca_SR*q_Ca_SR_global);
mu_Ca_di = R*T*ln(K_Ca_di*q_Ca_di_global);
mu_C_RyR = R*T*ln(K_C_RyR*q_C_RyR_global);
mu_CI_RyR = R*T*ln(K_CI_RyR*q_CI_RyR_global);
mu_I_RyR = R*T*ln(K_I_RyR*q_I_RyR_global);
mu_O_RyR = R*T*ln(K_O_RyR*q_O_RyR_global);
v_RyR = ppp;
v_OC = ppp;
v_CCI = ppp;
v_CII = ppp;
v_IO = ppp;
ode(q_Ca_SR, time) = qqq;
ode(q_Ca_di, time) = qqq;
ode(q_C_RyR, time) = qqq;
ode(q_CI_RyR, time) = qqq;
ode(q_I_RyR, time) = qqq;
ode(q_O_RyR, time) = qqq;
enddef;
def map between environment and RyR for
vars time and time;
vars q_Ca_SR_mRyR and q_Ca_SR;
vars q_Ca_SR and q_Ca_SR_global;
vars q_Ca_di_mRyR and q_Ca_di;
vars q_Ca_di and q_Ca_di_global;
vars q_C_RyR_mRyR and q_C_RyR;
vars q_C_RyR and q_C_RyR_global;
vars q_CI_RyR_mRyR and q_CI_RyR;
vars q_CI_RyR and q_CI_RyR_global;
vars q_I_RyR_mRyR and q_I_RyR;
vars q_I_RyR and q_I_RyR_global;
vars q_O_RyR_mRyR and q_O_RyR;
vars q_O_RyR and q_O_RyR_global;
enddef;
def map between RyR and RyR_parameters for
vars kappa_RyR and kappa_RyR;
vars kappa_OC and kappa_OC;
vars kappa_CCI and kappa_CCI;
vars kappa_CII and kappa_CII;
vars kappa_IO and kappa_IO;
vars K_Ca_SR and K_Ca_SR;
vars K_Ca_di and K_Ca_di;
vars K_C_RyR and K_C_RyR;
vars K_CI_RyR and K_CI_RyR;
vars K_I_RyR and K_I_RyR;
vars K_O_RyR and K_O_RyR;
enddef;
def map between constants and RyR for
vars R and R;
 vars T and T;
enddef;
enddef;