Location: BG_ABC @ 4ae7938a2662 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2024-12-04 14:10:09+13:00
Desc:
Add link to protein knowledge page
Permanent Source URI:
https://staging.physiomeproject.org/workspace/c2a/rawfile/4ae7938a26624dbb4d1f338ecce055621440f793/parameter_finder/output/TEMP.cellml.txt
Compare... Download Source 

def model individual_ABC 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_S_i: fmol {init: 1e-888, pub: out};
var q_S_o: fmol {init: 1e-888, pub: out};
var q_E_ADP: fmol {init: 1e-888, pub: out};
var q_E_ATP: fmol {init: 1e-888, pub: out};
var q_ATP: fmol {init: 1e-888, pub: out};
var q_ADP: fmol {init: 1e-888, pub: out};
var q_Pi: fmol {init: 1e-888, pub: out};
var q_S_E_ATP: fmol {init: 1e-888, pub: out};
var q_S_E_ADP: fmol {init: 1e-888, pub: out};
// From submodule
var v_ReABind	: fmol_per_sec {pub: in};
var v_ReSBind	: fmol_per_sec {pub: in};
var v_ReHyd	: fmol_per_sec {pub: in};
var v_ReRel: fmol_per_sec {pub: in};
ode(q_S_i, time) = vvv;
ode(q_S_o, time) = vvv;
ode(q_E_ADP, time) = vvv;
ode(q_E_ATP, time) = vvv;
ode(q_ATP, time) = vvv;
ode(q_ADP, time) = vvv;
ode(q_Pi, time) = vvv;
ode(q_S_E_ATP, time) = vvv;
ode(q_S_E_ADP, time) = vvv;
enddef;

def comp ABC_parameters as
var kappa_ReABind	: fmol_per_sec {init: 0.509703, pub: out};
var kappa_ReSBind	: fmol_per_sec {init: 1.85478e-07, pub: out};
var kappa_ReHyd	: fmol_per_sec {init: 185478, pub: out};
var kappa_ReRel: fmol_per_sec {init: 48186.7, pub: out};
var K_S_i: per_fmol {init: 1.58747e-11, pub: out};
var K_S_o: per_fmol {init: 6.46339e+08, pub: out};
var K_E_ADP: per_fmol {init: 0.000905319, pub: out};
var K_E_ATP: per_fmol {init: 5.7767, pub: out};
var K_ATP: per_fmol {init: 1.50077e+06, pub: out};
var K_ADP: per_fmol {init: 2.35199e-10, pub: out};
var K_Pi: per_fmol {init: 6.83676e-15, pub: out};
var K_S_E_ATP: per_fmol {init: 0.141881, pub: out};
var K_S_E_ADP: per_fmol {init: 0.546122, pub: out};
enddef;
def comp ABC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_ReABind	: fmol_per_sec {pub: in};
var kappa_ReSBind	: fmol_per_sec {pub: in};
var kappa_ReHyd	: fmol_per_sec {pub: in};
var kappa_ReRel: fmol_per_sec {pub: in};
var K_S_i: per_fmol {pub: in};
var K_S_o: per_fmol {pub: in};
var K_E_ADP: per_fmol {pub: in};
var K_E_ATP: per_fmol {pub: in};
var K_ATP: per_fmol {pub: in};
var K_ADP: per_fmol {pub: in};
var K_Pi: per_fmol {pub: in};
var K_S_E_ATP: per_fmol {pub: in};
var K_S_E_ADP: per_fmol {pub: in};
// Input from global environment
var q_S_i: fmol {pub: in};
var q_S_o: fmol {pub: in};
var q_E_ADP: fmol {pub: in};
var q_E_ATP: fmol {pub: in};
var q_ATP: fmol {pub: in};
var q_ADP: fmol {pub: in};
var q_Pi: fmol {pub: in};
var q_S_E_ATP: fmol {pub: in};
var q_S_E_ADP: fmol {pub: in};
// Constitutive parameters
var mu_S_i: J_per_mol;
var mu_S_o: J_per_mol;
var mu_E_ADP: J_per_mol;
var mu_E_ATP: J_per_mol;
var mu_ATP: J_per_mol;
var mu_ADP: J_per_mol;
var mu_Pi: J_per_mol;
var mu_S_E_ATP: J_per_mol;
var mu_S_E_ADP: J_per_mol;
var v_ReABind	: fmol_per_sec {pub: out};
var v_ReSBind	: fmol_per_sec {pub: out};
var v_ReHyd	: fmol_per_sec {pub: out};
var v_ReRel: fmol_per_sec {pub: out};
mu_S_i = R*T*ln(K_S_i*q_S_i);
mu_S_o = R*T*ln(K_S_o*q_S_o);
mu_E_ADP = R*T*ln(K_E_ADP*q_E_ADP);
mu_E_ATP = R*T*ln(K_E_ATP*q_E_ATP);
mu_ATP = R*T*ln(K_ATP*q_ATP);
mu_ADP = R*T*ln(K_ADP*q_ADP);
mu_Pi = R*T*ln(K_Pi*q_Pi);
mu_S_E_ATP = R*T*ln(K_S_E_ATP*q_S_E_ATP);
mu_S_E_ADP = R*T*ln(K_S_E_ADP*q_S_E_ADP);
v_ReABind	 = ppp;
v_ReSBind	 = ppp;
v_ReHyd	 = ppp;
v_ReRel = ppp;
enddef;
def map between environment and ABC for
vars time and time;
vars q_S_i and q_S_i;
vars q_S_o and q_S_o;
vars q_E_ADP and q_E_ADP;
vars q_E_ATP and q_E_ATP;
vars q_ATP and q_ATP;
vars q_ADP and q_ADP;
vars q_Pi and q_Pi;
vars q_S_E_ATP and q_S_E_ATP;
vars q_S_E_ADP and q_S_E_ADP;
vars v_ReABind	 and v_ReABind	;
vars v_ReSBind	 and v_ReSBind	;
vars v_ReHyd	 and v_ReHyd	;
vars v_ReRel and v_ReRel;
enddef;
def map between ABC and ABC_parameters for
vars kappa_ReABind	 and kappa_ReABind	;
vars kappa_ReSBind	 and kappa_ReSBind	;
vars kappa_ReHyd	 and kappa_ReHyd	;
vars kappa_ReRel and kappa_ReRel;
vars K_S_i and K_S_i;
vars K_S_o and K_S_o;
vars K_E_ADP and K_E_ADP;
vars K_E_ATP and K_E_ATP;
vars K_ATP and K_ATP;
vars K_ADP and K_ADP;
vars K_Pi and K_Pi;
vars K_S_E_ATP and K_S_E_ATP;
vars K_S_E_ADP and K_S_E_ADP;
enddef;
def map between constants and ABC for
vars R and R;
 vars T and T;
enddef;
enddef;