Location: BG_NBC @ 7d72968ae64a / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-25 14:19:21+12:00
Desc:
Fixing n_o in cellml
Permanent Source URI:
http://models.cellml.org/workspace/87f/rawfile/7d72968ae64a468d04e0487a5d88a8a8485c5e14/parameter_finder/output/TEMP.cellml.txt
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def model individual_NBC 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 fF using unit fF;
        unit fC using unit fC;
        unit per_second using unit per_second;
        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 pL using unit pL;
   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_Na_i: fmol {init: 1e-888, pub: out};
var q_Na_o: fmol {init: 1e-888, pub: out};
var q_HCO3_i: fmol {init: 1e-888, pub: out};
var q_HCO3_o: fmol {init: 1e-888, pub: out};
var q_S1_NBC: fmol {init: 1e-888, pub: out};
var q_S2_NBC: fmol {init: 1e-888, pub: out};
var q_S3_NBC: fmol {init: 1e-888, pub: out};
var q_S4_NBC: fmol {init: 1e-888, pub: out};
var q_S5_NBC: fmol {init: 1e-888, pub: out};
var q_S6_NBC: fmol {init: 1e-888, pub: out};
var q_H_i: fmol {init: 1e-888, pub: out};
var q_H_o: fmol {init: 1e-888, pub: out};
// From submodule
var v_R61_NBC: fmol_per_sec {pub: in};
var v_R12_NBC: fmol_per_sec {pub: in};
var v_R23_NBC: fmol_per_sec {pub: in};
var v_R34_NBC: fmol_per_sec {pub: in};
var v_R45_NBC: fmol_per_sec {pub: in};
var v_R56_NBC: fmol_per_sec {pub: in};
ode(q_Na_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_HCO3_i, time) = vvv;
ode(q_HCO3_o, time) = vvv;
ode(q_S1_NBC, time) = vvv;
ode(q_S2_NBC, time) = vvv;
ode(q_S3_NBC, time) = vvv;
ode(q_S4_NBC, time) = vvv;
ode(q_S5_NBC, time) = vvv;
ode(q_S6_NBC, time) = vvv;
ode(q_H_i, time) = vvv;
ode(q_H_o, time) = vvv;
enddef;

def comp NBC_parameters as
var kappa_R61_NBC: fmol_per_sec {init: 0.00544275, pub: out};
var kappa_R12_NBC: fmol_per_sec {init: 2805.48, pub: out};
var kappa_R23_NBC: fmol_per_sec {init: 2563.29, pub: out};
var kappa_R34_NBC: fmol_per_sec {init: 0.0272629, pub: out};
var kappa_R45_NBC: fmol_per_sec {init: 4.4897e-05, pub: out};
var kappa_R56_NBC: fmol_per_sec {init: 49.6861, pub: out};
var K_Na_i: per_fmol {init: 0.289138, pub: out};
var K_Na_o: per_fmol {init: 0.00668538, pub: out};
var K_HCO3_i: per_fmol {init: 5.98005, pub: out};
var K_HCO3_o: per_fmol {init: 4.33694e-05, pub: out};
var K_S1_NBC: per_fmol {init: 0.00283875, pub: out};
var K_S2_NBC: per_fmol {init: 0.478939, pub: out};
var K_S3_NBC: per_fmol {init: 8.63247e-07, pub: out};
var K_S4_NBC: per_fmol {init: 49.285, pub: out};
var K_S5_NBC: per_fmol {init: 27.0428, pub: out};
var K_S6_NBC: per_fmol {init: 0.0005054, pub: out};
var K_H_i: per_fmol {init: 0.328291, pub: out};
var K_H_o: per_fmol {init: 0.0291348, pub: out};
enddef;
def comp NBC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R61_NBC: fmol_per_sec {pub: in};
var kappa_R12_NBC: fmol_per_sec {pub: in};
var kappa_R23_NBC: fmol_per_sec {pub: in};
var kappa_R34_NBC: fmol_per_sec {pub: in};
var kappa_R45_NBC: fmol_per_sec {pub: in};
var kappa_R56_NBC: fmol_per_sec {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_HCO3_i: per_fmol {pub: in};
var K_HCO3_o: per_fmol {pub: in};
var K_S1_NBC: per_fmol {pub: in};
var K_S2_NBC: per_fmol {pub: in};
var K_S3_NBC: per_fmol {pub: in};
var K_S4_NBC: per_fmol {pub: in};
var K_S5_NBC: per_fmol {pub: in};
var K_S6_NBC: per_fmol {pub: in};
var K_H_i: per_fmol {pub: in};
var K_H_o: per_fmol {pub: in};
// Input from global environment
var q_Na_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_HCO3_i: fmol {pub: in};
var q_HCO3_o: fmol {pub: in};
var q_S1_NBC: fmol {pub: in};
var q_S2_NBC: fmol {pub: in};
var q_S3_NBC: fmol {pub: in};
var q_S4_NBC: fmol {pub: in};
var q_S5_NBC: fmol {pub: in};
var q_S6_NBC: fmol {pub: in};
var q_H_i: fmol {pub: in};
var q_H_o: fmol {pub: in};
// Constitutive parameters
var mu_Na_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_HCO3_i: J_per_mol;
var mu_HCO3_o: J_per_mol;
var mu_S1_NBC: J_per_mol;
var mu_S2_NBC: J_per_mol;
var mu_S3_NBC: J_per_mol;
var mu_S4_NBC: J_per_mol;
var mu_S5_NBC: J_per_mol;
var mu_S6_NBC: J_per_mol;
var mu_H_i: J_per_mol;
var mu_H_o: J_per_mol;
var v_R61_NBC: fmol_per_sec {pub: out};
var v_R12_NBC: fmol_per_sec {pub: out};
var v_R23_NBC: fmol_per_sec {pub: out};
var v_R34_NBC: fmol_per_sec {pub: out};
var v_R45_NBC: fmol_per_sec {pub: out};
var v_R56_NBC: fmol_per_sec {pub: out};
mu_Na_i = R*T*ln(K_Na_i*q_Na_i);
mu_Na_o = R*T*ln(K_Na_o*q_Na_o);
mu_HCO3_i = R*T*ln(K_HCO3_i*q_HCO3_i);
mu_HCO3_o = R*T*ln(K_HCO3_o*q_HCO3_o);
mu_S1_NBC = R*T*ln(K_S1_NBC*q_S1_NBC);
mu_S2_NBC = R*T*ln(K_S2_NBC*q_S2_NBC);
mu_S3_NBC = R*T*ln(K_S3_NBC*q_S3_NBC);
mu_S4_NBC = R*T*ln(K_S4_NBC*q_S4_NBC);
mu_S5_NBC = R*T*ln(K_S5_NBC*q_S5_NBC);
mu_S6_NBC = R*T*ln(K_S6_NBC*q_S6_NBC);
mu_H_i = R*T*ln(K_H_i*q_H_i);
mu_H_o = R*T*ln(K_H_o*q_H_o);
v_R61_NBC = kappa_R61_NBC*(ppp);
v_R12_NBC = kappa_R12_NBC*(ppp);
v_R23_NBC = kappa_R23_NBC*(ppp);
v_R34_NBC = kappa_R34_NBC*(ppp);
v_R45_NBC = kappa_R45_NBC*(ppp);
v_R56_NBC = kappa_R56_NBC*(ppp);
enddef;
def map between environment and NBC for
vars time and time;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_HCO3_i and q_HCO3_i;
vars q_HCO3_o and q_HCO3_o;
vars q_S1_NBC and q_S1_NBC;
vars q_S2_NBC and q_S2_NBC;
vars q_S3_NBC and q_S3_NBC;
vars q_S4_NBC and q_S4_NBC;
vars q_S5_NBC and q_S5_NBC;
vars q_S6_NBC and q_S6_NBC;
vars q_H_i and q_H_i;
vars q_H_o and q_H_o;
vars v_R61_NBC and v_R61_NBC;
vars v_R12_NBC and v_R12_NBC;
vars v_R23_NBC and v_R23_NBC;
vars v_R34_NBC and v_R34_NBC;
vars v_R45_NBC and v_R45_NBC;
vars v_R56_NBC and v_R56_NBC;
enddef;
def map between NBC and NBC_parameters for
vars kappa_R61_NBC and kappa_R61_NBC;
vars kappa_R12_NBC and kappa_R12_NBC;
vars kappa_R23_NBC and kappa_R23_NBC;
vars kappa_R34_NBC and kappa_R34_NBC;
vars kappa_R45_NBC and kappa_R45_NBC;
vars kappa_R56_NBC and kappa_R56_NBC;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_HCO3_i and K_HCO3_i;
vars K_HCO3_o and K_HCO3_o;
vars K_S1_NBC and K_S1_NBC;
vars K_S2_NBC and K_S2_NBC;
vars K_S3_NBC and K_S3_NBC;
vars K_S4_NBC and K_S4_NBC;
vars K_S5_NBC and K_S5_NBC;
vars K_S6_NBC and K_S6_NBC;
vars K_H_i and K_H_i;
vars K_H_o and K_H_o;
enddef;
def map between constants and NBC for
vars R and R;
 vars T and T;
enddef;
enddef;