- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2021-10-20 15:38:20+13:00
- Desc:
- Adding python solvers
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/700/rawfile/12fbc060fea3d9f9017ddf9c23f4e47a24d8a676/parameter_finder/BG_muscarinic_compositeTEMP.cellml.txt
def model FCU_composite 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 import using "LRGbinding_M2/BG_LRGbinding_M2.cellml" for
comp LRGbinding_M2 using comp LRGbinding_M2;
enddef;
def import using "GiProtein/BG_GiProtein.cellml" for
comp GiProtein using comp GiProtein;
enddef;
def comp BG_parameters as
var kappa_sig1_M2: fmol_per_sec {init: 3114.22, pub: out};
var kappa_sig2_M2: fmol_per_sec {init: 50.3536, pub: out};
var kappa_sig3_M2: fmol_per_sec {init: 10.6322, pub: out};
var kappa_sig4_M2: fmol_per_sec {init: 2.21912e+06, pub: out};
var kappa_act1_Gi: fmol_per_sec {init: 0.399172, pub: out};
var kappa_act2_Gi: fmol_per_sec {init: 0.000628818, pub: out};
var kappa_hyd_Gi: fmol_per_sec {init: 3.19289, pub: out};
var kappa_reassoc_Gi: fmol_per_sec {init: 1.60828e+06, pub: out};
var K_L_M2: per_fmol {init: 0.0561308, pub: out};
var K_R_M2: per_fmol {init: 0.0114466, pub: out};
var K_Gi: per_fmol {init: 41.2085, pub: out};
var K_LR_M2: per_fmol {init: 1.17774, pub: out};
var K_R_M2Gi: per_fmol {init: 177.204, pub: out};
var K_LR_M2Gi: per_fmol {init: 277.608, pub: out};
var K_aGi_GTP: per_fmol {init: 0.00773136, pub: out};
var K_beta_gamma_Gi: per_fmol {init: 0.000237095, pub: out};
var K_aGi_GDP: per_fmol {init: 0.00284638, pub: out};
var K_Pi: per_fmol {init: 8.75985e-05, pub: out};
enddef;
def comp environment as
var time: second;
var vol_myo: pL {init: 34.4, pub: out};
var freq: dimensionless {init: 500};
// stimulus
q_L_B1_init = sel
case sin(2{dimensionless}*freq*pi*time) > 0.5{dimensionless}:
1e-13{fmol};
otherwise:
1e-15{fmol};
endsel;
q_L_M2_init = sel
case cos(2{dimensionless}*freq*pi*time) > 0.5{dimensionless}:
1e-13{fmol};
otherwise:
1e-15{fmol};
endsel;
var q_L_M2_init: fmol {init: 1e-888};
var q_R_M2_init: fmol {init: 1e-888};
var q_Gi_init: fmol {init: 1e-888};
var q_LR_M2_init: fmol {init: 1e-888};
var q_R_M2Gi_init: fmol {init: 1e-888};
var q_LR_M2Gi_init: fmol {init: 1e-888};
var q_aGi_GTP_init: fmol {init: 1e-888};
var q_beta_gamma_Gi_init: fmol {init: 1e-888};
var q_aGi_GDP_init: fmol {init: 1e-888};
var q_Pi_init: fmol {init: 1e-888};
// Global value
var q_L_M2: fmol {pub: out};
var q_R_M2: fmol {pub: out};
var q_Gi: fmol {pub: out};
var q_LR_M2: fmol {pub: out};
var q_R_M2Gi: fmol {pub: out};
var q_LR_M2Gi: fmol {pub: out};
var q_aGi_GTP: fmol {pub: out};
var q_beta_gamma_Gi: fmol {pub: out};
var q_aGi_GDP: fmol {pub: out};
var q_Pi: fmol {pub: out};
// LRGbinding_M2 imports
var q_L_M2_mLRGbinding_M2: fmol {pub: in};
var q_R_M2_mLRGbinding_M2: fmol {pub: in};
var q_Gi_mLRGbinding_M2: fmol {pub: in};
var q_LR_M2_mLRGbinding_M2: fmol {pub: in};
var q_R_M2Gi_mLRGbinding_M2: fmol {pub: in};
var q_LR_M2Gi_mLRGbinding_M2: fmol {pub: in};
// GiProtein imports
var q_R_M2_mGiProtein: fmol {pub: in};
var q_Gi_mGiProtein: fmol {pub: in};
var q_R_M2Gi_mGiProtein: fmol {pub: in};
var q_LR_M2_mGiProtein: fmol {pub: in};
var q_LR_M2Gi_mGiProtein: fmol {pub: in};
var q_aGi_GTP_mGiProtein: fmol {pub: in};
var q_beta_gamma_Gi_mGiProtein: fmol {pub: in};
var q_aGi_GDP_mGiProtein: fmol {pub: in};
var q_Pi_mGiProtein: fmol {pub: in};
q_L_M2 = q_L_M2_init + q_L_M2_mLRGbinding_M2 ;
q_R_M2 = q_R_M2_init + q_R_M2_mLRGbinding_M2 + q_R_M2_mGiProtein ;
q_Gi = q_Gi_init + q_Gi_mLRGbinding_M2 + q_Gi_mGiProtein ;
q_LR_M2 = q_LR_M2_init + q_LR_M2_mLRGbinding_M2 + q_LR_M2_mGiProtein ;
q_R_M2Gi = q_R_M2Gi_init + q_R_M2Gi_mLRGbinding_M2 + q_R_M2Gi_mGiProtein ;
q_LR_M2Gi = q_LR_M2Gi_init + q_LR_M2Gi_mLRGbinding_M2 + q_LR_M2Gi_mGiProtein ;
q_aGi_GTP = q_aGi_GTP_init + q_aGi_GTP_mGiProtein ;
q_beta_gamma_Gi = q_beta_gamma_Gi_init + q_beta_gamma_Gi_mGiProtein ;
q_aGi_GDP = q_aGi_GDP_init + q_aGi_GDP_mGiProtein ;
q_Pi = q_Pi_init + q_Pi_mGiProtein ;
enddef;
def map between environment and LRGbinding_M2 for
vars time and time;
vars q_L_M2_mLRGbinding_M2 and q_L_M2;
vars q_L_M2 and q_L_M2_global;
vars q_R_M2_mLRGbinding_M2 and q_R_M2;
vars q_R_M2 and q_R_M2_global;
vars q_Gi_mLRGbinding_M2 and q_Gi;
vars q_Gi and q_Gi_global;
vars q_LR_M2_mLRGbinding_M2 and q_LR_M2;
vars q_LR_M2 and q_LR_M2_global;
vars q_R_M2Gi_mLRGbinding_M2 and q_R_M2Gi;
vars q_R_M2Gi and q_R_M2Gi_global;
vars q_LR_M2Gi_mLRGbinding_M2 and q_LR_M2Gi;
vars q_LR_M2Gi and q_LR_M2Gi_global;
enddef;
def map between environment and GiProtein for
vars time and time;
vars q_R_M2_mGiProtein and q_R_M2;
vars q_R_M2 and q_R_M2_global;
vars q_Gi_mGiProtein and q_Gi;
vars q_Gi and q_Gi_global;
vars q_R_M2Gi_mGiProtein and q_R_M2Gi;
vars q_R_M2Gi and q_R_M2Gi_global;
vars q_LR_M2_mGiProtein and q_LR_M2;
vars q_LR_M2 and q_LR_M2_global;
vars q_LR_M2Gi_mGiProtein and q_LR_M2Gi;
vars q_LR_M2Gi and q_LR_M2Gi_global;
vars q_aGi_GTP_mGiProtein and q_aGi_GTP;
vars q_aGi_GTP and q_aGi_GTP_global;
vars q_beta_gamma_Gi_mGiProtein and q_beta_gamma_Gi;
vars q_beta_gamma_Gi and q_beta_gamma_Gi_global;
vars q_aGi_GDP_mGiProtein and q_aGi_GDP;
vars q_aGi_GDP and q_aGi_GDP_global;
vars q_Pi_mGiProtein and q_Pi;
vars q_Pi and q_Pi_global;
enddef;
def map between BG_parameters and LRGbinding_M2 for
vars kappa_sig1_M2 and kappa_sig1_M2;
vars kappa_sig2_M2 and kappa_sig2_M2;
vars kappa_sig3_M2 and kappa_sig3_M2;
vars kappa_sig4_M2 and kappa_sig4_M2;
vars K_L_M2 and K_L_M2;
vars K_R_M2 and K_R_M2;
vars K_Gi and K_Gi;
vars K_LR_M2 and K_LR_M2;
vars K_R_M2Gi and K_R_M2Gi;
vars K_LR_M2Gi and K_LR_M2Gi;
enddef;
def map between BG_parameters and GiProtein for
vars kappa_act1_Gi and kappa_act1_Gi;
vars kappa_act2_Gi and kappa_act2_Gi;
vars kappa_hyd_Gi and kappa_hyd_Gi;
vars kappa_reassoc_Gi and kappa_reassoc_Gi;
vars K_R_M2 and K_R_M2;
vars K_Gi and K_Gi;
vars K_R_M2Gi and K_R_M2Gi;
vars K_LR_M2 and K_LR_M2;
vars K_LR_M2Gi and K_LR_M2Gi;
vars K_aGi_GTP and K_aGi_GTP;
vars K_beta_gamma_Gi and K_beta_gamma_Gi;
vars K_aGi_GDP and K_aGi_GDP;
vars K_Pi and K_Pi;
enddef;
def map between constants and LRGbinding_M2 for
vars R and R;
vars T and T;
enddef;
def map between constants and GiProtein for
vars R and R;
vars T and T;
enddef;
enddef;
