Location: BG_ns_Ca @ d238a25d7c74 / parameter_finder / output / TEMP.cellml.txt

Author:

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

Date:

2022-03-17 14:20:13+13:00

Desc:

Adding fluxes for Na and K species

Permanent Source URI:

https://models.physiomeproject.org/workspace/83b/rawfile/d238a25d7c74467569e0ea6aa73092bbcd9eb17e/parameter_finder/output/TEMP.cellml.txt

def model individual_ns_Ca 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};
var q_Na_i: fmol {init: 1e-888, pub: out};
var q_Na_o: fmol {init: 1e-888, pub: out};
var q_K_i: fmol {init: 1e-888, pub: out};
var q_K_o: fmol {init: 1e-888, pub: out};
// From submodule
var v_ns_Ca: fmol_per_sec {pub: in};
var v_ns_Na: fmol_per_sec {pub: in};
var v_ns_K: fmol_per_sec {pub: in};
ode(q_Ca_i, time) = vvv;
ode(q_Ca_o, time) = vvv;
ode(q_Na_i, time) = vvv;
ode(q_Na_o, time) = vvv;
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
enddef;

def comp ns_Ca_parameters as
var kappa_ns_Ca: fmol_per_sec {init: 0.013843, pub: out};
var kappa_ns_Na: fmol_per_sec {init: 0.0011334, pub: out};
var kappa_ns_K: fmol_per_sec {init: 0.00131116, pub: out};
var K_Ca_i: per_fmol {init: 0.00342024, pub: out};
var K_Ca_o: per_fmol {init: 0.0227048, pub: out};
var K_Na_i: per_fmol {init: 0.000978662, pub: out};
var K_Na_o: per_fmol {init: 0.00649671, pub: out};
var K_K_i: per_fmol {init: 0.00105262, pub: out};
var K_K_o: per_fmol {init: 0.00698765, pub: out};
enddef;
def comp ns_Ca as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_ns_Ca: fmol_per_sec {pub: in};
var kappa_ns_Na: fmol_per_sec {pub: in};
var kappa_ns_K: fmol_per_sec {pub: in};
var K_Ca_i: per_fmol {pub: in};
var K_Ca_o: per_fmol {pub: in};
var K_Na_i: per_fmol {pub: in};
var K_Na_o: per_fmol {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
// Input from global environment
var q_Ca_i: fmol {pub: in};
var q_Ca_o: fmol {pub: in};
var q_Na_i: fmol {pub: in};
var q_Na_o: fmol {pub: in};
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
// Constitutive parameters
var mu_Ca_i: J_per_mol;
var mu_Ca_o: J_per_mol;
var mu_Na_i: J_per_mol;
var mu_Na_o: J_per_mol;
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var v_ns_Ca: fmol_per_sec {pub: out};
var v_ns_Na: fmol_per_sec {pub: out};
var v_ns_K: 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);
mu_Na_i = R*T*ln(K_Na_i*q_Na_i);
mu_Na_o = R*T*ln(K_Na_o*q_Na_o);
mu_K_i = R*T*ln(K_K_i*q_K_i);
mu_K_o = R*T*ln(K_K_o*q_K_o);
v_ns_Ca = ppp;
v_ns_Na = ppp;
v_ns_K = ppp;
enddef;
def map between environment and ns_Ca for
vars time and time;
vars q_Ca_i and q_Ca_i;
vars q_Ca_o and q_Ca_o;
vars q_Na_i and q_Na_i;
vars q_Na_o and q_Na_o;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars v_ns_Ca and v_ns_Ca;
vars v_ns_Na and v_ns_Na;
vars v_ns_K and v_ns_K;
enddef;
def map between ns_Ca and ns_Ca_parameters for
vars kappa_ns_Ca and kappa_ns_Ca;
vars kappa_ns_Na and kappa_ns_Na;
vars kappa_ns_K and kappa_ns_K;
vars K_Ca_i and K_Ca_i;
vars K_Ca_o and K_Ca_o;
vars K_Na_i and K_Na_i;
vars K_Na_o and K_Na_o;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
enddef;
def map between constants and ns_Ca for
vars R and R;
 vars T and T;
enddef;
enddef;