- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2024-11-13 11:18:14+13:00
- Desc:
- Updating cellml and sedml
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/891/rawfile/0e12b0f14ccd4923dc8b6f7fd13ba9f3b0ca1d20/parameter_finder/output/TEMP.cellml.txt
def model individual_LCC_diadic 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_Ca_D: fmol {init: 1e-888, pub: out};
var q_Ca_o: fmol {init: 1e-888, pub: out};
var q_000_LCC: fmol {init: 1e-888, pub: out};
var q_010_LCC: fmol {init: 1e-888, pub: out};
var q_020_LCC: fmol {init: 1e-888, pub: out};
var q_100_LCC: fmol {init: 1e-888, pub: out};
var q_110_LCC: fmol {init: 1e-888, pub: out};
var q_120_LCC: fmol {init: 1e-888, pub: out};
var q_001_LCC: fmol {init: 1e-888, pub: out};
var q_011_LCC: fmol {init: 1e-888, pub: out};
var q_021_LCC: fmol {init: 1e-888, pub: out};
var q_101_LCC: fmol {init: 1e-888, pub: out};
var q_111_LCC: fmol {init: 1e-888, pub: out};
var q_121_LCC: fmol {init: 1e-888, pub: out};
// From submodule
var v_LCC_Ca1: fmol_per_sec {pub: in};
var v_LCC_Ca2: fmol_per_sec {pub: in};
var v_d000: fmol_per_sec {pub: in};
var v_d010: fmol_per_sec {pub: in};
var v_d020: fmol_per_sec {pub: in};
var v_d001: fmol_per_sec {pub: in};
var v_d011: fmol_per_sec {pub: in};
var v_d021: fmol_per_sec {pub: in};
var v_f1_000: fmol_per_sec {pub: in};
var v_f1_100: fmol_per_sec {pub: in};
var v_f1_001: fmol_per_sec {pub: in};
var v_f1_101: fmol_per_sec {pub: in};
var v_f2_000: fmol_per_sec {pub: in};
var v_f2_100: fmol_per_sec {pub: in};
var v_f2_001: fmol_per_sec {pub: in};
var v_f2_101: fmol_per_sec {pub: in};
var v_f3_010: fmol_per_sec {pub: in};
var v_f3_110: fmol_per_sec {pub: in};
var v_f3_011: fmol_per_sec {pub: in};
var v_f3_111: fmol_per_sec {pub: in};
var v_fCa000: fmol_per_sec {pub: in};
var v_fCa100: fmol_per_sec {pub: in};
var v_fCa010: fmol_per_sec {pub: in};
var v_fCa110: fmol_per_sec {pub: in};
var v_fCa020: fmol_per_sec {pub: in};
var v_fCa120: fmol_per_sec {pub: in};
ode(q_Ca_D, time) = vvv;
ode(q_Ca_o, time) = vvv;
ode(q_000_LCC, time) = vvv;
ode(q_010_LCC, time) = vvv;
ode(q_020_LCC, time) = vvv;
ode(q_100_LCC, time) = vvv;
ode(q_110_LCC, time) = vvv;
ode(q_120_LCC, time) = vvv;
ode(q_001_LCC, time) = vvv;
ode(q_011_LCC, time) = vvv;
ode(q_021_LCC, time) = vvv;
ode(q_101_LCC, time) = vvv;
ode(q_111_LCC, time) = vvv;
ode(q_121_LCC, time) = vvv;
enddef;
def comp LCC_diadic_parameters as
var kappa_LCC_Ca1: fmol_per_sec {init: 60.4388, pub: out};
var kappa_LCC_Ca2: fmol_per_sec {init: 79.5763, pub: out};
var kappa_d000: fmol_per_sec {init: 52.6837, pub: out};
var kappa_d010: fmol_per_sec {init: 2.66052, pub: out};
var kappa_d020: fmol_per_sec {init: 3.50295, pub: out};
var kappa_d001: fmol_per_sec {init: 0.246334, pub: out};
var kappa_d011: fmol_per_sec {init: 0.0124398, pub: out};
var kappa_d021: fmol_per_sec {init: 0.0163788, pub: out};
var kappa_f1_000: fmol_per_sec {init: 5.07473, pub: out};
var kappa_f1_100: fmol_per_sec {init: 25.1998, pub: out};
var kappa_f1_001: fmol_per_sec {init: 0.023728, pub: out};
var kappa_f1_101: fmol_per_sec {init: 0.117827, pub: out};
var kappa_f2_000: fmol_per_sec {init: 0.329839, pub: out};
var kappa_f2_100: fmol_per_sec {init: 1.6379, pub: out};
var kappa_f2_001: fmol_per_sec {init: 0.00154223, pub: out};
var kappa_f2_101: fmol_per_sec {init: 0.00765834, pub: out};
var kappa_f3_010: fmol_per_sec {init: 719.643, pub: out};
var kappa_f3_110: fmol_per_sec {init: 3573.57, pub: out};
var kappa_f3_011: fmol_per_sec {init: 3.36484, pub: out};
var kappa_f3_111: fmol_per_sec {init: 16.709, pub: out};
var kappa_fCa000: fmol_per_sec {init: 84344.4, pub: out};
var kappa_fCa100: fmol_per_sec {init: 418833, pub: out};
var kappa_fCa010: fmol_per_sec {init: 4259.38, pub: out};
var kappa_fCa110: fmol_per_sec {init: 21151, pub: out};
var kappa_fCa020: fmol_per_sec {init: 5608.07, pub: out};
var kappa_fCa120: fmol_per_sec {init: 27848.3, pub: out};
var K_Ca_D: per_fmol {init: 141.171, pub: out};
var K_Ca_o: per_fmol {init: 0.069128, pub: out};
var K_000_LCC: per_fmol {init: 9.23933, pub: out};
var K_010_LCC: per_fmol {init: 182.958, pub: out};
var K_020_LCC: per_fmol {init: 138.958, pub: out};
var K_100_LCC: per_fmol {init: 1.86061, pub: out};
var K_110_LCC: per_fmol {init: 36.8439, pub: out};
var K_120_LCC: per_fmol {init: 27.9833, pub: out};
var K_001_LCC: per_fmol {init: 1976.03, pub: out};
var K_011_LCC: per_fmol {init: 39129.4, pub: out};
var K_021_LCC: per_fmol {init: 29719.1, pub: out};
var K_101_LCC: per_fmol {init: 397.931, pub: out};
var K_111_LCC: per_fmol {init: 7879.85, pub: out};
var K_121_LCC: per_fmol {init: 5984.81, pub: out};
enddef;
def comp LCC_diadic as
var time: second {pub: in};
var R: J_per_K_per_mol {pub: in};
var T: kelvin {pub: in};
// parameters
var kappa_LCC_Ca1: fmol_per_sec {pub: in};
var kappa_LCC_Ca2: fmol_per_sec {pub: in};
var kappa_d000: fmol_per_sec {pub: in};
var kappa_d010: fmol_per_sec {pub: in};
var kappa_d020: fmol_per_sec {pub: in};
var kappa_d001: fmol_per_sec {pub: in};
var kappa_d011: fmol_per_sec {pub: in};
var kappa_d021: fmol_per_sec {pub: in};
var kappa_f1_000: fmol_per_sec {pub: in};
var kappa_f1_100: fmol_per_sec {pub: in};
var kappa_f1_001: fmol_per_sec {pub: in};
var kappa_f1_101: fmol_per_sec {pub: in};
var kappa_f2_000: fmol_per_sec {pub: in};
var kappa_f2_100: fmol_per_sec {pub: in};
var kappa_f2_001: fmol_per_sec {pub: in};
var kappa_f2_101: fmol_per_sec {pub: in};
var kappa_f3_010: fmol_per_sec {pub: in};
var kappa_f3_110: fmol_per_sec {pub: in};
var kappa_f3_011: fmol_per_sec {pub: in};
var kappa_f3_111: fmol_per_sec {pub: in};
var kappa_fCa000: fmol_per_sec {pub: in};
var kappa_fCa100: fmol_per_sec {pub: in};
var kappa_fCa010: fmol_per_sec {pub: in};
var kappa_fCa110: fmol_per_sec {pub: in};
var kappa_fCa020: fmol_per_sec {pub: in};
var kappa_fCa120: fmol_per_sec {pub: in};
var K_Ca_D: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
var K_000_LCC: per_fmol {pub: in};
var K_010_LCC: per_fmol {pub: in};
var K_020_LCC: per_fmol {pub: in};
var K_100_LCC: per_fmol {pub: in};
var K_110_LCC: per_fmol {pub: in};
var K_120_LCC: per_fmol {pub: in};
var K_001_LCC: per_fmol {pub: in};
var K_011_LCC: per_fmol {pub: in};
var K_021_LCC: per_fmol {pub: in};
var K_101_LCC: per_fmol {pub: in};
var K_111_LCC: per_fmol {pub: in};
var K_121_LCC: per_fmol {pub: in};
// Input from global environment
var q_Ca_D: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
var q_000_LCC: fmol {pub: in};
var q_010_LCC: fmol {pub: in};
var q_020_LCC: fmol {pub: in};
var q_100_LCC: fmol {pub: in};
var q_110_LCC: fmol {pub: in};
var q_120_LCC: fmol {pub: in};
var q_001_LCC: fmol {pub: in};
var q_011_LCC: fmol {pub: in};
var q_021_LCC: fmol {pub: in};
var q_101_LCC: fmol {pub: in};
var q_111_LCC: fmol {pub: in};
var q_121_LCC: fmol {pub: in};
// Constitutive parameters
var mu_Ca_D: J_per_mol;
var mu_Ca_o: J_per_mol;
var mu_000_LCC: J_per_mol;
var mu_010_LCC: J_per_mol;
var mu_020_LCC: J_per_mol;
var mu_100_LCC: J_per_mol;
var mu_110_LCC: J_per_mol;
var mu_120_LCC: J_per_mol;
var mu_001_LCC: J_per_mol;
var mu_011_LCC: J_per_mol;
var mu_021_LCC: J_per_mol;
var mu_101_LCC: J_per_mol;
var mu_111_LCC: J_per_mol;
var mu_121_LCC: J_per_mol;
var v_LCC_Ca1: fmol_per_sec {pub: out};
var v_LCC_Ca2: fmol_per_sec {pub: out};
var v_d000: fmol_per_sec {pub: out};
var v_d010: fmol_per_sec {pub: out};
var v_d020: fmol_per_sec {pub: out};
var v_d001: fmol_per_sec {pub: out};
var v_d011: fmol_per_sec {pub: out};
var v_d021: fmol_per_sec {pub: out};
var v_f1_000: fmol_per_sec {pub: out};
var v_f1_100: fmol_per_sec {pub: out};
var v_f1_001: fmol_per_sec {pub: out};
var v_f1_101: fmol_per_sec {pub: out};
var v_f2_000: fmol_per_sec {pub: out};
var v_f2_100: fmol_per_sec {pub: out};
var v_f2_001: fmol_per_sec {pub: out};
var v_f2_101: fmol_per_sec {pub: out};
var v_f3_010: fmol_per_sec {pub: out};
var v_f3_110: fmol_per_sec {pub: out};
var v_f3_011: fmol_per_sec {pub: out};
var v_f3_111: fmol_per_sec {pub: out};
var v_fCa000: fmol_per_sec {pub: out};
var v_fCa100: fmol_per_sec {pub: out};
var v_fCa010: fmol_per_sec {pub: out};
var v_fCa110: fmol_per_sec {pub: out};
var v_fCa020: fmol_per_sec {pub: out};
var v_fCa120: fmol_per_sec {pub: out};
mu_Ca_D = R*T*ln(K_Ca_D*q_Ca_D);
mu_Ca_o = R*T*ln(K_Ca_o*q_Ca_o);
mu_000_LCC = R*T*ln(K_000_LCC*q_000_LCC);
mu_010_LCC = R*T*ln(K_010_LCC*q_010_LCC);
mu_020_LCC = R*T*ln(K_020_LCC*q_020_LCC);
mu_100_LCC = R*T*ln(K_100_LCC*q_100_LCC);
mu_110_LCC = R*T*ln(K_110_LCC*q_110_LCC);
mu_120_LCC = R*T*ln(K_120_LCC*q_120_LCC);
mu_001_LCC = R*T*ln(K_001_LCC*q_001_LCC);
mu_011_LCC = R*T*ln(K_011_LCC*q_011_LCC);
mu_021_LCC = R*T*ln(K_021_LCC*q_021_LCC);
mu_101_LCC = R*T*ln(K_101_LCC*q_101_LCC);
mu_111_LCC = R*T*ln(K_111_LCC*q_111_LCC);
mu_121_LCC = R*T*ln(K_121_LCC*q_121_LCC);
v_LCC_Ca1 = ppp;
v_LCC_Ca2 = ppp;
v_d000 = ppp;
v_d010 = ppp;
v_d020 = ppp;
v_d001 = ppp;
v_d011 = ppp;
v_d021 = ppp;
v_f1_000 = ppp;
v_f1_100 = ppp;
v_f1_001 = ppp;
v_f1_101 = ppp;
v_f2_000 = ppp;
v_f2_100 = ppp;
v_f2_001 = ppp;
v_f2_101 = ppp;
v_f3_010 = ppp;
v_f3_110 = ppp;
v_f3_011 = ppp;
v_f3_111 = ppp;
v_fCa000 = ppp;
v_fCa100 = ppp;
v_fCa010 = ppp;
v_fCa110 = ppp;
v_fCa020 = ppp;
v_fCa120 = ppp;
enddef;
def map between environment and LCC_diadic for
vars time and time;
vars q_Ca_D and q_Ca_D;
vars q_Ca_o and q_Ca_o;
vars q_000_LCC and q_000_LCC;
vars q_010_LCC and q_010_LCC;
vars q_020_LCC and q_020_LCC;
vars q_100_LCC and q_100_LCC;
vars q_110_LCC and q_110_LCC;
vars q_120_LCC and q_120_LCC;
vars q_001_LCC and q_001_LCC;
vars q_011_LCC and q_011_LCC;
vars q_021_LCC and q_021_LCC;
vars q_101_LCC and q_101_LCC;
vars q_111_LCC and q_111_LCC;
vars q_121_LCC and q_121_LCC;
vars v_LCC_Ca1 and v_LCC_Ca1;
vars v_LCC_Ca2 and v_LCC_Ca2;
vars v_d000 and v_d000;
vars v_d010 and v_d010;
vars v_d020 and v_d020;
vars v_d001 and v_d001;
vars v_d011 and v_d011;
vars v_d021 and v_d021;
vars v_f1_000 and v_f1_000;
vars v_f1_100 and v_f1_100;
vars v_f1_001 and v_f1_001;
vars v_f1_101 and v_f1_101;
vars v_f2_000 and v_f2_000;
vars v_f2_100 and v_f2_100;
vars v_f2_001 and v_f2_001;
vars v_f2_101 and v_f2_101;
vars v_f3_010 and v_f3_010;
vars v_f3_110 and v_f3_110;
vars v_f3_011 and v_f3_011;
vars v_f3_111 and v_f3_111;
vars v_fCa000 and v_fCa000;
vars v_fCa100 and v_fCa100;
vars v_fCa010 and v_fCa010;
vars v_fCa110 and v_fCa110;
vars v_fCa020 and v_fCa020;
vars v_fCa120 and v_fCa120;
enddef;
def map between LCC_diadic and LCC_diadic_parameters for
vars kappa_LCC_Ca1 and kappa_LCC_Ca1;
vars kappa_LCC_Ca2 and kappa_LCC_Ca2;
vars kappa_d000 and kappa_d000;
vars kappa_d010 and kappa_d010;
vars kappa_d020 and kappa_d020;
vars kappa_d001 and kappa_d001;
vars kappa_d011 and kappa_d011;
vars kappa_d021 and kappa_d021;
vars kappa_f1_000 and kappa_f1_000;
vars kappa_f1_100 and kappa_f1_100;
vars kappa_f1_001 and kappa_f1_001;
vars kappa_f1_101 and kappa_f1_101;
vars kappa_f2_000 and kappa_f2_000;
vars kappa_f2_100 and kappa_f2_100;
vars kappa_f2_001 and kappa_f2_001;
vars kappa_f2_101 and kappa_f2_101;
vars kappa_f3_010 and kappa_f3_010;
vars kappa_f3_110 and kappa_f3_110;
vars kappa_f3_011 and kappa_f3_011;
vars kappa_f3_111 and kappa_f3_111;
vars kappa_fCa000 and kappa_fCa000;
vars kappa_fCa100 and kappa_fCa100;
vars kappa_fCa010 and kappa_fCa010;
vars kappa_fCa110 and kappa_fCa110;
vars kappa_fCa020 and kappa_fCa020;
vars kappa_fCa120 and kappa_fCa120;
vars K_Ca_D and K_Ca_D;
vars K_Ca_o and K_Ca_o;
vars K_000_LCC and K_000_LCC;
vars K_010_LCC and K_010_LCC;
vars K_020_LCC and K_020_LCC;
vars K_100_LCC and K_100_LCC;
vars K_110_LCC and K_110_LCC;
vars K_120_LCC and K_120_LCC;
vars K_001_LCC and K_001_LCC;
vars K_011_LCC and K_011_LCC;
vars K_021_LCC and K_021_LCC;
vars K_101_LCC and K_101_LCC;
vars K_111_LCC and K_111_LCC;
vars K_121_LCC and K_121_LCC;
enddef;
def map between constants and LCC_diadic for
vars R and R;
vars T and T;
enddef;
enddef;
