Location: BG_cGMP @ 2d57c741da49 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2025-04-09 09:22:28+12:00
Desc:
Adding xpo files. updating param finder folder with new stoich
Permanent Source URI:
https://staging.physiomeproject.org/workspace/856/rawfile/2d57c741da498eb46cef438bbb1ffaefbdb0f820/parameter_finder/output/TEMP.cellml.txt
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def model individual_cGMP 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_GTP: fmol {init: 1e-888, pub: out};
var q_E5c: fmol {init: 1e-888, pub: out};
var q_cGMP: fmol {init: 1e-888, pub: out};
var q_PDE: fmol {init: 1e-888, pub: out};
var q_GTP_E5c: fmol {init: 1e-888, pub: out};
var q_cGMP_PDE: fmol {init: 1e-888, pub: out};
var q_GMP: fmol {init: 1e-888, pub: out};
// From submodule
var v_R_1a_cGMP: fmol_per_sec {pub: in};
var v_R_1b_cGMP: fmol_per_sec {pub: in};
var v_R_2a_cGMP: fmol_per_sec {pub: in};
var v_R_2b_cGMP: fmol_per_sec {pub: in};
ode(q_GTP, time) = vvv;
ode(q_E5c, time) = vvv;
ode(q_cGMP, time) = vvv;
ode(q_PDE, time) = vvv;
ode(q_GTP_E5c, time) = vvv;
ode(q_cGMP_PDE, time) = vvv;
ode(q_GMP, time) = vvv;
enddef;

def comp cGMP_parameters as
var kappa_R_1a_cGMP: fmol_per_sec {init: 1772.99, pub: out};
var kappa_R_1b_cGMP: fmol_per_sec {init: 0.0302117, pub: out};
var kappa_R_2a_cGMP: fmol_per_sec {init: 73652.7, pub: out};
var kappa_R_2b_cGMP: fmol_per_sec {init: 0.0143623, pub: out};
var K_GTP: per_fmol {init: 1600.8, pub: out};
var K_E5c: per_fmol {init: 0.0255983, pub: out};
var K_cGMP: per_fmol {init: 0.0939434, pub: out};
var K_PDE: per_fmol {init: 10.5002, pub: out};
var K_GTP_E5c: per_fmol {init: 152.027, pub: out};
var K_cGMP_PDE: per_fmol {init: 7.31926, pub: out};
var K_GMP: per_fmol {init: 0.000481761, pub: out};
enddef;
def comp cGMP as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R_1a_cGMP: fmol_per_sec {pub: in};
var kappa_R_1b_cGMP: fmol_per_sec {pub: in};
var kappa_R_2a_cGMP: fmol_per_sec {pub: in};
var kappa_R_2b_cGMP: fmol_per_sec {pub: in};
var K_GTP: per_fmol {pub: in};
var K_E5c: per_fmol {pub: in};
var K_cGMP: per_fmol {pub: in};
var K_PDE: per_fmol {pub: in};
var K_GTP_E5c: per_fmol {pub: in};
var K_cGMP_PDE: per_fmol {pub: in};
var K_GMP: per_fmol {pub: in};
// Input from global environment
var q_GTP: fmol {pub: in};
var q_E5c: fmol {pub: in};
var q_cGMP: fmol {pub: in};
var q_PDE: fmol {pub: in};
var q_GTP_E5c: fmol {pub: in};
var q_cGMP_PDE: fmol {pub: in};
var q_GMP: fmol {pub: in};
// Constitutive parameters
var mu_GTP: J_per_mol;
var mu_E5c: J_per_mol;
var mu_cGMP: J_per_mol;
var mu_PDE: J_per_mol;
var mu_GTP_E5c: J_per_mol;
var mu_cGMP_PDE: J_per_mol;
var mu_GMP: J_per_mol;
var v_R_1a_cGMP: fmol_per_sec {pub: out};
var v_R_1b_cGMP: fmol_per_sec {pub: out};
var v_R_2a_cGMP: fmol_per_sec {pub: out};
var v_R_2b_cGMP: fmol_per_sec {pub: out};
mu_GTP = R*T*ln(K_GTP*q_GTP);
mu_E5c = R*T*ln(K_E5c*q_E5c);
mu_cGMP = R*T*ln(K_cGMP*q_cGMP);
mu_PDE = R*T*ln(K_PDE*q_PDE);
mu_GTP_E5c = R*T*ln(K_GTP_E5c*q_GTP_E5c);
mu_cGMP_PDE = R*T*ln(K_cGMP_PDE*q_cGMP_PDE);
mu_GMP = R*T*ln(K_GMP*q_GMP);
v_R_1a_cGMP = ppp;
v_R_1b_cGMP = ppp;
v_R_2a_cGMP = ppp;
v_R_2b_cGMP = ppp;
enddef;
def map between environment and cGMP for
vars time and time;
vars q_GTP and q_GTP;
vars q_E5c and q_E5c;
vars q_cGMP and q_cGMP;
vars q_PDE and q_PDE;
vars q_GTP_E5c and q_GTP_E5c;
vars q_cGMP_PDE and q_cGMP_PDE;
vars q_GMP and q_GMP;
vars v_R_1a_cGMP and v_R_1a_cGMP;
vars v_R_1b_cGMP and v_R_1b_cGMP;
vars v_R_2a_cGMP and v_R_2a_cGMP;
vars v_R_2b_cGMP and v_R_2b_cGMP;
enddef;
def map between cGMP and cGMP_parameters for
vars kappa_R_1a_cGMP and kappa_R_1a_cGMP;
vars kappa_R_1b_cGMP and kappa_R_1b_cGMP;
vars kappa_R_2a_cGMP and kappa_R_2a_cGMP;
vars kappa_R_2b_cGMP and kappa_R_2b_cGMP;
vars K_GTP and K_GTP;
vars K_E5c and K_E5c;
vars K_cGMP and K_cGMP;
vars K_PDE and K_PDE;
vars K_GTP_E5c and K_GTP_E5c;
vars K_cGMP_PDE and K_cGMP_PDE;
vars K_GMP and K_GMP;
enddef;
def map between constants and cGMP for
vars R and R;
 vars T and T;
enddef;
enddef;