Location: BG_CMDN_buffer @ bde7f0f7dbbc / parameter_finder / output / TEMP.cellml.txt

Author:

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

Date:

2022-03-03 14:21:00+13:00

Desc:

Changing Xi to X_i, and adding python param finder code

Permanent Source URI:

http://models.cellml.org/workspace/822/rawfile/bde7f0f7dbbcf3b0cbf2db1513d3aa347cfac547/parameter_finder/output/TEMP.cellml.txt

def model individual_CMDN_buffer 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_CMDN: fmol {init: 1e-888, pub: out};
var q_CMDN_Ca: fmol {init: 1e-888, pub: out};
// From submodule
var v_b2: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_CMDN, time) = vvv;
ode(q_CMDN_Ca, time) = vvv;
enddef;

def comp CMDN_buffer_parameters as
var kappa_b2: fmol_per_sec {init: 355.329, pub: out};
var K_Ca_i: per_fmol {init: 1.54215, pub: out};
var K_CMDN: per_fmol {init: 1.54215, pub: out};
var K_CMDN_Ca: per_fmol {init: 0.19471, pub: out};
enddef;
def comp CMDN_buffer as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_b2: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_CMDN: per_fmol {pub: in};
var K_CMDN_Ca: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_CMDN: fmol {pub: in};
var q_CMDN_Ca: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_CMDN: J_per_mol;
var mu_CMDN_Ca: J_per_mol;
var v_b2: fmol_per_sec {pub: out};
mu_Ca_i = R*T*ln(K_Ca_i*q_Ca_i);
mu_CMDN = R*T*ln(K_CMDN*q_CMDN);
mu_CMDN_Ca = R*T*ln(K_CMDN_Ca*q_CMDN_Ca);
v_b2 = ppp;
enddef;
def map between environment and CMDN_buffer for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_CMDN and q_CMDN;
vars q_CMDN_Ca and q_CMDN_Ca;
vars v_b2 and v_b2;
enddef;
def map between CMDN_buffer and CMDN_buffer_parameters for
vars kappa_b2 and kappa_b2;
vars K_Ca_i and K_Ca_i;
vars K_CMDN and K_CMDN;
vars K_CMDN_Ca and K_CMDN_Ca;
enddef;
def map between constants and CMDN_buffer for
vars R and R;
 vars T and T;
enddef;
enddef;