Location: BG_Ks @ 9d0bac38f32f / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-03-03 09:36:39+13:00
Desc:
Changing Xi to X_i, and adding python param finder code
Permanent Source URI:
https://staging.physiomeproject.org/workspace/82d/rawfile/9d0bac38f32f96494587904e6f6eb66283125565/parameter_finder/output/TEMP.cellml.txt
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def model individual_Ks_channel 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_Sa: fmol {init: 1e-888, pub: out};
var q_Sb: fmol {init: 1e-888, pub: out};
var q_Sc: fmol {init: 1e-888, pub: out};
var q_Sd: fmol {init: 1e-888, pub: out};
// From submodule
var v_Ks: fmol_per_sec {pub: in};
var v_x10: fmol_per_sec {pub: in};
var v_x11: fmol_per_sec {pub: in};
var v_x20: fmol_per_sec {pub: in};
var v_x21: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_Sa, time) = vvv;
ode(q_Sb, time) = vvv;
ode(q_Sc, time) = vvv;
ode(q_Sd, time) = vvv;
enddef;

def comp Ks_channel_parameters as
var kappa_Ks: fmol_per_sec {init: 4805.32, pub: out};
var kappa_x10: fmol_per_sec {init: 1.70139, pub: out};
var kappa_x11: fmol_per_sec {init: 1.79332, pub: out};
var kappa_x20: fmol_per_sec {init: 0.391403, pub: out};
var kappa_x21: fmol_per_sec {init: 0.395408, pub: out};
var K_K_i: per_fmol {init: 2.01513, pub: out};
var K_K_o: per_fmol {init: 13.3772, pub: out};
var K_Sa: per_fmol {init: 0.855402, pub: out};
var K_Sb: per_fmol {init: 0.846737, pub: out};
var K_Sc: per_fmol {init: 0.811553, pub: out};
var K_Sd: per_fmol {init: 0.803333, pub: out};
enddef;
def comp Ks_channel 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_x10: fmol_per_sec {pub: in};
var kappa_x11: fmol_per_sec {pub: in};
var kappa_x20: fmol_per_sec {pub: in};
var kappa_x21: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_Sa: per_fmol {pub: in};
var K_Sb: per_fmol {pub: in};
var K_Sc: per_fmol {pub: in};
var K_Sd: per_fmol {pub: in};
// Input from global environment
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_Sa: fmol {pub: in};
var q_Sb: fmol {pub: in};
var q_Sc: fmol {pub: in};
var q_Sd: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_Sa: J_per_mol;
var mu_Sb: J_per_mol;
var mu_Sc: J_per_mol;
var mu_Sd: J_per_mol;
var v_Ks: fmol_per_sec {pub: out};
var v_x10: fmol_per_sec {pub: out};
var v_x11: fmol_per_sec {pub: out};
var v_x20: fmol_per_sec {pub: out};
var v_x21: 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_Sa = R*T*ln(K_Sa*q_Sa);
mu_Sb = R*T*ln(K_Sb*q_Sb);
mu_Sc = R*T*ln(K_Sc*q_Sc);
mu_Sd = R*T*ln(K_Sd*q_Sd);
v_Ks = ppp;
v_x10 = ppp;
v_x11 = ppp;
v_x20 = ppp;
v_x21 = ppp;
enddef;
def map between environment and Ks_channel for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_Sa and q_Sa;
vars q_Sb and q_Sb;
vars q_Sc and q_Sc;
vars q_Sd and q_Sd;
vars v_Ks and v_Ks;
vars v_x10 and v_x10;
vars v_x11 and v_x11;
vars v_x20 and v_x20;
vars v_x21 and v_x21;
enddef;
def map between Ks_channel and Ks_channel_parameters for
vars kappa_Ks and kappa_Ks;
vars kappa_x10 and kappa_x10;
vars kappa_x11 and kappa_x11;
vars kappa_x20 and kappa_x20;
vars kappa_x21 and kappa_x21;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_Sa and K_Sa;
vars K_Sb and K_Sb;
vars K_Sc and K_Sc;
vars K_Sd and K_Sd;
enddef;
def map between constants and Ks_channel for
vars R and R;
 vars T and T;
enddef;
enddef;