Location: BG_AE1_Weinstein @ abd6b152f2b3 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-20 13:09:26+12:00
Desc:
Update comments
Permanent Source URI:
https://models.physiomeproject.org/workspace/877/rawfile/abd6b152f2b3fd16c4db2d8dcc0d203b2ad35c38/parameter_finder/output/TEMP.cellml.txt
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def model individual_AE1 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_Cl_i: fmol {init: 1e-888, pub: out};
var q_Cl_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_AE1_i: fmol {init: 1e-888, pub: out};
var q_AE1_o: fmol {init: 1e-888, pub: out};
var q_AE1_Cl_i: fmol {init: 1e-888, pub: out};
var q_AE1_Cl_o: fmol {init: 1e-888, pub: out};
var q_AE1_HCO3_i: fmol {init: 1e-888, pub: out};
var q_AE1_HCO3_o: fmol {init: 1e-888, pub: out};
// From submodule
var v_1_AE1: fmol_per_sec {pub: in};
var v_2_AE1: fmol_per_sec {pub: in};
var v_3_AE1: fmol_per_sec {pub: in};
var v_4_AE1: fmol_per_sec {pub: in};
var v_5_AE1: fmol_per_sec {pub: in};
var v_6_AE1: fmol_per_sec {pub: in};
ode(q_Cl_i, time) = vvv;
ode(q_Cl_o, time) = vvv;
ode(q_HCO3_i, time) = vvv;
ode(q_HCO3_o, time) = vvv;
ode(q_AE1_i, time) = vvv;
ode(q_AE1_o, time) = vvv;
ode(q_AE1_Cl_i, time) = vvv;
ode(q_AE1_Cl_o, time) = vvv;
ode(q_AE1_HCO3_i, time) = vvv;
ode(q_AE1_HCO3_o, time) = vvv;
enddef;

def comp AE1_parameters as
var kappa_1_AE1: fmol_per_sec {init: 8390.34, pub: out};
var kappa_2_AE1: fmol_per_sec {init: 0.0943074, pub: out};
var kappa_3_AE1: fmol_per_sec {init: 77301.2, pub: out};
var kappa_4_AE1: fmol_per_sec {init: 124606, pub: out};
var kappa_5_AE1: fmol_per_sec {init: 0.0849584, pub: out};
var kappa_6_AE1: fmol_per_sec {init: 13489.8, pub: out};
var K_Cl_i: per_fmol {init: 6.55349e-06, pub: out};
var K_Cl_o: per_fmol {init: 4.80434e-05, pub: out};
var K_HCO3_i: per_fmol {init: 4.06557e-06, pub: out};
var K_HCO3_o: per_fmol {init: 2.98819e-05, pub: out};
var K_AE1_i: per_fmol {init: 1.11903e-05, pub: out};
var K_AE1_o: per_fmol {init: 0.000172276, pub: out};
var K_AE1_Cl_i: per_fmol {init: 0.00154005, pub: out};
var K_AE1_Cl_o: per_fmol {init: 0.0496603, pub: out};
var K_AE1_HCO3_i: per_fmol {init: 0.00378337, pub: out};
var K_AE1_HCO3_o: per_fmol {init: 0.122315, pub: out};
enddef;
def comp AE1 as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_1_AE1: fmol_per_sec {pub: in};
var kappa_2_AE1: fmol_per_sec {pub: in};
var kappa_3_AE1: fmol_per_sec {pub: in};
var kappa_4_AE1: fmol_per_sec {pub: in};
var kappa_5_AE1: fmol_per_sec {pub: in};
var kappa_6_AE1: fmol_per_sec {pub: in};
var K_Cl_i: per_fmol {pub: in};
var K_Cl_o: per_fmol {pub: in};
var K_HCO3_i: per_fmol {pub: in};
var K_HCO3_o: per_fmol {pub: in};
var K_AE1_i: per_fmol {pub: in};
var K_AE1_o: per_fmol {pub: in};
var K_AE1_Cl_i: per_fmol {pub: in};
var K_AE1_Cl_o: per_fmol {pub: in};
var K_AE1_HCO3_i: per_fmol {pub: in};
var K_AE1_HCO3_o: per_fmol {pub: in};
// Input from global environment
var q_Cl_i: fmol {pub: in};
var q_Cl_o: fmol {pub: in};
var q_HCO3_i: fmol {pub: in};
var q_HCO3_o: fmol {pub: in};
var q_AE1_i: fmol {pub: in};
var q_AE1_o: fmol {pub: in};
var q_AE1_Cl_i: fmol {pub: in};
var q_AE1_Cl_o: fmol {pub: in};
var q_AE1_HCO3_i: fmol {pub: in};
var q_AE1_HCO3_o: fmol {pub: in};
// Constitutive parameters
var mu_Cl_i: J_per_mol;
var mu_Cl_o: J_per_mol;
var mu_HCO3_i: J_per_mol;
var mu_HCO3_o: J_per_mol;
var mu_AE1_i: J_per_mol;
var mu_AE1_o: J_per_mol;
var mu_AE1_Cl_i: J_per_mol;
var mu_AE1_Cl_o: J_per_mol;
var mu_AE1_HCO3_i: J_per_mol;
var mu_AE1_HCO3_o: J_per_mol;
var v_1_AE1: fmol_per_sec {pub: out};
var v_2_AE1: fmol_per_sec {pub: out};
var v_3_AE1: fmol_per_sec {pub: out};
var v_4_AE1: fmol_per_sec {pub: out};
var v_5_AE1: fmol_per_sec {pub: out};
var v_6_AE1: fmol_per_sec {pub: out};
mu_Cl_i = R*T*ln(K_Cl_i*q_Cl_i);
mu_Cl_o = R*T*ln(K_Cl_o*q_Cl_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_AE1_i = R*T*ln(K_AE1_i*q_AE1_i);
mu_AE1_o = R*T*ln(K_AE1_o*q_AE1_o);
mu_AE1_Cl_i = R*T*ln(K_AE1_Cl_i*q_AE1_Cl_i);
mu_AE1_Cl_o = R*T*ln(K_AE1_Cl_o*q_AE1_Cl_o);
mu_AE1_HCO3_i = R*T*ln(K_AE1_HCO3_i*q_AE1_HCO3_i);
mu_AE1_HCO3_o = R*T*ln(K_AE1_HCO3_o*q_AE1_HCO3_o);
v_1_AE1 = ppp;
v_2_AE1 = ppp;
v_3_AE1 = ppp;
v_4_AE1 = ppp;
v_5_AE1 = ppp;
v_6_AE1 = ppp;
enddef;
def map between environment and AE1 for
vars time and time;
vars q_Cl_i and q_Cl_i;
vars q_Cl_o and q_Cl_o;
vars q_HCO3_i and q_HCO3_i;
vars q_HCO3_o and q_HCO3_o;
vars q_AE1_i and q_AE1_i;
vars q_AE1_o and q_AE1_o;
vars q_AE1_Cl_i and q_AE1_Cl_i;
vars q_AE1_Cl_o and q_AE1_Cl_o;
vars q_AE1_HCO3_i and q_AE1_HCO3_i;
vars q_AE1_HCO3_o and q_AE1_HCO3_o;
vars v_1_AE1 and v_1_AE1;
vars v_2_AE1 and v_2_AE1;
vars v_3_AE1 and v_3_AE1;
vars v_4_AE1 and v_4_AE1;
vars v_5_AE1 and v_5_AE1;
vars v_6_AE1 and v_6_AE1;
enddef;
def map between AE1 and AE1_parameters for
vars kappa_1_AE1 and kappa_1_AE1;
vars kappa_2_AE1 and kappa_2_AE1;
vars kappa_3_AE1 and kappa_3_AE1;
vars kappa_4_AE1 and kappa_4_AE1;
vars kappa_5_AE1 and kappa_5_AE1;
vars kappa_6_AE1 and kappa_6_AE1;
vars K_Cl_i and K_Cl_i;
vars K_Cl_o and K_Cl_o;
vars K_HCO3_i and K_HCO3_i;
vars K_HCO3_o and K_HCO3_o;
vars K_AE1_i and K_AE1_i;
vars K_AE1_o and K_AE1_o;
vars K_AE1_Cl_i and K_AE1_Cl_i;
vars K_AE1_Cl_o and K_AE1_Cl_o;
vars K_AE1_HCO3_i and K_AE1_HCO3_i;
vars K_AE1_HCO3_o and K_AE1_HCO3_o;
enddef;
def map between constants and AE1 for
vars R and R;
 vars T and T;
enddef;
enddef;