- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-05-27 16:22:39+12:00
- Desc:
- Adding BG pic and separatring q_trash
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/b2d/rawfile/9ff3d929d90c32cdd2bbbe5328a93b0d2de1fc22/parameter_finder/output/TEMP.cellml.txt
def model individual_RTK 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_L: fmol {init: 1e-888, pub: out};
var q_K1: fmol {init: 1e-888, pub: out};
var q_K2: fmol {init: 1e-888, pub: out};
var q_LK1: fmol {init: 1e-888, pub: out};
var q_P: fmol {init: 1e-888, pub: out};
var q_LK1K2: fmol {init: 1e-888, pub: out};
var q_LK1K2P: fmol {init: 1e-888, pub: out};
var q_Ubiq: fmol {init: 1e-888, pub: out};
var q_LKKPU: fmol {init: 1e-888, pub: out};
var q_trash: fmol {init: 1e-888, pub: out};
// From submodule
var v_Re1: fmol_per_sec {pub: in};
var v_Re2: fmol_per_sec {pub: in};
var v_Re3: fmol_per_sec {pub: in};
var v_Re4: fmol_per_sec {pub: in};
var v_Re5: fmol_per_sec {pub: in};
var v_Re6: fmol_per_sec {pub: in};
ode(q_L, time) = vvv;
ode(q_K1, time) = vvv;
ode(q_K2, time) = vvv;
ode(q_LK1, time) = vvv;
ode(q_P, time) = vvv;
ode(q_LK1K2, time) = vvv;
ode(q_LK1K2P, time) = vvv;
ode(q_Ubiq, time) = vvv;
ode(q_LKKPU, time) = vvv;
ode(q_trash, time) = vvv;
enddef;
def comp RTK_parameters as
var kappa_Re1: fmol_per_sec {init: 8.62541e-08, pub: out};
var kappa_Re2: fmol_per_sec {init: 0.743977, pub: out};
var kappa_Re3: fmol_per_sec {init: 0.00227928, pub: out};
var kappa_Re4: fmol_per_sec {init: 3.62771e-07, pub: out};
var kappa_Re5: fmol_per_sec {init: 3627.71, pub: out};
var kappa_Re6: fmol_per_sec {init: 362771, pub: out};
var K_L: per_fmol {init: 3.90735e+10, pub: out};
var K_K1: per_fmol {init: 2.50739e-05, pub: out};
var K_K2: per_fmol {init: 3370.25, pub: out};
var K_LK1: per_fmol {init: 0.337025, pub: out};
var K_P: per_fmol {init: 9.48862e+12, pub: out};
var K_LK1K2: per_fmol {init: 3.90735e-08, pub: out};
var K_LK1K2P: per_fmol {init: 1.27539e-05, pub: out};
var K_Ubiq: per_fmol {init: 1.82645e+12, pub: out};
var K_LKKPU: per_fmol {init: 0.0801325, pub: out};
var K_trash: per_fmol {init: 8.01325e-14, pub: out};
enddef;
def comp RTK as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_Re1: fmol_per_sec {pub: in};
var kappa_Re2: fmol_per_sec {pub: in};
var kappa_Re3: fmol_per_sec {pub: in};
var kappa_Re4: fmol_per_sec {pub: in};
var kappa_Re5: fmol_per_sec {pub: in};
var kappa_Re6: fmol_per_sec {pub: in};
var K_L: per_fmol {pub: in};
var K_K1: per_fmol {pub: in};
var K_K2: per_fmol {pub: in};
var K_LK1: per_fmol {pub: in};
var K_P: per_fmol {pub: in};
var K_LK1K2: per_fmol {pub: in};
var K_LK1K2P: per_fmol {pub: in};
var K_Ubiq: per_fmol {pub: in};
var K_LKKPU: per_fmol {pub: in};
var K_trash: per_fmol {pub: in};
// Input from global environment
var q_L: fmol {pub: in};
var q_K1: fmol {pub: in};
var q_K2: fmol {pub: in};
var q_LK1: fmol {pub: in};
var q_P: fmol {pub: in};
var q_LK1K2: fmol {pub: in};
var q_LK1K2P: fmol {pub: in};
var q_Ubiq: fmol {pub: in};
var q_LKKPU: fmol {pub: in};
var q_trash: fmol {pub: in};
// Constitutive parameters
var mu_L: J_per_mol;
var mu_K1: J_per_mol;
var mu_K2: J_per_mol;
var mu_LK1: J_per_mol;
var mu_P: J_per_mol;
var mu_LK1K2: J_per_mol;
var mu_LK1K2P: J_per_mol;
var mu_Ubiq: J_per_mol;
var mu_LKKPU: J_per_mol;
var mu_trash: J_per_mol;
var v_Re1: fmol_per_sec {pub: out};
var v_Re2: fmol_per_sec {pub: out};
var v_Re3: fmol_per_sec {pub: out};
var v_Re4: fmol_per_sec {pub: out};
var v_Re5: fmol_per_sec {pub: out};
var v_Re6: fmol_per_sec {pub: out};
mu_L = R*T*ln(K_L*q_L);
mu_K1 = R*T*ln(K_K1*q_K1);
mu_K2 = R*T*ln(K_K2*q_K2);
mu_LK1 = R*T*ln(K_LK1*q_LK1);
mu_P = R*T*ln(K_P*q_P);
mu_LK1K2 = R*T*ln(K_LK1K2*q_LK1K2);
mu_LK1K2P = R*T*ln(K_LK1K2P*q_LK1K2P);
mu_Ubiq = R*T*ln(K_Ubiq*q_Ubiq);
mu_LKKPU = R*T*ln(K_LKKPU*q_LKKPU);
mu_trash = R*T*ln(K_trash*q_trash);
v_Re1 = kappa_Re1*ppp;
v_Re2 = kappa_Re2*ppp;
v_Re3 = kappa_Re3*ppp;
v_Re4 = kappa_Re4*ppp;
v_Re5 = kappa_Re5*ppp;
v_Re6 = kappa_Re6*ppp;
enddef;
def map between environment and RTK for
vars time and time;
vars q_L and q_L;
vars q_K1 and q_K1;
vars q_K2 and q_K2;
vars q_LK1 and q_LK1;
vars q_P and q_P;
vars q_LK1K2 and q_LK1K2;
vars q_LK1K2P and q_LK1K2P;
vars q_Ubiq and q_Ubiq;
vars q_LKKPU and q_LKKPU;
vars q_trash and q_trash;
vars v_Re1 and v_Re1;
vars v_Re2 and v_Re2;
vars v_Re3 and v_Re3;
vars v_Re4 and v_Re4;
vars v_Re5 and v_Re5;
vars v_Re6 and v_Re6;
enddef;
def map between RTK and RTK_parameters for
vars kappa_Re1 and kappa_Re1;
vars kappa_Re2 and kappa_Re2;
vars kappa_Re3 and kappa_Re3;
vars kappa_Re4 and kappa_Re4;
vars kappa_Re5 and kappa_Re5;
vars kappa_Re6 and kappa_Re6;
vars K_L and K_L;
vars K_K1 and K_K1;
vars K_K2 and K_K2;
vars K_LK1 and K_LK1;
vars K_P and K_P;
vars K_LK1K2 and K_LK1K2;
vars K_LK1K2P and K_LK1K2P;
vars K_Ubiq and K_Ubiq;
vars K_LKKPU and K_LKKPU;
vars K_trash and K_trash;
enddef;
def map between constants and RTK for
vars R and R;
vars T and T;
enddef;
enddef;
