Location: BG_IPR @ e96fcf69494a / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-06-30 14:25:17+12:00
Desc:
Renaming Siekmann files to nondefault; using DeYoung instead
Permanent Source URI:
https://staging.physiomeproject.org/workspace/8ab/rawfile/e96fcf69494a24946ba1e4aad50ee4991d8e92e9/parameter_finder/output/TEMP.cellml.txt
Compare... Download Source 

def model individual_IPR 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_i: fmol {init: 1e-888, pub: out};
var q_Ca_SR: fmol {init: 1e-888, pub: out};
var q_IP3: fmol {init: 1e-888, pub: out};
var q_C1: fmol {init: 1e-888, pub: out};
var q_C2: fmol {init: 1e-888, pub: out};
var q_C3: fmol {init: 1e-888, pub: out};
var q_C4: fmol {init: 1e-888, pub: out};
var q_O5: fmol {init: 1e-888, pub: out};
var q_O6: fmol {init: 1e-888, pub: out};
// From submodule
var v_R_IPR: fmol_per_sec {pub: in};
var v_R12: fmol_per_sec {pub: in};
var v_R23: fmol_per_sec {pub: in};
var v_R24: fmol_per_sec {pub: in};
var v_R26: fmol_per_sec {pub: in};
var v_R45: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_Ca_SR, time) = vvv;
ode(q_IP3, time) = vvv;
ode(q_C1, time) = vvv;
ode(q_C2, time) = vvv;
ode(q_C3, time) = vvv;
ode(q_C4, time) = vvv;
ode(q_O5, time) = vvv;
ode(q_O6, time) = vvv;
enddef;

def comp IPR_parameters as
var kappa_R_IPR: fmol_per_sec {init: 0.135721, pub: out};
var kappa_R12: fmol_per_sec {init: 0.627589, pub: out};
var kappa_R23: fmol_per_sec {init: 0.0213951, pub: out};
var kappa_R24: fmol_per_sec {init: 1.06975, pub: out};
var kappa_R26: fmol_per_sec {init: 74.8828, pub: out};
var kappa_R45: fmol_per_sec {init: 117673, pub: out};
var K_Ca_i: per_fmol {init: 0.0993, pub: out};
var K_Ca_SR: per_fmol {init: 0.0993, pub: out};
var K_IP3: per_fmol {init: 0.269542, pub: out};
var K_C1: per_fmol {init: 1975.81, pub: out};
var K_C2: per_fmol {init: 140.219, pub: out};
var K_C3: per_fmol {init: 3225.04, pub: out};
var K_C4: per_fmol {init: 9.34794e-05, pub: out};
var K_O5: per_fmol {init: 0.0282988, pub: out};
var K_O6: per_fmol {init: 53.5503, pub: out};
enddef;
def comp IPR as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R_IPR: fmol_per_sec {pub: in};
var kappa_R12: fmol_per_sec {pub: in};
var kappa_R23: fmol_per_sec {pub: in};
var kappa_R24: fmol_per_sec {pub: in};
var kappa_R26: fmol_per_sec {pub: in};
var kappa_R45: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_SR: per_fmol {pub: in};
var K_IP3: per_fmol {pub: in};
var K_C1: per_fmol {pub: in};
var K_C2: per_fmol {pub: in};
var K_C3: per_fmol {pub: in};
var K_C4: per_fmol {pub: in};
var K_O5: per_fmol {pub: in};
var K_O6: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_Ca_SR: fmol {pub: in};
var q_IP3: fmol {pub: in};
var q_C1: fmol {pub: in};
var q_C2: fmol {pub: in};
var q_C3: fmol {pub: in};
var q_C4: fmol {pub: in};
var q_O5: fmol {pub: in};
var q_O6: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_Ca_SR: J_per_mol;
var mu_IP3: J_per_mol;
var mu_C1: J_per_mol;
var mu_C2: J_per_mol;
var mu_C3: J_per_mol;
var mu_C4: J_per_mol;
var mu_O5: J_per_mol;
var mu_O6: J_per_mol;
var v_R_IPR: fmol_per_sec {pub: out};
var v_R12: fmol_per_sec {pub: out};
var v_R23: fmol_per_sec {pub: out};
var v_R24: fmol_per_sec {pub: out};
var v_R26: fmol_per_sec {pub: out};
var v_R45: fmol_per_sec {pub: out};
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Ca_SR = R*T*ln(K_Ca_SR*q_Ca_SR);
mu_IP3 = R*T*ln(K_IP3*q_IP3);
mu_C1 = R*T*ln(K_C1*q_C1);
mu_C2 = R*T*ln(K_C2*q_C2);
mu_C3 = R*T*ln(K_C3*q_C3);
mu_C4 = R*T*ln(K_C4*q_C4);
mu_O5 = R*T*ln(K_O5*q_O5);
mu_O6 = R*T*ln(K_O6*q_O6);
v_R_IPR = kappa_R_IPR*ppp;
v_R12 = kappa_R12*ppp;
v_R23 = kappa_R23*ppp;
v_R24 = kappa_R24*ppp;
v_R26 = kappa_R26*ppp;
v_R45 = kappa_R45*ppp;
enddef;
def map between environment and IPR for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_Ca_SR and q_Ca_SR;
vars q_IP3 and q_IP3;
vars q_C1 and q_C1;
vars q_C2 and q_C2;
vars q_C3 and q_C3;
vars q_C4 and q_C4;
vars q_O5 and q_O5;
vars q_O6 and q_O6;
vars v_R_IPR and v_R_IPR;
vars v_R12 and v_R12;
vars v_R23 and v_R23;
vars v_R24 and v_R24;
vars v_R26 and v_R26;
vars v_R45 and v_R45;
enddef;
def map between IPR and IPR_parameters for
vars kappa_R_IPR and kappa_R_IPR;
vars kappa_R12 and kappa_R12;
vars kappa_R23 and kappa_R23;
vars kappa_R24 and kappa_R24;
vars kappa_R26 and kappa_R26;
vars kappa_R45 and kappa_R45;
vars K_Ca_i and K_Ca_i;
vars K_Ca_SR and K_Ca_SR;
vars K_IP3 and K_IP3;
vars K_C1 and K_C1;
vars K_C2 and K_C2;
vars K_C3 and K_C3;
vars K_C4 and K_C4;
vars K_O5 and K_O5;
vars K_O6 and K_O6;
enddef;
def map between constants and IPR for
vars R and R;
 vars T and T;
enddef;
enddef;