Location: BG_TCC @ 06f090addb49 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2024-11-13 10:26:46+13:00
Desc:
Updating cellml and sedml
Permanent Source URI:
https://models.physiomeproject.org/workspace/831/rawfile/06f090addb4968d12531197d463345e0b2012d2a/parameter_finder/output/TEMP.cellml.txt
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def model individual_TCC 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_Ca_i: fmol {init: 1e-888, pub: out};
var q_Ca_o: fmol {init: 1e-888, pub: out};
var q_S00_TCC: fmol {init: 1e-888, pub: out};
var q_S10_TCC: fmol {init: 1e-888, pub: out};
var q_S01_TCC: fmol {init: 1e-888, pub: out};
var q_S11_TCC: fmol {init: 1e-888, pub: out};
// From submodule
var v_TCC: fmol_per_sec {pub: in};
var v_R1_TCC: fmol_per_sec {pub: in};
var v_R2_TCC: fmol_per_sec {pub: in};
var v_R3_TCC: fmol_per_sec {pub: in};
var v_R4_TCC: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_Ca_o, time) = vvv;
ode(q_S00_TCC, time) = vvv;
ode(q_S10_TCC, time) = vvv;
ode(q_S01_TCC, time) = vvv;
ode(q_S11_TCC, time) = vvv;
enddef;

def comp TCC_parameters as
var kappa_TCC: fmol_per_sec {init: 5935.83, pub: out};
var kappa_R1_TCC: fmol_per_sec {init: 40.0387, pub: out};
var kappa_R2_TCC: fmol_per_sec {init: 0.137081, pub: out};
var kappa_R3_TCC: fmol_per_sec {init: 0.0426788, pub: out};
var kappa_R4_TCC: fmol_per_sec {init: 0.235519, pub: out};
var K_Ca_i: per_fmol {init: 20.7667, pub: out};
var K_Ca_o: per_fmol {init: 23.5985, pub: out};
var K_S00_TCC: per_fmol {init: 0.0666161, pub: out};
var K_S10_TCC: per_fmol {init: 0.0120716, pub: out};
var K_S01_TCC: per_fmol {init: 19.4573, pub: out};
var K_S11_TCC: per_fmol {init: 3.52589, pub: out};
enddef;
def comp TCC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_TCC: fmol_per_sec {pub: in};
var kappa_R1_TCC: fmol_per_sec {pub: in};
var kappa_R2_TCC: fmol_per_sec {pub: in};
var kappa_R3_TCC: fmol_per_sec {pub: in};
var kappa_R4_TCC: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
var K_S00_TCC: per_fmol {pub: in};
var K_S10_TCC: per_fmol {pub: in};
var K_S01_TCC: per_fmol {pub: in};
var K_S11_TCC: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
var q_S00_TCC: fmol {pub: in};
var q_S10_TCC: fmol {pub: in};
var q_S01_TCC: fmol {pub: in};
var q_S11_TCC: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_Ca_o: J_per_mol;
var mu_S00_TCC: J_per_mol;
var mu_S10_TCC: J_per_mol;
var mu_S01_TCC: J_per_mol;
var mu_S11_TCC: J_per_mol;
var v_TCC: fmol_per_sec {pub: out};
var v_R1_TCC: fmol_per_sec {pub: out};
var v_R2_TCC: fmol_per_sec {pub: out};
var v_R3_TCC: fmol_per_sec {pub: out};
var v_R4_TCC: fmol_per_sec {pub: out};
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Ca_o = R*T*ln(K_Ca_o*q_Ca_o);
mu_S00_TCC = R*T*ln(K_S00_TCC*q_S00_TCC);
mu_S10_TCC = R*T*ln(K_S10_TCC*q_S10_TCC);
mu_S01_TCC = R*T*ln(K_S01_TCC*q_S01_TCC);
mu_S11_TCC = R*T*ln(K_S11_TCC*q_S11_TCC);
v_TCC = ppp;
v_R1_TCC = ppp;
v_R2_TCC = ppp;
v_R3_TCC = ppp;
v_R4_TCC = ppp;
enddef;
def map between environment and TCC for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_Ca_o and q_Ca_o;
vars q_S00_TCC and q_S00_TCC;
vars q_S10_TCC and q_S10_TCC;
vars q_S01_TCC and q_S01_TCC;
vars q_S11_TCC and q_S11_TCC;
vars v_TCC and v_TCC;
vars v_R1_TCC and v_R1_TCC;
vars v_R2_TCC and v_R2_TCC;
vars v_R3_TCC and v_R3_TCC;
vars v_R4_TCC and v_R4_TCC;
enddef;
def map between TCC and TCC_parameters for
vars kappa_TCC and kappa_TCC;
vars kappa_R1_TCC and kappa_R1_TCC;
vars kappa_R2_TCC and kappa_R2_TCC;
vars kappa_R3_TCC and kappa_R3_TCC;
vars kappa_R4_TCC and kappa_R4_TCC;
vars K_Ca_i and K_Ca_i;
vars K_Ca_o and K_Ca_o;
vars K_S00_TCC and K_S00_TCC;
vars K_S10_TCC and K_S10_TCC;
vars K_S01_TCC and K_S01_TCC;
vars K_S11_TCC and K_S11_TCC;
enddef;
def map between constants and TCC for
vars R and R;
 vars T and T;
enddef;
enddef;