Location: BG_funny @ 724670f52ae3 / matlab_parameter_fitting / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-30 09:05:01+13:00
Desc:
With channel density checked using patch clamp against kinetic model. K and Na have diff channel densities
Permanent Source URI:
https://models.cellml.org/workspace/838/rawfile/724670f52ae35574ca5a9d3dbfac57ab5173e105/matlab_parameter_fitting/output/TEMP.cellml.txt
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def model individual_to 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: fmol {init: 1e-888, pub: out};
var q_S10: fmol {init: 1e-888, pub: out};
var q_S20: fmol {init: 1e-888, pub: out};
var q_S30: fmol {init: 1e-888, pub: out};
var q_S01: fmol {init: 1e-888, pub: out};
var q_S11: fmol {init: 1e-888, pub: out};
var q_S21: fmol {init: 1e-888, pub: out};
var q_S31: fmol {init: 1e-888, pub: out};
// From submodule
var v_to: fmol_per_sec {pub: in};
var v_z00: fmol_per_sec {pub: in};
var v_z01: fmol_per_sec {pub: in};
var v_z10: fmol_per_sec {pub: in};
var v_z11: fmol_per_sec {pub: in};
var v_z20: fmol_per_sec {pub: in};
var v_z21: fmol_per_sec {pub: in};
var v_y00: fmol_per_sec {pub: in};
var v_y10: fmol_per_sec {pub: in};
var v_y20: fmol_per_sec {pub: in};
var v_y30: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_S00, time) = vvv;
ode(q_S10, time) = vvv;
ode(q_S20, time) = vvv;
ode(q_S30, time) = vvv;
ode(q_S01, time) = vvv;
ode(q_S11, time) = vvv;
ode(q_S21, time) = vvv;
ode(q_S31, time) = vvv;
enddef;

def comp to_parameters as
var kappa_to: fmol_per_sec {init: 4553.87, pub: out};
var kappa_z00: fmol_per_sec {init: 192.53, pub: out};
var kappa_z01: fmol_per_sec {init: 3.81216, pub: out};
var kappa_z10: fmol_per_sec {init: 1135.74, pub: out};
var kappa_z11: fmol_per_sec {init: 22.4882, pub: out};
var kappa_z20: fmol_per_sec {init: 1674.95, pub: out};
var kappa_z21: fmol_per_sec {init: 33.1647, pub: out};
var kappa_y00: fmol_per_sec {init: 0.0529623, pub: out};
var kappa_y10: fmol_per_sec {init: 0.468641, pub: out};
var kappa_y20: fmol_per_sec {init: 1.38227, pub: out};
var kappa_y30: fmol_per_sec {init: 1.35902, pub: out};
var K_K_i: per_fmol {init: 1.9617, pub: out};
var K_K_o: per_fmol {init: 13.0225, pub: out};
var K_S00: per_fmol {init: 26.7487, pub: out};
var K_S10: per_fmol {init: 3.02293, pub: out};
var K_S20: per_fmol {init: 1.02489, pub: out};
var K_S30: per_fmol {init: 1.04242, pub: out};
var K_S01: per_fmol {init: 1350.92, pub: out};
var K_S11: per_fmol {init: 152.67, pub: out};
var K_S21: per_fmol {init: 51.761, pub: out};
var K_S31: per_fmol {init: 52.6467, pub: out};
enddef;
def comp to as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_to: fmol_per_sec {pub: in};
var kappa_z00: fmol_per_sec {pub: in};
var kappa_z01: fmol_per_sec {pub: in};
var kappa_z10: fmol_per_sec {pub: in};
var kappa_z11: fmol_per_sec {pub: in};
var kappa_z20: fmol_per_sec {pub: in};
var kappa_z21: fmol_per_sec {pub: in};
var kappa_y00: fmol_per_sec {pub: in};
var kappa_y10: fmol_per_sec {pub: in};
var kappa_y20: fmol_per_sec {pub: in};
var kappa_y30: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_S00: per_fmol {pub: in};
var K_S10: per_fmol {pub: in};
var K_S20: per_fmol {pub: in};
var K_S30: per_fmol {pub: in};
var K_S01: per_fmol {pub: in};
var K_S11: per_fmol {pub: in};
var K_S21: per_fmol {pub: in};
var K_S31: 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: fmol {pub: in};
var q_S10: fmol {pub: in};
var q_S20: fmol {pub: in};
var q_S30: fmol {pub: in};
var q_S01: fmol {pub: in};
var q_S11: fmol {pub: in};
var q_S21: fmol {pub: in};
var q_S31: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_S00: J_per_mol;
var mu_S10: J_per_mol;
var mu_S20: J_per_mol;
var mu_S30: J_per_mol;
var mu_S01: J_per_mol;
var mu_S11: J_per_mol;
var mu_S21: J_per_mol;
var mu_S31: J_per_mol;
var v_to: fmol_per_sec {pub: out};
var v_z00: fmol_per_sec {pub: out};
var v_z01: fmol_per_sec {pub: out};
var v_z10: fmol_per_sec {pub: out};
var v_z11: fmol_per_sec {pub: out};
var v_z20: fmol_per_sec {pub: out};
var v_z21: fmol_per_sec {pub: out};
var v_y00: fmol_per_sec {pub: out};
var v_y10: fmol_per_sec {pub: out};
var v_y20: fmol_per_sec {pub: out};
var v_y30: 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 = R*T*ln(K_S00*q_S00);
mu_S10 = R*T*ln(K_S10*q_S10);
mu_S20 = R*T*ln(K_S20*q_S20);
mu_S30 = R*T*ln(K_S30*q_S30);
mu_S01 = R*T*ln(K_S01*q_S01);
mu_S11 = R*T*ln(K_S11*q_S11);
mu_S21 = R*T*ln(K_S21*q_S21);
mu_S31 = R*T*ln(K_S31*q_S31);
v_to = ppp;
v_z00 = ppp;
v_z01 = ppp;
v_z10 = ppp;
v_z11 = ppp;
v_z20 = ppp;
v_z21 = ppp;
v_y00 = ppp;
v_y10 = ppp;
v_y20 = ppp;
v_y30 = ppp;
enddef;
def map between environment and to for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_S00 and q_S00;
vars q_S10 and q_S10;
vars q_S20 and q_S20;
vars q_S30 and q_S30;
vars q_S01 and q_S01;
vars q_S11 and q_S11;
vars q_S21 and q_S21;
vars q_S31 and q_S31;
vars v_to and v_to;
vars v_z00 and v_z00;
vars v_z01 and v_z01;
vars v_z10 and v_z10;
vars v_z11 and v_z11;
vars v_z20 and v_z20;
vars v_z21 and v_z21;
vars v_y00 and v_y00;
vars v_y10 and v_y10;
vars v_y20 and v_y20;
vars v_y30 and v_y30;
enddef;
def map between to and to_parameters for
vars kappa_to and kappa_to;
vars kappa_z00 and kappa_z00;
vars kappa_z01 and kappa_z01;
vars kappa_z10 and kappa_z10;
vars kappa_z11 and kappa_z11;
vars kappa_z20 and kappa_z20;
vars kappa_z21 and kappa_z21;
vars kappa_y00 and kappa_y00;
vars kappa_y10 and kappa_y10;
vars kappa_y20 and kappa_y20;
vars kappa_y30 and kappa_y30;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_S00 and K_S00;
vars K_S10 and K_S10;
vars K_S20 and K_S20;
vars K_S30 and K_S30;
vars K_S01 and K_S01;
vars K_S11 and K_S11;
vars K_S21 and K_S21;
vars K_S31 and K_S31;
enddef;
def map between constants and to for
vars R and R;
 vars T and T;
enddef;
enddef;