Location: BG_NCX @ a33eddc15290 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-03 13:30:12+13:00
Desc:
Changing Xi to X_i, and adding python param finder code
Permanent Source URI:
https://models.physiomeproject.org/workspace/828/rawfile/a33eddc15290b8fb2e1417369aa5d3b7be82130a/parameter_finder/output/TEMP.cellml.txt
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def model individual_NCX 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_1_NCX: fmol {init: 1e-888, pub: out};
var q_2_NCX: fmol {init: 1e-888, pub: out};
var q_3_NCX: fmol {init: 1e-888, pub: out};
var q_4_NCX: fmol {init: 1e-888, pub: out};
var q_5_NCX: fmol {init: 1e-888, pub: out};
var q_6_NCX: fmol {init: 1e-888, pub: out};
var q_Na_i: fmol {init: 1e-888, pub: out};
var q_Ca_i: fmol {init: 1e-888, pub: out};
var q_Na_o: fmol {init: 1e-888, pub: out};
var q_Ca_o: fmol {init: 1e-888, pub: out};
// From submodule
var v_1_NCX: fmol_per_sec {pub: in};
var v_2_NCX: fmol_per_sec {pub: in};
var v_3_NCX: fmol_per_sec {pub: in};
var v_4_NCX: fmol_per_sec {pub: in};
var v_5_NCX: fmol_per_sec {pub: in};
var v_6_NCX: fmol_per_sec {pub: in};
ode(q_1_NCX, time) = vvv;
ode(q_2_NCX, time) = vvv;
ode(q_3_NCX, time) = vvv;
ode(q_4_NCX, time) = vvv;
ode(q_5_NCX, time) = vvv;
ode(q_6_NCX, time) = vvv;
ode(q_Na_i, time) = vvv;
ode(q_Ca_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_Ca_o, time) = vvv;
enddef;

def comp NCX_parameters as
var kappa_1_NCX: fmol_per_sec {init: 180120, pub: out};
var kappa_2_NCX: fmol_per_sec {init: 4.11924e+06, pub: out};
var kappa_3_NCX: fmol_per_sec {init: 1331.58, pub: out};
var kappa_4_NCX: fmol_per_sec {init: 4.11924e+06, pub: out};
var kappa_5_NCX: fmol_per_sec {init: 180120, pub: out};
var kappa_6_NCX: fmol_per_sec {init: 1.24489, pub: out};
var K_1_NCX: per_fmol {init: 2.28377e+08, pub: out};
var K_2_NCX: per_fmol {init: 31.0615, pub: out};
var K_3_NCX: per_fmol {init: 113898, pub: out};
var K_4_NCX: per_fmol {init: 613742, pub: out};
var K_5_NCX: per_fmol {init: 6470.36, pub: out};
var K_6_NCX: per_fmol {init: 284.414, pub: out};
var K_Na_i: per_fmol {init: 0.00639903, pub: out};
var K_Ca_i: per_fmol {init: 1.49546, pub: out};
var K_Na_o: per_fmol {init: 0.210759, pub: out};
var K_Ca_o: per_fmol {init: 1212.47, pub: out};
enddef;
def comp NCX as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_1_NCX: fmol_per_sec {pub: in};
var kappa_2_NCX: fmol_per_sec {pub: in};
var kappa_3_NCX: fmol_per_sec {pub: in};
var kappa_4_NCX: fmol_per_sec {pub: in};
var kappa_5_NCX: fmol_per_sec {pub: in};
var kappa_6_NCX: fmol_per_sec {pub: in};
var K_1_NCX: per_fmol {pub: in};
var K_2_NCX: per_fmol {pub: in};
var K_3_NCX: per_fmol {pub: in};
var K_4_NCX: per_fmol {pub: in};
var K_5_NCX: per_fmol {pub: in};
var K_6_NCX: per_fmol {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
// Input from global environment
var q_1_NCX: fmol {pub: in};
var q_2_NCX: fmol {pub: in};
var q_3_NCX: fmol {pub: in};
var q_4_NCX: fmol {pub: in};
var q_5_NCX: fmol {pub: in};
var q_6_NCX: fmol {pub: in};
var q_Na_i: fmol {pub: in};
var q_Ca_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
// Constitutive parameters
var mu_1_NCX: J_per_mol;
var mu_2_NCX: J_per_mol;
var mu_3_NCX: J_per_mol;
var mu_4_NCX: J_per_mol;
var mu_5_NCX: J_per_mol;
var mu_6_NCX: J_per_mol;
var mu_Na_i: J_per_mol;
var mu_Ca_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_Ca_o: J_per_mol;
var v_1_NCX: fmol_per_sec {pub: out};
var v_2_NCX: fmol_per_sec {pub: out};
var v_3_NCX: fmol_per_sec {pub: out};
var v_4_NCX: fmol_per_sec {pub: out};
var v_5_NCX: fmol_per_sec {pub: out};
var v_6_NCX: fmol_per_sec {pub: out};
mu_1_NCX = R*T*ln(K_1_NCX*q_1_NCX);
mu_2_NCX = R*T*ln(K_2_NCX*q_2_NCX);
mu_3_NCX = R*T*ln(K_3_NCX*q_3_NCX);
mu_4_NCX = R*T*ln(K_4_NCX*q_4_NCX);
mu_5_NCX = R*T*ln(K_5_NCX*q_5_NCX);
mu_6_NCX = R*T*ln(K_6_NCX*q_6_NCX);
mu_Na_i = R*T*ln(K_Na_i*q_Na_i);
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Na_o = R*T*ln(K_Na_o*q_Na_o);
mu_Ca_o = R*T*ln(K_Ca_o*q_Ca_o);
v_1_NCX = ppp;
v_2_NCX = ppp;
v_3_NCX = ppp;
v_4_NCX = ppp;
v_5_NCX = ppp;
v_6_NCX = ppp;
enddef;
def map between environment and NCX for
vars time and time;
vars q_1_NCX and q_1_NCX;
vars q_2_NCX and q_2_NCX;
vars q_3_NCX and q_3_NCX;
vars q_4_NCX and q_4_NCX;
vars q_5_NCX and q_5_NCX;
vars q_6_NCX and q_6_NCX;
vars q_Na_i and q_Na_i;
vars q_Ca_i and q_Ca_i;
vars q_Na_o and q_Na_o;
vars q_Ca_o and q_Ca_o;
vars v_1_NCX and v_1_NCX;
vars v_2_NCX and v_2_NCX;
vars v_3_NCX and v_3_NCX;
vars v_4_NCX and v_4_NCX;
vars v_5_NCX and v_5_NCX;
vars v_6_NCX and v_6_NCX;
enddef;
def map between NCX and NCX_parameters for
vars kappa_1_NCX and kappa_1_NCX;
vars kappa_2_NCX and kappa_2_NCX;
vars kappa_3_NCX and kappa_3_NCX;
vars kappa_4_NCX and kappa_4_NCX;
vars kappa_5_NCX and kappa_5_NCX;
vars kappa_6_NCX and kappa_6_NCX;
vars K_1_NCX and K_1_NCX;
vars K_2_NCX and K_2_NCX;
vars K_3_NCX and K_3_NCX;
vars K_4_NCX and K_4_NCX;
vars K_5_NCX and K_5_NCX;
vars K_6_NCX and K_6_NCX;
vars K_Na_i and K_Na_i;
vars K_Ca_i and K_Ca_i;
vars K_Na_o and K_Na_o;
vars K_Ca_o and K_Ca_o;
enddef;
def map between constants and NCX for
vars R and R;
 vars T and T;
enddef;
enddef;