Location: BG_HaiMurphy @ c39f6c56cf0a / parameter_finder / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-02-08 16:06:56+13:00
Desc:
Using 2 sets of parameters depending on the timepoint
Permanent Source URI:
https://staging.physiomeproject.org/workspace/818/rawfile/c39f6c56cf0ad6b322fdc8135641b4f0427f5de8/parameter_finder/TEMP.cellml.txt
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def model individual_HaiMurphy 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_A_init: fmol {init: 1e-888};
var q_M_init: fmol {init: 1e-888};
var q_Mp_init: fmol {init: 1e-888};
var q_AM_init: fmol {init: 1e-888};
var q_AMp_init: fmol {init: 1e-888};
var q_Pi_init: fmol {init: 1e-888};
// Global value
var q_A: fmol {pub: out};
var q_M: fmol {pub: out};
var q_Mp: fmol {pub: out};
var q_AM: fmol {pub: out};
var q_AMp: fmol {pub: out};
var q_Pi: fmol {pub: out};
// From submodule
var q_A_mHaiMurphy: fmol {pub: in};
var q_M_mHaiMurphy: fmol {pub: in};
var q_Mp_mHaiMurphy: fmol {pub: in};
var q_AM_mHaiMurphy: fmol {pub: in};
var q_AMp_mHaiMurphy: fmol {pub: in};
var q_Pi_mHaiMurphy: fmol {pub: in};
q_A = q_A_mHaiMurphy + q_A_init;
q_M = q_M_mHaiMurphy + q_M_init;
q_Mp = q_Mp_mHaiMurphy + q_Mp_init;
q_AM = q_AM_mHaiMurphy + q_AM_init;
q_AMp = q_AMp_mHaiMurphy + q_AMp_init;
q_Pi = q_Pi_mHaiMurphy + q_Pi_init;
enddef;

def comp HaiMurphy_parameters as
var kappa_R_12: fmol_per_sec {init: 0.525428, pub: out};
var kappa_R_34: fmol_per_sec {init: 0.420342, pub: out};
var kappa_R_56: fmol_per_sec {init: 2.10171, pub: out};
var kappa_R_78: fmol_per_sec {init: 0.0654128, pub: out};
var K_A: per_fmol {init: 0.0242694, pub: out};
var K_M: per_fmol {init: 0.0212922, pub: out};
var K_Mp: per_fmol {init: 0.0331345, pub: out};
var K_AM: per_fmol {init: 0.00444405, pub: out};
var K_AMp: per_fmol {init: 0.00691574, pub: out};
var K_Pi: per_fmol {init: 0.0497616, pub: out};
enddef;
def comp HaiMurphy as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R_12: fmol_per_sec {pub: in};
var kappa_R_34: fmol_per_sec {pub: in};
var kappa_R_56: fmol_per_sec {pub: in};
var kappa_R_78: fmol_per_sec {pub: in};
var K_A: per_fmol {pub: in};
var K_M: per_fmol {pub: in};
var K_Mp: per_fmol {pub: in};
var K_AM: per_fmol {pub: in};
var K_AMp: per_fmol {pub: in};
var K_Pi: per_fmol {pub: in};
// Input from global environment
var q_A_global: fmol {pub: in};
var q_M_global: fmol {pub: in};
var q_Mp_global: fmol {pub: in};
var q_AM_global: fmol {pub: in};
var q_AMp_global: fmol {pub: in};
var q_Pi_global: fmol {pub: in};
// Output to global environment
var q_A: fmol {init: 1e-16, pub: out};
var q_M: fmol {init: 1e-16, pub: out};
var q_Mp: fmol {init: 1e-16, pub: out};
var q_AM: fmol {init: 1e-16, pub: out};
var q_AMp: fmol {init: 1e-16, pub: out};
var q_Pi: fmol {init: 1e-16, pub: out};
// Constitutive parameters
var mu_A: J_per_mol;
var mu_M: J_per_mol;
var mu_Mp: J_per_mol;
var mu_AM: J_per_mol;
var mu_AMp: J_per_mol;
var mu_Pi: J_per_mol;
var v_R_12: fmol_per_sec;
var v_R_34: fmol_per_sec;
var v_R_56: fmol_per_sec;
var v_R_78: fmol_per_sec;
mu_A = R*T*ln(K_A*q_A_global);
mu_M = R*T*ln(K_M*q_M_global);
mu_Mp = R*T*ln(K_Mp*q_Mp_global);
mu_AM = R*T*ln(K_AM*q_AM_global);
mu_AMp = R*T*ln(K_AMp*q_AMp_global);
mu_Pi = R*T*ln(K_Pi*q_Pi_global);
v_R_12 = ppp;
v_R_34 = ppp;
v_R_56 = ppp;
v_R_78 = ppp;
ode(q_A, time) = qqq;
ode(q_M, time) = qqq;
ode(q_Mp, time) = qqq;
ode(q_AM, time) = qqq;
ode(q_AMp, time) = qqq;
ode(q_Pi, time) = qqq;
enddef;
def map between environment and HaiMurphy for
vars time and time;
vars q_A_mHaiMurphy and q_A;
vars q_A and q_A_global;
vars q_M_mHaiMurphy and q_M;
vars q_M and q_M_global;
vars q_Mp_mHaiMurphy and q_Mp;
vars q_Mp and q_Mp_global;
vars q_AM_mHaiMurphy and q_AM;
vars q_AM and q_AM_global;
vars q_AMp_mHaiMurphy and q_AMp;
vars q_AMp and q_AMp_global;
vars q_Pi_mHaiMurphy and q_Pi;
vars q_Pi and q_Pi_global;
enddef;
def map between HaiMurphy and HaiMurphy_parameters for
vars kappa_R_12 and kappa_R_12;
vars kappa_R_34 and kappa_R_34;
vars kappa_R_56 and kappa_R_56;
vars kappa_R_78 and kappa_R_78;
vars K_A and K_A;
vars K_M and K_M;
vars K_Mp and K_Mp;
vars K_AM and K_AM;
vars K_AMp and K_AMp;
vars K_Pi and K_Pi;
enddef;
def map between constants and HaiMurphy for
vars R and R;
 vars T and T;
enddef;
enddef;