Location: BG_CaB @ ca1cba607bf6 / parameter_finder / output / TEMP.cellml.txt

Author:

Shelley Fong <s.fong@auckland.ac.nz>

Date:

2022-03-02 16:50:27+13:00

Desc:

Changing Xi to X_i, and adding python param finder code

Permanent Source URI:

https://staging.physiomeproject.org/workspace/82a/rawfile/ca1cba607bf6f3067449fc29fd7e03360c99f5a4/parameter_finder/output/TEMP.cellml.txt

def model individual_Ca_background 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_i: fmol {init: 1e-888, pub: out};
var q_Ca_o: fmol {init: 1e-888, pub: out};
// From submodule
var v_CaB: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_Ca_o, time) = vvv;
enddef;

def comp Ca_background_parameters as
var kappa_CaB: fmol_per_sec {init: 10294.6, pub: out};
var K_Ca_i: per_fmol {init: 2.94948, pub: out};
var K_Ca_o: per_fmol {init: 19.5797, pub: out};
enddef;
def comp Ca_background as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_CaB: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_Ca_o: J_per_mol;
var v_CaB: fmol_per_sec {pub: out};
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_Ca_o = R*T*ln(K_Ca_o*q_Ca_o);
v_CaB = ppp;
enddef;
def map between environment and Ca_background for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_Ca_o and q_Ca_o;
vars v_CaB and v_CaB;
enddef;
def map between Ca_background and Ca_background_parameters for
vars kappa_CaB and kappa_CaB;
vars K_Ca_i and K_Ca_i;
vars K_Ca_o and K_Ca_o;
enddef;
def map between constants and Ca_background for
vars R and R;
 vars T and T;
enddef;
enddef;