Location: Kraeutler_Logic_Models @ 2d361c0a2cff / parameter_finder / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2021-12-20 15:33:22+13:00
Desc:
Removing wrong folder
Permanent Source URI:
http://models.cellml.org/workspace/7e8/rawfile/2d361c0a2cffe551fc9a01a53def99f0c9cd1a17/parameter_finder/TEMP.cellml.txt
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def model individual_KrToy 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-018};
var q_B_init: fmol {init: 1e-018};
var q_Ci_init: fmol {init: 1e-018};
var q_C_init: fmol {init: 1e-018};
var q_Di_init: fmol {init: 1e-018};
var q_D_init: fmol {init: 1e-018};
var q_Ei_init: fmol {init: 1e-018};
var q_E_init: fmol {init: 1e-018};
var q_ACi_init: fmol {init: 1e-018};
var q_ECi_init: fmol {init: 1e-018};
var q_BDi_init: fmol {init: 1e-018};
var q_CEi_init: fmol {init: 1e-018};
var q_E1_init: fmol {init: 1e-018};
var q_DE1_init: fmol {init: 1e-018};
// Global value
var q_A: fmol {pub: out};
var q_B: fmol {pub: out};
var q_Ci: fmol {pub: out};
var q_C: fmol {pub: out};
var q_Di: fmol {pub: out};
var q_D: fmol {pub: out};
var q_Ei: fmol {pub: out};
var q_E: fmol {pub: out};
var q_ACi: fmol {pub: out};
var q_ECi: fmol {pub: out};
var q_BDi: fmol {pub: out};
var q_CEi: fmol {pub: out};
var q_E1: fmol {pub: out};
var q_DE1: fmol {pub: out};
// From submodule
var q_A_mKrToy: fmol {pub: in};
var q_B_mKrToy: fmol {pub: in};
var q_Ci_mKrToy: fmol {pub: in};
var q_C_mKrToy: fmol {pub: in};
var q_Di_mKrToy: fmol {pub: in};
var q_D_mKrToy: fmol {pub: in};
var q_Ei_mKrToy: fmol {pub: in};
var q_E_mKrToy: fmol {pub: in};
var q_ACi_mKrToy: fmol {pub: in};
var q_ECi_mKrToy: fmol {pub: in};
var q_BDi_mKrToy: fmol {pub: in};
var q_CEi_mKrToy: fmol {pub: in};
var q_E1_mKrToy: fmol {pub: in};
var q_DE1_mKrToy: fmol {pub: in};
q_A = q_A_mKrToy + q_A_init;
q_B = q_B_mKrToy + q_B_init;
q_Ci = q_Ci_mKrToy + q_Ci_init;
q_C = q_C_mKrToy + q_C_init;
q_Di = q_Di_mKrToy + q_Di_init;
q_D = q_D_mKrToy + q_D_init;
q_Ei = q_Ei_mKrToy + q_Ei_init;
q_E = q_E_mKrToy + q_E_init;
q_ACi = q_ACi_mKrToy + q_ACi_init;
q_ECi = q_ECi_mKrToy + q_ECi_init;
q_BDi = q_BDi_mKrToy + q_BDi_init;
q_CEi = q_CEi_mKrToy + q_CEi_init;
q_E1 = q_E1_mKrToy + q_E1_init;
q_DE1 = q_DE1_mKrToy + q_DE1_init;
enddef;

def comp KrToy_parameters as
var kappa_Re_AC1: fmol_per_sec {init: 16102.9, pub: out};
var kappa_Re_AC2: fmol_per_sec {init: 0.0299955, pub: out};
var kappa_Re_EC1: fmol_per_sec {init: 15065.5, pub: out};
var kappa_Re_EC2: fmol_per_sec {init: 0.028063, pub: out};
var kappa_Re_BD1: fmol_per_sec {init: 17211.7, pub: out};
var kappa_Re_BD2: fmol_per_sec {init: 0.032061, pub: out};
var kappa_Re_AND_CE1: fmol_per_sec {init: 15065.5, pub: out};
var kappa_Re_AND_CE2: fmol_per_sec {init: 0.028063, pub: out};
var kappa_Re_AND_DE1: fmol_per_sec {init: 19663.8, pub: out};
var kappa_Re_AND_DE2: fmol_per_sec {init: 0.0366284, pub: out};
var K_A: per_fmol {init: 0.164205, pub: out};
var K_B: per_fmol {init: 0.200515, pub: out};
var K_Ci: per_fmol {init: 0.319591, pub: out};
var K_C: per_fmol {init: 0.319591, pub: out};
var K_Di: per_fmol {init: 0.244856, pub: out};
var K_D: per_fmol {init: 0.244856, pub: out};
var K_Ei: per_fmol {init: 0.175512, pub: out};
var K_E: per_fmol {init: 0.175512, pub: out};
var K_ACi: per_fmol {init: 2.48575, pub: out};
var K_ECi: per_fmol {init: 2.65692, pub: out};
var K_BDi: per_fmol {init: 2.32561, pub: out};
var K_CEi: per_fmol {init: 2.65692, pub: out};
var K_E1: per_fmol {init: 0.175512, pub: out};
var K_DE1: per_fmol {init: 2.03561, pub: out};
enddef;
def comp KrToy as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_Re_AC1: fmol_per_sec {pub: in};
var kappa_Re_AC2: fmol_per_sec {pub: in};
var kappa_Re_EC1: fmol_per_sec {pub: in};
var kappa_Re_EC2: fmol_per_sec {pub: in};
var kappa_Re_BD1: fmol_per_sec {pub: in};
var kappa_Re_BD2: fmol_per_sec {pub: in};
var kappa_Re_AND_CE1: fmol_per_sec {pub: in};
var kappa_Re_AND_CE2: fmol_per_sec {pub: in};
var kappa_Re_AND_DE1: fmol_per_sec {pub: in};
var kappa_Re_AND_DE2: fmol_per_sec {pub: in};
var K_A: per_fmol {pub: in};
var K_B: per_fmol {pub: in};
var K_Ci: per_fmol {pub: in};
var K_C: per_fmol {pub: in};
var K_Di: per_fmol {pub: in};
var K_D: per_fmol {pub: in};
var K_Ei: per_fmol {pub: in};
var K_E: per_fmol {pub: in};
var K_ACi: per_fmol {pub: in};
var K_ECi: per_fmol {pub: in};
var K_BDi: per_fmol {pub: in};
var K_CEi: per_fmol {pub: in};
var K_E1: per_fmol {pub: in};
var K_DE1: per_fmol {pub: in};
// Input from global environment
var q_A_global: fmol {pub: in};
var q_B_global: fmol {pub: in};
var q_Ci_global: fmol {pub: in};
var q_C_global: fmol {pub: in};
var q_Di_global: fmol {pub: in};
var q_D_global: fmol {pub: in};
var q_Ei_global: fmol {pub: in};
var q_E_global: fmol {pub: in};
var q_ACi_global: fmol {pub: in};
var q_ECi_global: fmol {pub: in};
var q_BDi_global: fmol {pub: in};
var q_CEi_global: fmol {pub: in};
var q_E1_global: fmol {pub: in};
var q_DE1_global: fmol {pub: in};
// Output to global environment
var q_A: fmol {init: 1e-16, pub: out};
var q_B: fmol {init: 1e-16, pub: out};
var q_Ci: fmol {init: 1e-16, pub: out};
var q_C: fmol {init: 1e-16, pub: out};
var q_Di: fmol {init: 1e-16, pub: out};
var q_D: fmol {init: 1e-16, pub: out};
var q_Ei: fmol {init: 1e-16, pub: out};
var q_E: fmol {init: 1e-16, pub: out};
var q_ACi: fmol {init: 1e-16, pub: out};
var q_ECi: fmol {init: 1e-16, pub: out};
var q_BDi: fmol {init: 1e-16, pub: out};
var q_CEi: fmol {init: 1e-16, pub: out};
var q_E1: fmol {init: 1e-16, pub: out};
var q_DE1: fmol {init: 1e-16, pub: out};
// Constitutive parameters
var mu_A: J_per_mol;
var mu_B: J_per_mol;
var mu_Ci: J_per_mol;
var mu_C: J_per_mol;
var mu_Di: J_per_mol;
var mu_D: J_per_mol;
var mu_Ei: J_per_mol;
var mu_E: J_per_mol;
var mu_ACi: J_per_mol;
var mu_ECi: J_per_mol;
var mu_BDi: J_per_mol;
var mu_CEi: J_per_mol;
var mu_E1: J_per_mol;
var mu_DE1: J_per_mol;
var v_Re_AC1: fmol_per_sec;
var v_Re_AC2: fmol_per_sec;
var v_Re_EC1: fmol_per_sec;
var v_Re_EC2: fmol_per_sec;
var v_Re_BD1: fmol_per_sec;
var v_Re_BD2: fmol_per_sec;
var v_Re_AND_CE1: fmol_per_sec;
var v_Re_AND_CE2: fmol_per_sec;
var v_Re_AND_DE1: fmol_per_sec;
var v_Re_AND_DE2: fmol_per_sec;
mu_A = R*T*ln(K_A*q_A_global);
mu_B = R*T*ln(K_B*q_B_global);
mu_Ci = R*T*ln(K_Ci*q_Ci_global);
mu_C = R*T*ln(K_C*q_C_global);
mu_Di = R*T*ln(K_Di*q_Di_global);
mu_D = R*T*ln(K_D*q_D_global);
mu_Ei = R*T*ln(K_Ei*q_Ei_global);
mu_E = R*T*ln(K_E*q_E_global);
mu_ACi = R*T*ln(K_ACi*q_ACi_global);
mu_ECi = R*T*ln(K_ECi*q_ECi_global);
mu_BDi = R*T*ln(K_BDi*q_BDi_global);
mu_CEi = R*T*ln(K_CEi*q_CEi_global);
mu_E1 = R*T*ln(K_E1*q_E1_global);
mu_DE1 = R*T*ln(K_DE1*q_DE1_global);
v_Re_AC1 = kappa_Re_AC1*(ppp);
v_Re_AC2 = kappa_Re_AC2*(ppp);
v_Re_EC1 = kappa_Re_EC1*(ppp);
v_Re_EC2 = kappa_Re_EC2*(ppp);
v_Re_BD1 = kappa_Re_BD1*(ppp);
v_Re_BD2 = kappa_Re_BD2*(ppp);
v_Re_AND_CE1 = kappa_Re_AND_CE1*(ppp);
v_Re_AND_CE2 = kappa_Re_AND_CE2*(ppp);
v_Re_AND_DE1 = kappa_Re_AND_DE1*(ppp);
v_Re_AND_DE2 = kappa_Re_AND_DE2*(ppp);
ode(q_A, time) = qqq;
ode(q_B, time) = qqq;
ode(q_Ci, time) = qqq;
ode(q_C, time) = qqq;
ode(q_Di, time) = qqq;
ode(q_D, time) = qqq;
ode(q_Ei, time) = qqq;
ode(q_E, time) = qqq;
ode(q_ACi, time) = qqq;
ode(q_ECi, time) = qqq;
ode(q_BDi, time) = qqq;
ode(q_CEi, time) = qqq;
ode(q_E1, time) = qqq;
ode(q_DE1, time) = qqq;
enddef;
def map between environment and KrToy for
vars time and time;
vars q_A_mKrToy and q_A;
vars q_A and q_A_global;
vars q_B_mKrToy and q_B;
vars q_B and q_B_global;
vars q_Ci_mKrToy and q_Ci;
vars q_Ci and q_Ci_global;
vars q_C_mKrToy and q_C;
vars q_C and q_C_global;
vars q_Di_mKrToy and q_Di;
vars q_Di and q_Di_global;
vars q_D_mKrToy and q_D;
vars q_D and q_D_global;
vars q_Ei_mKrToy and q_Ei;
vars q_Ei and q_Ei_global;
vars q_E_mKrToy and q_E;
vars q_E and q_E_global;
vars q_ACi_mKrToy and q_ACi;
vars q_ACi and q_ACi_global;
vars q_ECi_mKrToy and q_ECi;
vars q_ECi and q_ECi_global;
vars q_BDi_mKrToy and q_BDi;
vars q_BDi and q_BDi_global;
vars q_CEi_mKrToy and q_CEi;
vars q_CEi and q_CEi_global;
vars q_E1_mKrToy and q_E1;
vars q_E1 and q_E1_global;
vars q_DE1_mKrToy and q_DE1;
vars q_DE1 and q_DE1_global;
enddef;
def map between KrToy and KrToy_parameters for
vars kappa_Re_AC1 and kappa_Re_AC1;
vars kappa_Re_AC2 and kappa_Re_AC2;
vars kappa_Re_EC1 and kappa_Re_EC1;
vars kappa_Re_EC2 and kappa_Re_EC2;
vars kappa_Re_BD1 and kappa_Re_BD1;
vars kappa_Re_BD2 and kappa_Re_BD2;
vars kappa_Re_AND_CE1 and kappa_Re_AND_CE1;
vars kappa_Re_AND_CE2 and kappa_Re_AND_CE2;
vars kappa_Re_AND_DE1 and kappa_Re_AND_DE1;
vars kappa_Re_AND_DE2 and kappa_Re_AND_DE2;
vars K_A and K_A;
vars K_B and K_B;
vars K_Ci and K_Ci;
vars K_C and K_C;
vars K_Di and K_Di;
vars K_D and K_D;
vars K_Ei and K_Ei;
vars K_E and K_E;
vars K_ACi and K_ACi;
vars K_ECi and K_ECi;
vars K_BDi and K_BDi;
vars K_CEi and K_CEi;
vars K_E1 and K_E1;
vars K_DE1 and K_DE1;
enddef;
def map between constants and KrToy for
vars R and R;
 vars T and T;
enddef;
enddef;