Location: BG_cAMP @ fa9b0dc5a19a / parameter_finder / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-01-14 14:28:02+13:00
Desc:
fleshed rst
Permanent Source URI:
https://models.physiomeproject.org/workspace/674/rawfile/fa9b0dc5a19adca2aa290d3c3f402a045f3e576b/parameter_finder/TEMP.cellml.txt
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def model individual_cAMP 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_ATP_init: fmol {init: 1e-888};
var q_cAMP_init: fmol {init: 1e-888};
var q_AC_init: fmol {init: 1e-888};
var q_AC_ATP_init: fmol {init: 1e-888};
var q_a_Gs_GTP_AC_init: fmol {init: 1e-888};
var q_a_Gs_GTP_AC_ATP_init: fmol {init: 1e-888};
var q_FSK_AC_init: fmol {init: 1e-888};
var q_FSK_AC_ATP_init: fmol {init: 1e-888};
var q_PDE_init: fmol {init: 1e-888};
var q_PDE_cAMP_init: fmol {init: 1e-888};
var q_five_AMP_init: fmol {init: 1e-888};
var q_IBMX_init: fmol {init: 1e-888};
var q_PDEinh_init: fmol {init: 1e-888};
var q_a_Gs_GTP_init: fmol {init: 1e-888};
var q_FSK_init: fmol {init: 1e-888};
var q_a_Gi_GTP_init: fmol {init: 1e-888};
var q_ACinh_init: fmol {init: 1e-888};
var q_PPi_init: fmol {init: 1e-888};
// Global value
var q_ATP: fmol {pub: out};
var q_cAMP: fmol {pub: out};
var q_AC: fmol {pub: out};
var q_AC_ATP: fmol {pub: out};
var q_a_Gs_GTP_AC: fmol {pub: out};
var q_a_Gs_GTP_AC_ATP: fmol {pub: out};
var q_FSK_AC: fmol {pub: out};
var q_FSK_AC_ATP: fmol {pub: out};
var q_PDE: fmol {pub: out};
var q_PDE_cAMP: fmol {pub: out};
var q_five_AMP: fmol {pub: out};
var q_IBMX: fmol {pub: out};
var q_PDEinh: fmol {pub: out};
var q_a_Gs_GTP: fmol {pub: out};
var q_FSK: fmol {pub: out};
var q_a_Gi_GTP: fmol {pub: out};
var q_ACinh: fmol {pub: out};
var q_PPi: fmol {pub: out};
// From submodule
var q_ATP_mcAMP: fmol {pub: in};
var q_cAMP_mcAMP: fmol {pub: in};
var q_AC_mcAMP: fmol {pub: in};
var q_AC_ATP_mcAMP: fmol {pub: in};
var q_a_Gs_GTP_AC_mcAMP: fmol {pub: in};
var q_a_Gs_GTP_AC_ATP_mcAMP: fmol {pub: in};
var q_FSK_AC_mcAMP: fmol {pub: in};
var q_FSK_AC_ATP_mcAMP: fmol {pub: in};
var q_PDE_mcAMP: fmol {pub: in};
var q_PDE_cAMP_mcAMP: fmol {pub: in};
var q_five_AMP_mcAMP: fmol {pub: in};
var q_IBMX_mcAMP: fmol {pub: in};
var q_PDEinh_mcAMP: fmol {pub: in};
var q_a_Gs_GTP_mcAMP: fmol {pub: in};
var q_FSK_mcAMP: fmol {pub: in};
var q_a_Gi_GTP_mcAMP: fmol {pub: in};
var q_ACinh_mcAMP: fmol {pub: in};
var q_PPi_mcAMP: fmol {pub: in};
q_ATP = q_ATP_mcAMP + q_ATP_init;
q_cAMP = q_cAMP_mcAMP + q_cAMP_init;
q_AC = q_AC_mcAMP + q_AC_init;
q_AC_ATP = q_AC_ATP_mcAMP + q_AC_ATP_init;
q_a_Gs_GTP_AC = q_a_Gs_GTP_AC_mcAMP + q_a_Gs_GTP_AC_init;
q_a_Gs_GTP_AC_ATP = q_a_Gs_GTP_AC_ATP_mcAMP + q_a_Gs_GTP_AC_ATP_init;
q_FSK_AC = q_FSK_AC_mcAMP + q_FSK_AC_init;
q_FSK_AC_ATP = q_FSK_AC_ATP_mcAMP + q_FSK_AC_ATP_init;
q_PDE = q_PDE_mcAMP + q_PDE_init;
q_PDE_cAMP = q_PDE_cAMP_mcAMP + q_PDE_cAMP_init;
q_five_AMP = q_five_AMP_mcAMP + q_five_AMP_init;
q_IBMX = q_IBMX_mcAMP + q_IBMX_init;
q_PDEinh = q_PDEinh_mcAMP + q_PDEinh_init;
q_a_Gs_GTP = q_a_Gs_GTP_mcAMP + q_a_Gs_GTP_init;
q_FSK = q_FSK_mcAMP + q_FSK_init;
q_a_Gi_GTP = q_a_Gi_GTP_mcAMP + q_a_Gi_GTP_init;
q_ACinh = q_ACinh_mcAMP + q_ACinh_init;
q_PPi = q_PPi_mcAMP + q_PPi_init;
enddef;

def comp cAMP_parameters as
var kappa_1a: fmol_per_sec {init: 9.47329e+06, pub: out};
var kappa_1b: fmol_per_sec {init: 0.00197793, pub: out};
var kappa_2a: fmol_per_sec {init: 176000, pub: out};
var kappa_2b: fmol_per_sec {init: 0.047492, pub: out};
var kappa_3a: fmol_per_sec {init: 5.07667e+08, pub: out};
var kappa_3b: fmol_per_sec {init: 5.9031e-17, pub: out};
var kappa_4a: fmol_per_sec {init: 36084.5, pub: out};
var kappa_4b: fmol_per_sec {init: 0.138787, pub: out};
var kappa_5: fmol_per_sec {init: 751.564, pub: out};
var kappa_6: fmol_per_sec {init: 556.617, pub: out};
var kappa_7: fmol_per_sec {init: 160555, pub: out};
var kappa_GiAC: fmol_per_sec {init: 685.521, pub: out};
var K_ATP: per_fmol {init: 9.19362e-06, pub: out};
var K_cAMP: per_fmol {init: 0.0102598, pub: out};
var K_AC: per_fmol {init: 9.02358, pub: out};
var K_AC_ATP: per_fmol {init: 2.93942, pub: out};
var K_a_Gs_GTP_AC: per_fmol {init: 52.2258, pub: out};
var K_a_Gs_GTP_AC_ATP: per_fmol {init: 5.20284, pub: out};
var K_FSK_AC: per_fmol {init: 0.181058, pub: out};
var K_FSK_AC_ATP: per_fmol {init: 0.0492449, pub: out};
var K_PDE: per_fmol {init: 2.28256, pub: out};
var K_PDE_cAMP: per_fmol {init: 1.04728, pub: out};
var K_five_AMP: per_fmol {init: 0.0102598, pub: out};
var K_IBMX: per_fmol {init: 0.01642, pub: out};
var K_PDEinh: per_fmol {init: 38.679, pub: out};
var K_a_Gs_GTP: per_fmol {init: 0.420618, pub: out};
var K_FSK: per_fmol {init: 1.32565e-05, pub: out};
var K_a_Gi_GTP: per_fmol {init: 0.013661, pub: out};
var K_ACinh: per_fmol {init: 42.4053, pub: out};
var K_PPi: per_fmol {init: 2.60488e-05, pub: out};
enddef;
def comp cAMP as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_1a: fmol_per_sec {pub: in};
var kappa_1b: fmol_per_sec {pub: in};
var kappa_2a: fmol_per_sec {pub: in};
var kappa_2b: fmol_per_sec {pub: in};
var kappa_3a: fmol_per_sec {pub: in};
var kappa_3b: fmol_per_sec {pub: in};
var kappa_4a: fmol_per_sec {pub: in};
var kappa_4b: fmol_per_sec {pub: in};
var kappa_5: fmol_per_sec {pub: in};
var kappa_6: fmol_per_sec {pub: in};
var kappa_7: fmol_per_sec {pub: in};
var kappa_GiAC: fmol_per_sec {pub: in};
var K_ATP: per_fmol {pub: in};
var K_cAMP: per_fmol {pub: in};
var K_AC: per_fmol {pub: in};
var K_AC_ATP: per_fmol {pub: in};
var K_a_Gs_GTP_AC: per_fmol {pub: in};
var K_a_Gs_GTP_AC_ATP: per_fmol {pub: in};
var K_FSK_AC: per_fmol {pub: in};
var K_FSK_AC_ATP: per_fmol {pub: in};
var K_PDE: per_fmol {pub: in};
var K_PDE_cAMP: per_fmol {pub: in};
var K_five_AMP: per_fmol {pub: in};
var K_IBMX: per_fmol {pub: in};
var K_PDEinh: per_fmol {pub: in};
var K_a_Gs_GTP: per_fmol {pub: in};
var K_FSK: per_fmol {pub: in};
var K_a_Gi_GTP: per_fmol {pub: in};
var K_ACinh: per_fmol {pub: in};
var K_PPi: per_fmol {pub: in};
// Input from global environment
var q_ATP_global: fmol {pub: in};
var q_cAMP_global: fmol {pub: in};
var q_AC_global: fmol {pub: in};
var q_AC_ATP_global: fmol {pub: in};
var q_a_Gs_GTP_AC_global: fmol {pub: in};
var q_a_Gs_GTP_AC_ATP_global: fmol {pub: in};
var q_FSK_AC_global: fmol {pub: in};
var q_FSK_AC_ATP_global: fmol {pub: in};
var q_PDE_global: fmol {pub: in};
var q_PDE_cAMP_global: fmol {pub: in};
var q_five_AMP_global: fmol {pub: in};
var q_IBMX_global: fmol {pub: in};
var q_PDEinh_global: fmol {pub: in};
var q_a_Gs_GTP_global: fmol {pub: in};
var q_FSK_global: fmol {pub: in};
var q_a_Gi_GTP_global: fmol {pub: in};
var q_ACinh_global: fmol {pub: in};
var q_PPi_global: fmol {pub: in};
// Output to global environment
var q_ATP: fmol {init: 1e-16, pub: out};
var q_cAMP: fmol {init: 1e-16, pub: out};
var q_AC: fmol {init: 1e-16, pub: out};
var q_AC_ATP: fmol {init: 1e-16, pub: out};
var q_a_Gs_GTP_AC: fmol {init: 1e-16, pub: out};
var q_a_Gs_GTP_AC_ATP: fmol {init: 1e-16, pub: out};
var q_FSK_AC: fmol {init: 1e-16, pub: out};
var q_FSK_AC_ATP: fmol {init: 1e-16, pub: out};
var q_PDE: fmol {init: 1e-16, pub: out};
var q_PDE_cAMP: fmol {init: 1e-16, pub: out};
var q_five_AMP: fmol {init: 1e-16, pub: out};
var q_IBMX: fmol {init: 1e-16, pub: out};
var q_PDEinh: fmol {init: 1e-16, pub: out};
var q_a_Gs_GTP: fmol {init: 1e-16, pub: out};
var q_FSK: fmol {init: 1e-16, pub: out};
var q_a_Gi_GTP: fmol {init: 1e-16, pub: out};
var q_ACinh: fmol {init: 1e-16, pub: out};
var q_PPi: fmol {init: 1e-16, pub: out};
// Constitutive parameters
var mu_ATP: J_per_mol;
var mu_cAMP: J_per_mol;
var mu_AC: J_per_mol;
var mu_AC_ATP: J_per_mol;
var mu_a_Gs_GTP_AC: J_per_mol;
var mu_a_Gs_GTP_AC_ATP: J_per_mol;
var mu_FSK_AC: J_per_mol;
var mu_FSK_AC_ATP: J_per_mol;
var mu_PDE: J_per_mol;
var mu_PDE_cAMP: J_per_mol;
var mu_five_AMP: J_per_mol;
var mu_IBMX: J_per_mol;
var mu_PDEinh: J_per_mol;
var mu_a_Gs_GTP: J_per_mol;
var mu_FSK: J_per_mol;
var mu_a_Gi_GTP: J_per_mol;
var mu_ACinh: J_per_mol;
var mu_PPi: J_per_mol;
var v_1a: fmol_per_sec;
var v_1b: fmol_per_sec;
var v_2a: fmol_per_sec;
var v_2b: fmol_per_sec;
var v_3a: fmol_per_sec;
var v_3b: fmol_per_sec;
var v_4a: fmol_per_sec;
var v_4b: fmol_per_sec;
var v_5: fmol_per_sec;
var v_6: fmol_per_sec;
var v_7: fmol_per_sec;
var v_GiAC: fmol_per_sec;
mu_ATP = R*T*ln(K_ATP*q_ATP_global);
mu_cAMP = R*T*ln(K_cAMP*q_cAMP_global);
mu_AC = R*T*ln(K_AC*q_AC_global);
mu_AC_ATP = R*T*ln(K_AC_ATP*q_AC_ATP_global);
mu_a_Gs_GTP_AC = R*T*ln(K_a_Gs_GTP_AC*q_a_Gs_GTP_AC_global);
mu_a_Gs_GTP_AC_ATP = R*T*ln(K_a_Gs_GTP_AC_ATP*q_a_Gs_GTP_AC_ATP_global);
mu_FSK_AC = R*T*ln(K_FSK_AC*q_FSK_AC_global);
mu_FSK_AC_ATP = R*T*ln(K_FSK_AC_ATP*q_FSK_AC_ATP_global);
mu_PDE = R*T*ln(K_PDE*q_PDE_global);
mu_PDE_cAMP = R*T*ln(K_PDE_cAMP*q_PDE_cAMP_global);
mu_five_AMP = R*T*ln(K_five_AMP*q_five_AMP_global);
mu_IBMX = R*T*ln(K_IBMX*q_IBMX_global);
mu_PDEinh = R*T*ln(K_PDEinh*q_PDEinh_global);
mu_a_Gs_GTP = R*T*ln(K_a_Gs_GTP*q_a_Gs_GTP_global);
mu_FSK = R*T*ln(K_FSK*q_FSK_global);
mu_a_Gi_GTP = R*T*ln(K_a_Gi_GTP*q_a_Gi_GTP_global);
mu_ACinh = R*T*ln(K_ACinh*q_ACinh_global);
mu_PPi = R*T*ln(K_PPi*q_PPi_global);
v_1a = ppp;
v_1b = ppp;
v_2a = ppp;
v_2b = ppp;
v_3a = ppp;
v_3b = ppp;
v_4a = ppp;
v_4b = ppp;
v_5 = ppp;
v_6 = ppp;
v_7 = ppp;
v_GiAC = ppp;
ode(q_ATP, time) = qqq;
ode(q_cAMP, time) = qqq;
ode(q_AC, time) = qqq;
ode(q_AC_ATP, time) = qqq;
ode(q_a_Gs_GTP_AC, time) = qqq;
ode(q_a_Gs_GTP_AC_ATP, time) = qqq;
ode(q_FSK_AC, time) = qqq;
ode(q_FSK_AC_ATP, time) = qqq;
ode(q_PDE, time) = qqq;
ode(q_PDE_cAMP, time) = qqq;
ode(q_five_AMP, time) = qqq;
ode(q_IBMX, time) = qqq;
ode(q_PDEinh, time) = qqq;
ode(q_a_Gs_GTP, time) = qqq;
ode(q_FSK, time) = qqq;
ode(q_a_Gi_GTP, time) = qqq;
ode(q_ACinh, time) = qqq;
ode(q_PPi, time) = qqq;
enddef;
def map between environment and cAMP for
vars time and time;
vars q_ATP_mcAMP and q_ATP;
vars q_ATP and q_ATP_global;
vars q_cAMP_mcAMP and q_cAMP;
vars q_cAMP and q_cAMP_global;
vars q_AC_mcAMP and q_AC;
vars q_AC and q_AC_global;
vars q_AC_ATP_mcAMP and q_AC_ATP;
vars q_AC_ATP and q_AC_ATP_global;
vars q_a_Gs_GTP_AC_mcAMP and q_a_Gs_GTP_AC;
vars q_a_Gs_GTP_AC and q_a_Gs_GTP_AC_global;
vars q_a_Gs_GTP_AC_ATP_mcAMP and q_a_Gs_GTP_AC_ATP;
vars q_a_Gs_GTP_AC_ATP and q_a_Gs_GTP_AC_ATP_global;
vars q_FSK_AC_mcAMP and q_FSK_AC;
vars q_FSK_AC and q_FSK_AC_global;
vars q_FSK_AC_ATP_mcAMP and q_FSK_AC_ATP;
vars q_FSK_AC_ATP and q_FSK_AC_ATP_global;
vars q_PDE_mcAMP and q_PDE;
vars q_PDE and q_PDE_global;
vars q_PDE_cAMP_mcAMP and q_PDE_cAMP;
vars q_PDE_cAMP and q_PDE_cAMP_global;
vars q_five_AMP_mcAMP and q_five_AMP;
vars q_five_AMP and q_five_AMP_global;
vars q_IBMX_mcAMP and q_IBMX;
vars q_IBMX and q_IBMX_global;
vars q_PDEinh_mcAMP and q_PDEinh;
vars q_PDEinh and q_PDEinh_global;
vars q_a_Gs_GTP_mcAMP and q_a_Gs_GTP;
vars q_a_Gs_GTP and q_a_Gs_GTP_global;
vars q_FSK_mcAMP and q_FSK;
vars q_FSK and q_FSK_global;
vars q_a_Gi_GTP_mcAMP and q_a_Gi_GTP;
vars q_a_Gi_GTP and q_a_Gi_GTP_global;
vars q_ACinh_mcAMP and q_ACinh;
vars q_ACinh and q_ACinh_global;
vars q_PPi_mcAMP and q_PPi;
vars q_PPi and q_PPi_global;
enddef;
def map between cAMP and cAMP_parameters for
vars kappa_1a and kappa_1a;
vars kappa_1b and kappa_1b;
vars kappa_2a and kappa_2a;
vars kappa_2b and kappa_2b;
vars kappa_3a and kappa_3a;
vars kappa_3b and kappa_3b;
vars kappa_4a and kappa_4a;
vars kappa_4b and kappa_4b;
vars kappa_5 and kappa_5;
vars kappa_6 and kappa_6;
vars kappa_7 and kappa_7;
vars kappa_GiAC and kappa_GiAC;
vars K_ATP and K_ATP;
vars K_cAMP and K_cAMP;
vars K_AC and K_AC;
vars K_AC_ATP and K_AC_ATP;
vars K_a_Gs_GTP_AC and K_a_Gs_GTP_AC;
vars K_a_Gs_GTP_AC_ATP and K_a_Gs_GTP_AC_ATP;
vars K_FSK_AC and K_FSK_AC;
vars K_FSK_AC_ATP and K_FSK_AC_ATP;
vars K_PDE and K_PDE;
vars K_PDE_cAMP and K_PDE_cAMP;
vars K_five_AMP and K_five_AMP;
vars K_IBMX and K_IBMX;
vars K_PDEinh and K_PDEinh;
vars K_a_Gs_GTP and K_a_Gs_GTP;
vars K_FSK and K_FSK;
vars K_a_Gi_GTP and K_a_Gi_GTP;
vars K_ACinh and K_ACinh;
vars K_PPi and K_PPi;
enddef;
def map between constants and cAMP for
vars R and R;
 vars T and T;
enddef;
enddef;