Location: BG_sGC @ 764c22a66180 / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <sfon036@UoA.auckland.ac.nz>
Date:
2022-05-13 11:56:11+12:00
Desc:
Fixing equations
Permanent Source URI:
https://models.physiomeproject.org/workspace/857/rawfile/764c22a661800aa2d3173388426c3b88d31ebc80/parameter_finder/output/TEMP.cellml.txt
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def model individual_sGC 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_B: fmol {init: 1e-888, pub: out};
var q_NO: fmol {init: 1e-888, pub: out};
var q_E6c: 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_NO_product: fmol {init: 1e-888, pub: out};
// From submodule
var v_R_1_sGC: fmol_per_sec {pub: in};
var v_R_2_sGC: fmol_per_sec {pub: in};
var v_R_3_sGC: fmol_per_sec {pub: in};
var v_R_4_sGC: fmol_per_sec {pub: in};
var v_R_DNO_sGC: fmol_per_sec {pub: in};
ode(q_B, time) = vvv;
ode(q_NO, time) = vvv;
ode(q_E6c, time) = vvv;
ode(q_E5c, time) = vvv;
ode(q_cGMP, time) = vvv;
ode(q_NO_product, time) = vvv;
enddef;

def comp sGC_parameters as
var kappa_R_1_sGC: fmol_per_sec {init: 123.75, pub: out};
var kappa_R_2_sGC: fmol_per_sec {init: 0.12375, pub: out};
var kappa_R_3_sGC: fmol_per_sec {init: 0.12375, pub: out};
var kappa_R_4_sGC: fmol_per_sec {init: 0.00185625, pub: out};
var kappa_R_DNO_sGC: fmol_per_sec {init: 6.66667e-06, pub: out};
var K_B: per_fmol {init: 0.145208, pub: out};
var K_NO: per_fmol {init: 404.313, pub: out};
var K_E6c: per_fmol {init: 0.217811, pub: out};
var K_E5c: per_fmol {init: 0.00217811, pub: out};
var K_cGMP: per_fmol {init: 7.29923, pub: out};
var K_NO_product: per_fmol {init: 40.4313, pub: out};
enddef;
def comp sGC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R_1_sGC: fmol_per_sec {pub: in};
var kappa_R_2_sGC: fmol_per_sec {pub: in};
var kappa_R_3_sGC: fmol_per_sec {pub: in};
var kappa_R_4_sGC: fmol_per_sec {pub: in};
var kappa_R_DNO_sGC: fmol_per_sec {pub: in};
var K_B: per_fmol {pub: in};
var K_NO: per_fmol {pub: in};
var K_E6c: per_fmol {pub: in};
var K_E5c: per_fmol {pub: in};
var K_cGMP: per_fmol {pub: in};
var K_NO_product: per_fmol {pub: in};
// Input from global environment
var q_B: fmol {pub: in};
var q_NO: fmol {pub: in};
var q_E6c: fmol {pub: in};
var q_E5c: fmol {pub: in};
var q_cGMP: fmol {pub: in};
var q_NO_product: fmol {pub: in};
// Constitutive parameters
var mu_B: J_per_mol;
var mu_NO: J_per_mol;
var mu_E6c: J_per_mol;
var mu_E5c: J_per_mol;
var mu_cGMP: J_per_mol;
var mu_NO_product: J_per_mol;
var v_R_1_sGC: fmol_per_sec {pub: out};
var v_R_2_sGC: fmol_per_sec {pub: out};
var v_R_3_sGC: fmol_per_sec {pub: out};
var v_R_4_sGC: fmol_per_sec {pub: out};
var v_R_DNO_sGC: fmol_per_sec {pub: out};
mu_B = R*T*ln(K_B*q_B);
mu_NO = R*T*ln(K_NO*q_NO);
mu_E6c = R*T*ln(K_E6c*q_E6c);
mu_E5c = R*T*ln(K_E5c*q_E5c);
mu_cGMP = R*T*ln(K_cGMP*q_cGMP);
mu_NO_product = R*T*ln(K_NO_product*q_NO_product);
v_R_1_sGC = ppp;
v_R_2_sGC = ppp;
v_R_3_sGC = ppp;
v_R_4_sGC = ppp;
v_R_DNO_sGC = ppp;
enddef;
def map between environment and sGC for
vars time and time;
vars q_B and q_B;
vars q_NO and q_NO;
vars q_E6c and q_E6c;
vars q_E5c and q_E5c;
vars q_cGMP and q_cGMP;
vars q_NO_product and q_NO_product;
vars v_R_1_sGC and v_R_1_sGC;
vars v_R_2_sGC and v_R_2_sGC;
vars v_R_3_sGC and v_R_3_sGC;
vars v_R_4_sGC and v_R_4_sGC;
vars v_R_DNO_sGC and v_R_DNO_sGC;
enddef;
def map between sGC and sGC_parameters for
vars kappa_R_1_sGC and kappa_R_1_sGC;
vars kappa_R_2_sGC and kappa_R_2_sGC;
vars kappa_R_3_sGC and kappa_R_3_sGC;
vars kappa_R_4_sGC and kappa_R_4_sGC;
vars kappa_R_DNO_sGC and kappa_R_DNO_sGC;
vars K_B and K_B;
vars K_NO and K_NO;
vars K_E6c and K_E6c;
vars K_E5c and K_E5c;
vars K_cGMP and K_cGMP;
vars K_NO_product and K_NO_product;
enddef;
def map between constants and sGC for
vars R and R;
 vars T and T;
enddef;
enddef;