Location: BG_PLC @ 5065a066ecea / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-05-02 13:21:42+12:00
Desc:
Making exposure files
Permanent Source URI:
https://models.physiomeproject.org/workspace/848/rawfile/5065a066ecead2260e7b91da029b4eac898d2f68/parameter_finder/output/TEMP.cellml.txt
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def model individual_PLC 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_DAG: fmol {init: 1e-888, pub: out};
var q_PC: fmol {init: 1e-888, pub: out};
var q_IP3: fmol {init: 1e-888, pub: out};
var q_Ino: fmol {init: 1e-888, pub: out};
var q_PLC: fmol {init: 1e-888, pub: out};
var q_Gq: fmol {init: 1e-888, pub: out};
var q_Ca: fmol {init: 1e-888, pub: out};
var q_Gq_PLC: fmol {init: 1e-888, pub: out};
var q_Ca_PLC: fmol {init: 1e-888, pub: out};
var q_Ca_Gq_PLC: fmol {init: 1e-888, pub: out};
var q_G_GDP: fmol {init: 1e-888, pub: out};
var q_PIP2: fmol {init: 1e-888, pub: out};
var q_CaPLC_PIP2: fmol {init: 1e-888, pub: out};
var q_CaGqPLC_PIP2: fmol {init: 1e-888, pub: out};
// From submodule
var v_R0_PLC: fmol_per_sec {pub: in};
var v_R1_PLC: fmol_per_sec {pub: in};
var v_R2a_PLC: fmol_per_sec {pub: in};
var v_R2b_PLC: fmol_per_sec {pub: in};
var v_R3a_PLC: fmol_per_sec {pub: in};
var v_R3b_PLC: fmol_per_sec {pub: in};
var v_R4_PLC: fmol_per_sec {pub: in};
var v_R5_PLC: fmol_per_sec {pub: in};
var v_R6_PLC: fmol_per_sec {pub: in};
var v_R7_PLC: fmol_per_sec {pub: in};
var v_R8_PLC: fmol_per_sec {pub: in};
ode(q_DAG, time) = vvv;
ode(q_PC, time) = vvv;
ode(q_IP3, time) = vvv;
ode(q_Ino, time) = vvv;
ode(q_PLC, time) = vvv;
ode(q_Gq, time) = vvv;
ode(q_Ca, time) = vvv;
ode(q_Gq_PLC, time) = vvv;
ode(q_Ca_PLC, time) = vvv;
ode(q_Ca_Gq_PLC, time) = vvv;
ode(q_G_GDP, time) = vvv;
ode(q_PIP2, time) = vvv;
ode(q_CaPLC_PIP2, time) = vvv;
ode(q_CaGqPLC_PIP2, time) = vvv;
enddef;

def comp PLC_parameters as
var kappa_R0_PLC: fmol_per_sec {init: 0.0475807, pub: out};
var kappa_R1_PLC: fmol_per_sec {init: 0.121538, pub: out};
var kappa_R2a_PLC: fmol_per_sec {init: 70395.1, pub: out};
var kappa_R2b_PLC: fmol_per_sec {init: 2.70328, pub: out};
var kappa_R3a_PLC: fmol_per_sec {init: 10988.5, pub: out};
var kappa_R3b_PLC: fmol_per_sec {init: 0.00553812, pub: out};
var kappa_R4_PLC: fmol_per_sec {init: 4.56488, pub: out};
var kappa_R5_PLC: fmol_per_sec {init: 3.86201, pub: out};
var kappa_R6_PLC: fmol_per_sec {init: 0.71257, pub: out};
var kappa_R7_PLC: fmol_per_sec {init: 2.99279e-05, pub: out};
var kappa_R8_PLC: fmol_per_sec {init: 0.00947718, pub: out};
var K_DAG: per_fmol {init: 0.849741, pub: out};
var K_PC: per_fmol {init: 0.00566494, pub: out};
var K_IP3: per_fmol {init: 5.54437, pub: out};
var K_Ino: per_fmol {init: 0.00221775, pub: out};
var K_PLC: per_fmol {init: 0.00108946, pub: out};
var K_Gq: per_fmol {init: 7.25233e-05, pub: out};
var K_Ca: per_fmol {init: 7.30437e-05, pub: out};
var K_Gq_PLC: per_fmol {init: 0.0697931, pub: out};
var K_Ca_PLC: per_fmol {init: 0.0590468, pub: out};
var K_Ca_Gq_PLC: per_fmol {init: 0.378267, pub: out};
var K_G_GDP: per_fmol {init: 7.25233e-05, pub: out};
var K_PIP2: per_fmol {init: 17.4789, pub: out};
var K_CaPLC_PIP2: per_fmol {init: 19.1442, pub: out};
var K_CaGqPLC_PIP2: per_fmol {init: 486.703, pub: out};
enddef;
def comp PLC as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_R0_PLC: fmol_per_sec {pub: in};
var kappa_R1_PLC: fmol_per_sec {pub: in};
var kappa_R2a_PLC: fmol_per_sec {pub: in};
var kappa_R2b_PLC: fmol_per_sec {pub: in};
var kappa_R3a_PLC: fmol_per_sec {pub: in};
var kappa_R3b_PLC: fmol_per_sec {pub: in};
var kappa_R4_PLC: fmol_per_sec {pub: in};
var kappa_R5_PLC: fmol_per_sec {pub: in};
var kappa_R6_PLC: fmol_per_sec {pub: in};
var kappa_R7_PLC: fmol_per_sec {pub: in};
var kappa_R8_PLC: fmol_per_sec {pub: in};
var K_DAG: per_fmol {pub: in};
var K_PC: per_fmol {pub: in};
var K_IP3: per_fmol {pub: in};
var K_Ino: per_fmol {pub: in};
var K_PLC: per_fmol {pub: in};
var K_Gq: per_fmol {pub: in};
var K_Ca: per_fmol {pub: in};
var K_Gq_PLC: per_fmol {pub: in};
var K_Ca_PLC: per_fmol {pub: in};
var K_Ca_Gq_PLC: per_fmol {pub: in};
var K_G_GDP: per_fmol {pub: in};
var K_PIP2: per_fmol {pub: in};
var K_CaPLC_PIP2: per_fmol {pub: in};
var K_CaGqPLC_PIP2: per_fmol {pub: in};
// Input from global environment
var q_DAG: fmol {pub: in};
var q_PC: fmol {pub: in};
var q_IP3: fmol {pub: in};
var q_Ino: fmol {pub: in};
var q_PLC: fmol {pub: in};
var q_Gq: fmol {pub: in};
var q_Ca: fmol {pub: in};
var q_Gq_PLC: fmol {pub: in};
var q_Ca_PLC: fmol {pub: in};
var q_Ca_Gq_PLC: fmol {pub: in};
var q_G_GDP: fmol {pub: in};
var q_PIP2: fmol {pub: in};
var q_CaPLC_PIP2: fmol {pub: in};
var q_CaGqPLC_PIP2: fmol {pub: in};
// Constitutive parameters
var mu_DAG: J_per_mol;
var mu_PC: J_per_mol;
var mu_IP3: J_per_mol;
var mu_Ino: J_per_mol;
var mu_PLC: J_per_mol;
var mu_Gq: J_per_mol;
var mu_Ca: J_per_mol;
var mu_Gq_PLC: J_per_mol;
var mu_Ca_PLC: J_per_mol;
var mu_Ca_Gq_PLC: J_per_mol;
var mu_G_GDP: J_per_mol;
var mu_PIP2: J_per_mol;
var mu_CaPLC_PIP2: J_per_mol;
var mu_CaGqPLC_PIP2: J_per_mol;
var v_R0_PLC: fmol_per_sec {pub: out};
var v_R1_PLC: fmol_per_sec {pub: out};
var v_R2a_PLC: fmol_per_sec {pub: out};
var v_R2b_PLC: fmol_per_sec {pub: out};
var v_R3a_PLC: fmol_per_sec {pub: out};
var v_R3b_PLC: fmol_per_sec {pub: out};
var v_R4_PLC: fmol_per_sec {pub: out};
var v_R5_PLC: fmol_per_sec {pub: out};
var v_R6_PLC: fmol_per_sec {pub: out};
var v_R7_PLC: fmol_per_sec {pub: out};
var v_R8_PLC: fmol_per_sec {pub: out};
mu_DAG = R*T*ln(K_DAG*q_DAG);
mu_PC = R*T*ln(K_PC*q_PC);
mu_IP3 = R*T*ln(K_IP3*q_IP3);
mu_Ino = R*T*ln(K_Ino*q_Ino);
mu_PLC = R*T*ln(K_PLC*q_PLC);
mu_Gq = R*T*ln(K_Gq*q_Gq);
mu_Ca = R*T*ln(K_Ca*q_Ca);
mu_Gq_PLC = R*T*ln(K_Gq_PLC*q_Gq_PLC);
mu_Ca_PLC = R*T*ln(K_Ca_PLC*q_Ca_PLC);
mu_Ca_Gq_PLC = R*T*ln(K_Ca_Gq_PLC*q_Ca_Gq_PLC);
mu_G_GDP = R*T*ln(K_G_GDP*q_G_GDP);
mu_PIP2 = R*T*ln(K_PIP2*q_PIP2);
mu_CaPLC_PIP2 = R*T*ln(K_CaPLC_PIP2*q_CaPLC_PIP2);
mu_CaGqPLC_PIP2 = R*T*ln(K_CaGqPLC_PIP2*q_CaGqPLC_PIP2);
v_R0_PLC = ppp;
v_R1_PLC = ppp;
v_R2a_PLC = ppp;
v_R2b_PLC = ppp;
v_R3a_PLC = ppp;
v_R3b_PLC = ppp;
v_R4_PLC = ppp;
v_R5_PLC = ppp;
v_R6_PLC = ppp;
v_R7_PLC = ppp;
v_R8_PLC = ppp;
enddef;
def map between environment and PLC for
vars time and time;
vars q_DAG and q_DAG;
vars q_PC and q_PC;
vars q_IP3 and q_IP3;
vars q_Ino and q_Ino;
vars q_PLC and q_PLC;
vars q_Gq and q_Gq;
vars q_Ca and q_Ca;
vars q_Gq_PLC and q_Gq_PLC;
vars q_Ca_PLC and q_Ca_PLC;
vars q_Ca_Gq_PLC and q_Ca_Gq_PLC;
vars q_G_GDP and q_G_GDP;
vars q_PIP2 and q_PIP2;
vars q_CaPLC_PIP2 and q_CaPLC_PIP2;
vars q_CaGqPLC_PIP2 and q_CaGqPLC_PIP2;
vars v_R0_PLC and v_R0_PLC;
vars v_R1_PLC and v_R1_PLC;
vars v_R2a_PLC and v_R2a_PLC;
vars v_R2b_PLC and v_R2b_PLC;
vars v_R3a_PLC and v_R3a_PLC;
vars v_R3b_PLC and v_R3b_PLC;
vars v_R4_PLC and v_R4_PLC;
vars v_R5_PLC and v_R5_PLC;
vars v_R6_PLC and v_R6_PLC;
vars v_R7_PLC and v_R7_PLC;
vars v_R8_PLC and v_R8_PLC;
enddef;
def map between PLC and PLC_parameters for
vars kappa_R0_PLC and kappa_R0_PLC;
vars kappa_R1_PLC and kappa_R1_PLC;
vars kappa_R2a_PLC and kappa_R2a_PLC;
vars kappa_R2b_PLC and kappa_R2b_PLC;
vars kappa_R3a_PLC and kappa_R3a_PLC;
vars kappa_R3b_PLC and kappa_R3b_PLC;
vars kappa_R4_PLC and kappa_R4_PLC;
vars kappa_R5_PLC and kappa_R5_PLC;
vars kappa_R6_PLC and kappa_R6_PLC;
vars kappa_R7_PLC and kappa_R7_PLC;
vars kappa_R8_PLC and kappa_R8_PLC;
vars K_DAG and K_DAG;
vars K_PC and K_PC;
vars K_IP3 and K_IP3;
vars K_Ino and K_Ino;
vars K_PLC and K_PLC;
vars K_Gq and K_Gq;
vars K_Ca and K_Ca;
vars K_Gq_PLC and K_Gq_PLC;
vars K_Ca_PLC and K_Ca_PLC;
vars K_Ca_Gq_PLC and K_Ca_Gq_PLC;
vars K_G_GDP and K_G_GDP;
vars K_PIP2 and K_PIP2;
vars K_CaPLC_PIP2 and K_CaPLC_PIP2;
vars K_CaGqPLC_PIP2 and K_CaGqPLC_PIP2;
enddef;
def map between constants and PLC for
vars R and R;
 vars T and T;
enddef;
enddef;