Location: BG_Ks @ ef4b8640984c / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-04-08 14:02:01+12:00
Desc:
Fitting to kinetic hybrid model of LRd + Kernik
Permanent Source URI:
https://models.physiomeproject.org/workspace/82d/rawfile/ef4b8640984c620ac0534355377346919cffdeb6/parameter_finder/output/TEMP.cellml.txt
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def model individual_Ks 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_S_Ks00: fmol {init: 1e-888, pub: out};
var q_S_Ks01: fmol {init: 1e-888, pub: out};
var q_S_Ks10: fmol {init: 1e-888, pub: out};
var q_S_Ks11: fmol {init: 1e-888, pub: out};
// From submodule
var v_Ks: fmol_per_sec {pub: in};
var v_xs1: fmol_per_sec {pub: in};
var v_xs2: fmol_per_sec {pub: in};
var v_xs3: fmol_per_sec {pub: in};
var v_xs4: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_S_Ks00, time) = vvv;
ode(q_S_Ks01, time) = vvv;
ode(q_S_Ks10, time) = vvv;
ode(q_S_Ks11, time) = vvv;
enddef;

def comp Ks_parameters as
var kappa_Ks: fmol_per_sec {init: 1.21097, pub: out};
var kappa_xs1: fmol_per_sec {init: 0.0131575, pub: out};
var kappa_xs2: fmol_per_sec {init: 0.0469146, pub: out};
var kappa_xs3: fmol_per_sec {init: 0.0131575, pub: out};
var kappa_xs4: fmol_per_sec {init: 0.0469146, pub: out};
var K_K_i: per_fmol {init: 0.0319895, pub: out};
var K_K_o: per_fmol {init: 0.212358, pub: out};
var K_S_Ks00: per_fmol {init: 0.0885882, pub: out};
var K_S_Ks01: per_fmol {init: 0.0248451, pub: out};
var K_S_Ks10: per_fmol {init: 0.0248451, pub: out};
var K_S_Ks11: per_fmol {init: 0.00696797, pub: out};
enddef;
def comp Ks as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_Ks: fmol_per_sec {pub: in};
var kappa_xs1: fmol_per_sec {pub: in};
var kappa_xs2: fmol_per_sec {pub: in};
var kappa_xs3: fmol_per_sec {pub: in};
var kappa_xs4: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_S_Ks00: per_fmol {pub: in};
var K_S_Ks01: per_fmol {pub: in};
var K_S_Ks10: per_fmol {pub: in};
var K_S_Ks11: per_fmol {pub: in};
// Input from global environment
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_S_Ks00: fmol {pub: in};
var q_S_Ks01: fmol {pub: in};
var q_S_Ks10: fmol {pub: in};
var q_S_Ks11: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_S_Ks00: J_per_mol;
var mu_S_Ks01: J_per_mol;
var mu_S_Ks10: J_per_mol;
var mu_S_Ks11: J_per_mol;
var v_Ks: fmol_per_sec {pub: out};
var v_xs1: fmol_per_sec {pub: out};
var v_xs2: fmol_per_sec {pub: out};
var v_xs3: fmol_per_sec {pub: out};
var v_xs4: 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_S_Ks00 = R*T*ln(K_S_Ks00*q_S_Ks00);
mu_S_Ks01 = R*T*ln(K_S_Ks01*q_S_Ks01);
mu_S_Ks10 = R*T*ln(K_S_Ks10*q_S_Ks10);
mu_S_Ks11 = R*T*ln(K_S_Ks11*q_S_Ks11);
v_Ks = ppp;
v_xs1 = ppp;
v_xs2 = ppp;
v_xs3 = ppp;
v_xs4 = ppp;
enddef;
def map between environment and Ks for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_S_Ks00 and q_S_Ks00;
vars q_S_Ks01 and q_S_Ks01;
vars q_S_Ks10 and q_S_Ks10;
vars q_S_Ks11 and q_S_Ks11;
vars v_Ks and v_Ks;
vars v_xs1 and v_xs1;
vars v_xs2 and v_xs2;
vars v_xs3 and v_xs3;
vars v_xs4 and v_xs4;
enddef;
def map between Ks and Ks_parameters for
vars kappa_Ks and kappa_Ks;
vars kappa_xs1 and kappa_xs1;
vars kappa_xs2 and kappa_xs2;
vars kappa_xs3 and kappa_xs3;
vars kappa_xs4 and kappa_xs4;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_S_Ks00 and K_S_Ks00;
vars K_S_Ks01 and K_S_Ks01;
vars K_S_Ks10 and K_S_Ks10;
vars K_S_Ks11 and K_S_Ks11;
enddef;
def map between constants and Ks for
vars R and R;
 vars T and T;
enddef;
enddef;