- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2022-05-16 09:58:52+12:00
- Desc:
- Fix tab/space in RST
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/860/rawfile/680764a384e9850b39d5b1521c67ac32a4364b2c/parameter_finder/output/TEMP.cellml.txt
def model FCU_guanylylCyclase 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 "HaiMurphy/BG_HaiMurphy.cellml" for
comp HaiMurphy using comp HaiMurphy;
enddef;
def import using "cGMP/BG_cGMP.cellml" for
comp cGMP using comp cGMP;
enddef;
def import using "sGC/BG_sGC.cellml" for
comp sGC using comp sGC;
enddef;
def comp BG_parameters as
var kappa_R_12: fmol_per_sec {init: 0.00829214, pub: out};
var kappa_R_34: fmol_per_sec {init: 36.9764, pub: out};
var kappa_R_56: fmol_per_sec {init: 0.149259, pub: out};
var kappa_R_78: fmol_per_sec {init: 0.0496283, pub: out};
var kappa_R_1a_cGMP: fmol_per_sec {init: 598.068, pub: out};
var kappa_R_1b_cGMP: fmol_per_sec {init: 0.0101911, pub: out};
var kappa_R_2a_cGMP: fmol_per_sec {init: 52461.9, pub: out};
var kappa_R_2b_cGMP: fmol_per_sec {init: 0.000511503, pub: out};
var kappa_R_1_sGC: fmol_per_sec {init: 275.976, pub: out};
var kappa_R_2_sGC: fmol_per_sec {init: 0.275976, pub: out};
var kappa_R_3_sGC: fmol_per_sec {init: 0.275976, pub: out};
var kappa_R_4_sGC: fmol_per_sec {init: 0.00413964, pub: out};
var kappa_R_DNO_sGC: fmol_per_sec {init: 6.66667e-06, pub: out};
var K_A: per_fmol {init: 0.926192, pub: out};
var K_M: per_fmol {init: 17.622, pub: out};
var K_Mp: per_fmol {init: 0.0525589, pub: out};
var K_AM: per_fmol {init: 0.906741, pub: out};
var K_AMp: per_fmol {init: 0.00270443, pub: out};
var K_Pi: per_fmol {init: 321.965, pub: out};
var K_Ca_i: per_fmol {init: 7.29529, pub: out};
var K_cGMP: per_fmol {init: 27.0801, pub: out};
var K_GTP: per_fmol {init: 461445, pub: out};
var K_E5c: per_fmol {init: 0.00362351, pub: out};
var K_PDE: per_fmol {init: 0.703891, pub: out};
var K_GTP_E5c: per_fmol {init: 1672.05, pub: out};
var K_cGMP_PDE: per_fmol {init: 38.1229, pub: out};
var K_GMP: per_fmol {init: 2.77745, pub: out};
var K_Eb: per_fmol {init: 0.241567, pub: out};
var K_NO: per_fmol {init: 1500, pub: out};
var K_E6c: per_fmol {init: 0.362351, pub: out};
var K_NO_product: per_fmol {init: 150, pub: out};
enddef;
def comp environment as
var t: second {pub: out};
var vol_myo: pL {init: 1, pub: out};
var freq: dimensionless {init: 500};
var q_A: fmol {init: 1e-888, pub: out};
var q_M: fmol {init: 1e-888, pub: out};
var q_Mp: fmol {init: 1e-888, pub: out};
var q_AM: fmol {init: 1e-888, pub: out};
var q_AMp: fmol {init: 1e-888, pub: out};
var q_Pi: fmol {init: 1e-888, pub: out};
var q_Ca_i: fmol {init: 1e-888, pub: out};
var q_cGMP: fmol {init: 1e-888, pub: out};
var q_GTP: fmol {init: 1e-888, pub: out};
var q_E5c: fmol {init: 1e-888, pub: out};
var q_PDE: fmol {init: 1e-888, pub: out};
var q_GTP_E5c: fmol {init: 1e-888, pub: out};
var q_cGMP_PDE: fmol {init: 1e-888, pub: out};
var q_GMP: fmol {init: 1e-888, pub: out};
var q_Eb: 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_NO_product: fmol {init: 1e-888, pub: out};
// HaiMurphy imports
var v_R_12: fmol_per_sec {pub: in};
var v_R_34: fmol_per_sec {pub: in};
var v_R_56: fmol_per_sec {pub: in};
var v_R_78: fmol_per_sec {pub: in};
// cGMP imports
var v_R_1a_cGMP: fmol_per_sec {pub: in};
var v_R_1b_cGMP: fmol_per_sec {pub: in};
var v_R_2a_cGMP: fmol_per_sec {pub: in};
var v_R_2b_cGMP: fmol_per_sec {pub: in};
// sGC imports
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_A, time) = + v_mHaiMurphy ;
ode(q_M, time) = + v_mHaiMurphy ;
ode(q_Mp, time) = + v_mHaiMurphy ;
ode(q_AM, time) = + v_mHaiMurphy ;
ode(q_AMp, time) = + v_mHaiMurphy ;
ode(q_Pi, time) = + v_mHaiMurphy ;
ode(q_Ca_i, time) = + v_mHaiMurphy ;
ode(q_cGMP, time) = + v_mHaiMurphy + v_mcGMP + v_msGC ;
ode(q_GTP, time) = + v_mcGMP ;
ode(q_E5c, time) = + v_mcGMP + v_msGC ;
ode(q_PDE, time) = + v_mcGMP ;
ode(q_GTP_E5c, time) = + v_mcGMP ;
ode(q_cGMP_PDE, time) = + v_mcGMP ;
ode(q_GMP, time) = + v_mcGMP ;
ode(q_Eb, time) = + v_msGC ;
ode(q_NO, time) = + v_msGC ;
ode(q_E6c, time) = + v_msGC ;
ode(q_NO_product, time) = + v_msGC ;
enddef;
def map between environment and HaiMurphy for
vars time and time;
vars q_A and q_A;
vars q_M and q_M;
vars q_Mp and q_Mp;
vars q_AM and q_AM;
vars q_AMp and q_AMp;
vars q_Pi and q_Pi;
vars q_Ca_i and q_Ca_i;
vars q_cGMP and q_cGMP;
vars v_R_12 and v_R_12;
vars v_R_34 and v_R_34;
vars v_R_56 and v_R_56;
vars v_R_78 and v_R_78;
vars q_mem and q_mem;
vars I_mem and q_mem_mHaiMurphy;
enddef;
def map between environment and cGMP for
vars time and time;
vars q_GTP and q_GTP;
vars q_E5c and q_E5c;
vars q_cGMP and q_cGMP;
vars q_PDE and q_PDE;
vars q_GTP_E5c and q_GTP_E5c;
vars q_cGMP_PDE and q_cGMP_PDE;
vars q_GMP and q_GMP;
vars v_R_1a_cGMP and v_R_1a_cGMP;
vars v_R_1b_cGMP and v_R_1b_cGMP;
vars v_R_2a_cGMP and v_R_2a_cGMP;
vars v_R_2b_cGMP and v_R_2b_cGMP;
vars q_mem and q_mem;
vars I_mem and q_mem_mcGMP;
enddef;
def map between environment and sGC for
vars time and time;
vars q_Eb and q_Eb;
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;
vars q_mem and q_mem;
vars I_mem and q_mem_msGC;
enddef;
def map between BG_parameters and HaiMurphy for
vars kappa_R_12 and kappa_R_12;
vars kappa_R_34 and kappa_R_34;
vars kappa_R_56 and kappa_R_56;
vars kappa_R_78 and kappa_R_78;
vars K_A and K_A;
vars K_M and K_M;
vars K_Mp and K_Mp;
vars K_AM and K_AM;
vars K_AMp and K_AMp;
vars K_Pi and K_Pi;
vars K_Ca_i and K_Ca_i;
vars K_cGMP and K_cGMP;
enddef;
def map between BG_parameters and cGMP for
vars kappa_R_1a_cGMP and kappa_R_1a_cGMP;
vars kappa_R_1b_cGMP and kappa_R_1b_cGMP;
vars kappa_R_2a_cGMP and kappa_R_2a_cGMP;
vars kappa_R_2b_cGMP and kappa_R_2b_cGMP;
vars K_GTP and K_GTP;
vars K_E5c and K_E5c;
vars K_cGMP and K_cGMP;
vars K_PDE and K_PDE;
vars K_GTP_E5c and K_GTP_E5c;
vars K_cGMP_PDE and K_cGMP_PDE;
vars K_GMP and K_GMP;
enddef;
def map between BG_parameters and sGC 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_Eb and K_Eb;
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 HaiMurphy for
vars R and R;
vars T and T;
enddef;
def map between constants and cGMP for
vars R and R;
vars T and T;
enddef;
def map between constants and sGC for
vars R and R;
vars T and T;
enddef;
enddef;
