Location: BG_to_channel @ 4a21648d8c2b / parameter_finder / output / TEMP.cellml.txt

Author:
Shelley Fong <s.fong@auckland.ac.nz>
Date:
2022-04-11 14:50:29+12:00
Desc:
Changing method of number of channels present. Guess density. Using SA of human iPSC for Kernik. Updating volumes
Permanent Source URI:
https://models.physiomeproject.org/workspace/82e/rawfile/4a21648d8c2b1aa210932de4caa4c938d5a1215a/parameter_finder/output/TEMP.cellml.txt
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def model individual_TO 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_K_i: fmol {init: 1e-888, pub: out};
var q_K_o: fmol {init: 1e-888, pub: out};
var q_r0s0_TO: fmol {init: 1e-888, pub: out};
var q_r1s0_TO: fmol {init: 1e-888, pub: out};
var q_r0s1_TO: fmol {init: 1e-888, pub: out};
var q_r1s1_TO: fmol {init: 1e-888, pub: out};
// From submodule
var v_TO: fmol_per_sec {pub: in};
var v_gTO_1: fmol_per_sec {pub: in};
var v_gTO_2: fmol_per_sec {pub: in};
var v_gTO_3: fmol_per_sec {pub: in};
var v_gTO_4: fmol_per_sec {pub: in};
ode(q_K_i, time) = vvv;
ode(q_K_o, time) = vvv;
ode(q_r0s0_TO, time) = vvv;
ode(q_r1s0_TO, time) = vvv;
ode(q_r0s1_TO, time) = vvv;
ode(q_r1s1_TO, time) = vvv;
enddef;

def comp TO_parameters as
var kappa_TO: fmol_per_sec {init: 120.645, pub: out};
var kappa_gTO_1: fmol_per_sec {init: 10.0063, pub: out};
var kappa_gTO_2: fmol_per_sec {init: 0.053573, pub: out};
var kappa_gTO_3: fmol_per_sec {init: 0.0622138, pub: out};
var kappa_gTO_4: fmol_per_sec {init: 0.0155957, pub: out};
var K_K_i: per_fmol {init: 2.96061, pub: out};
var K_K_o: per_fmol {init: 3.36433, pub: out};
var K_r0s0_TO: per_fmol {init: 0.00553253, pub: out};
var K_r1s0_TO: per_fmol {init: 0.0220702, pub: out};
var K_r0s1_TO: per_fmol {init: 1.03336, pub: out};
var K_r1s1_TO: per_fmol {init: 4.12222, pub: out};
enddef;
def comp TO as
        var time: second {pub: in};
        var R: J_per_K_per_mol {pub: in};
        var T: kelvin {pub: in};
        // parameters
var kappa_TO: fmol_per_sec {pub: in};
var kappa_gTO_1: fmol_per_sec {pub: in};
var kappa_gTO_2: fmol_per_sec {pub: in};
var kappa_gTO_3: fmol_per_sec {pub: in};
var kappa_gTO_4: fmol_per_sec {pub: in};
var K_K_i: per_fmol {pub: in};
var K_K_o: per_fmol {pub: in};
var K_r0s0_TO: per_fmol {pub: in};
var K_r1s0_TO: per_fmol {pub: in};
var K_r0s1_TO: per_fmol {pub: in};
var K_r1s1_TO: per_fmol {pub: in};
// Input from global environment
var q_K_i: fmol {pub: in};
var q_K_o: fmol {pub: in};
var q_r0s0_TO: fmol {pub: in};
var q_r1s0_TO: fmol {pub: in};
var q_r0s1_TO: fmol {pub: in};
var q_r1s1_TO: fmol {pub: in};
// Constitutive parameters
var mu_K_i: J_per_mol;
var mu_K_o: J_per_mol;
var mu_r0s0_TO: J_per_mol;
var mu_r1s0_TO: J_per_mol;
var mu_r0s1_TO: J_per_mol;
var mu_r1s1_TO: J_per_mol;
var v_TO: fmol_per_sec {pub: out};
var v_gTO_1: fmol_per_sec {pub: out};
var v_gTO_2: fmol_per_sec {pub: out};
var v_gTO_3: fmol_per_sec {pub: out};
var v_gTO_4: fmol_per_sec {pub: out};
mu_K_i = R*T*ln(K_K_i*q_K_i);
mu_K_o = R*T*ln(K_K_o*q_K_o);
mu_r0s0_TO = R*T*ln(K_r0s0_TO*q_r0s0_TO);
mu_r1s0_TO = R*T*ln(K_r1s0_TO*q_r1s0_TO);
mu_r0s1_TO = R*T*ln(K_r0s1_TO*q_r0s1_TO);
mu_r1s1_TO = R*T*ln(K_r1s1_TO*q_r1s1_TO);
v_TO = ppp;
v_gTO_1 = ppp;
v_gTO_2 = ppp;
v_gTO_3 = ppp;
v_gTO_4 = ppp;
enddef;
def map between environment and TO for
vars time and time;
vars q_K_i and q_K_i;
vars q_K_o and q_K_o;
vars q_r0s0_TO and q_r0s0_TO;
vars q_r1s0_TO and q_r1s0_TO;
vars q_r0s1_TO and q_r0s1_TO;
vars q_r1s1_TO and q_r1s1_TO;
vars v_TO and v_TO;
vars v_gTO_1 and v_gTO_1;
vars v_gTO_2 and v_gTO_2;
vars v_gTO_3 and v_gTO_3;
vars v_gTO_4 and v_gTO_4;
enddef;
def map between TO and TO_parameters for
vars kappa_TO and kappa_TO;
vars kappa_gTO_1 and kappa_gTO_1;
vars kappa_gTO_2 and kappa_gTO_2;
vars kappa_gTO_3 and kappa_gTO_3;
vars kappa_gTO_4 and kappa_gTO_4;
vars K_K_i and K_K_i;
vars K_K_o and K_K_o;
vars K_r0s0_TO and K_r0s0_TO;
vars K_r1s0_TO and K_r1s0_TO;
vars K_r0s1_TO and K_r0s1_TO;
vars K_r1s1_TO and K_r1s1_TO;
enddef;
def map between constants and TO for
vars R and R;
 vars T and T;
enddef;
enddef;