Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =22;
end
% There are a total of 4 entries in each of the rate and state variable arrays.
% There are a total of 26 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('t in component GLUT2_BG (second)');
LEGEND_CONSTANTS(:,1) = strpad('R in component params_BG (J_per_K_mol)');
LEGEND_CONSTANTS(:,2) = strpad('T in component params_BG (kelvin)');
LEGEND_CONSTANTS(:,3) = strpad('K_Ai in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,24) = strpad('q_init_Ai in component params_BG (fmol)');
LEGEND_CONSTANTS(:,4) = strpad('K_Ao in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,21) = strpad('q_init_Ao in component params_BG (fmol)');
LEGEND_CONSTANTS(:,5) = strpad('K_1 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,6) = strpad('q_init_1 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,7) = strpad('K_2 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,8) = strpad('q_init_2 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,9) = strpad('K_3 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,10) = strpad('q_init_3 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,11) = strpad('K_4 in component params_BG (per_fmol)');
LEGEND_CONSTANTS(:,12) = strpad('q_init_4 in component params_BG (fmol)');
LEGEND_CONSTANTS(:,13) = strpad('kappa_r1 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,14) = strpad('kappa_r2 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,15) = strpad('kappa_r3 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,16) = strpad('kappa_r4 in component params_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,26) = strpad('mu_Ai in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,17) = strpad('v_Ai in component GLUT2_BG (fmol_per_s)');
LEGEND_CONSTANTS(:,23) = strpad('mu_Ao in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,18) = strpad('v_Ao in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,1) = strpad('mu_1 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,19) = strpad('v_1 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,2) = strpad('mu_2 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,20) = strpad('v_2 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,3) = strpad('mu_3 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,21) = strpad('v_3 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,4) = strpad('mu_4 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,22) = strpad('v_4 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,5) = strpad('A_f_r1 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,7) = strpad('v_r1 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,6) = strpad('A_r_r1 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,8) = strpad('A_f_r2 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,10) = strpad('v_r2 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,9) = strpad('A_r_r2 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,11) = strpad('A_f_r3 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,15) = strpad('v_r3 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,13) = strpad('A_r_r3 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,12) = strpad('A_f_r4 in component GLUT2_BG (J_per_mol)');
LEGEND_ALGEBRAIC(:,16) = strpad('v_r4 in component GLUT2_BG (fmol_per_s)');
LEGEND_ALGEBRAIC(:,14) = strpad('A_r_r4 in component GLUT2_BG (J_per_mol)');
LEGEND_CONSTANTS(:,25) = strpad('q_Ai in component GLUT2_BG (fmol)');
LEGEND_CONSTANTS(:,22) = strpad('q_Ao in component GLUT2_BG (fmol)');
LEGEND_STATES(:,1) = strpad('q_1 in component GLUT2_BG (fmol)');
LEGEND_STATES(:,2) = strpad('q_2 in component GLUT2_BG (fmol)');
LEGEND_STATES(:,3) = strpad('q_3 in component GLUT2_BG (fmol)');
LEGEND_STATES(:,4) = strpad('q_4 in component GLUT2_BG (fmol)');
LEGEND_CONSTANTS(:,17) = strpad('V_i in component params_BG (pL)');
LEGEND_CONSTANTS(:,18) = strpad('g_i in component params_BG (mM)');
LEGEND_CONSTANTS(:,19) = strpad('g_o in component params_BG (mM)');
LEGEND_CONSTANTS(:,20) = strpad('V_o in component params_BG (pL)');
LEGEND_RATES(:,1) = strpad('d/dt q_1 in component GLUT2_BG (fmol)');
LEGEND_RATES(:,2) = strpad('d/dt q_2 in component GLUT2_BG (fmol)');
LEGEND_RATES(:,3) = strpad('d/dt q_3 in component GLUT2_BG (fmol)');
LEGEND_RATES(:,4) = strpad('d/dt q_4 in component GLUT2_BG (fmol)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
CONSTANTS(:,1) = 8.31;
CONSTANTS(:,2) = 273.15;
CONSTANTS(:,3) = 149.65;
CONSTANTS(:,4) = 149.65;
CONSTANTS(:,5) = 33.20;
CONSTANTS(:,6) = 0.0017;
CONSTANTS(:,7) = 4.25e+03;
CONSTANTS(:,8) = 0.0017;
CONSTANTS(:,9) = 344.59;
CONSTANTS(:,10) = 0.0017;
CONSTANTS(:,11) = 1.99;
CONSTANTS(:,12) = 0.0017;
CONSTANTS(:,13) = 0.36;
CONSTANTS(:,14) = 0.26;
CONSTANTS(:,15) = 1.01e+05;
CONSTANTS(:,16) = 1.01e+04;
CONSTANTS(:,17) = 0.09;
CONSTANTS(:,18) = 10;
CONSTANTS(:,19) = 1e-5;
CONSTANTS(:,20) = 0.09;
CONSTANTS(:,21) = CONSTANTS(:,19).*CONSTANTS(:,20);
CONSTANTS(:,22) = CONSTANTS(:,21);
CONSTANTS(:,23) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,4).*CONSTANTS(:,22));
CONSTANTS(:,24) = CONSTANTS(:,18).*CONSTANTS(:,17);
CONSTANTS(:,25) = CONSTANTS(:,24);
CONSTANTS(:,26) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,3).*CONSTANTS(:,25));
STATES(:,1) = CONSTANTS(:,6);
STATES(:,2) = CONSTANTS(:,8);
STATES(:,3) = CONSTANTS(:,10);
STATES(:,4) = CONSTANTS(:,12);
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,4) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,4));
ALGEBRAIC(:,5) = ALGEBRAIC(:,4);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,5).*STATES(:,1));
ALGEBRAIC(:,6) = ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,13).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,11) = CONSTANTS(:,23)+ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,7).*STATES(:,2));
ALGEBRAIC(:,13) = ALGEBRAIC(:,2);
ALGEBRAIC(:,15) = CONSTANTS(:,15).*(exp(ALGEBRAIC(:,11)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,19) = ALGEBRAIC(:,7) - ALGEBRAIC(:,15);
RATES(:,1) = ALGEBRAIC(:,19);
ALGEBRAIC(:,8) = ALGEBRAIC(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,9).*STATES(:,3));
ALGEBRAIC(:,9) = ALGEBRAIC(:,3);
ALGEBRAIC(:,10) = CONSTANTS(:,14).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,20) = ALGEBRAIC(:,15) - ALGEBRAIC(:,10);
RATES(:,2) = ALGEBRAIC(:,20);
ALGEBRAIC(:,12) = ALGEBRAIC(:,3);
ALGEBRAIC(:,14) = CONSTANTS(:,26)+ALGEBRAIC(:,4);
ALGEBRAIC(:,16) = CONSTANTS(:,16).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,21) = ALGEBRAIC(:,10) - ALGEBRAIC(:,16);
RATES(:,3) = ALGEBRAIC(:,21);
ALGEBRAIC(:,22) = ALGEBRAIC(:,16) - ALGEBRAIC(:,7);
RATES(:,4) = ALGEBRAIC(:,22);
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,4) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,4));
ALGEBRAIC(:,5) = ALGEBRAIC(:,4);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,5).*STATES(:,1));
ALGEBRAIC(:,6) = ALGEBRAIC(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,13).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,11) = CONSTANTS(:,23)+ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,7).*STATES(:,2));
ALGEBRAIC(:,13) = ALGEBRAIC(:,2);
ALGEBRAIC(:,15) = CONSTANTS(:,15).*(exp(ALGEBRAIC(:,11)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,19) = ALGEBRAIC(:,7) - ALGEBRAIC(:,15);
ALGEBRAIC(:,8) = ALGEBRAIC(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,9).*STATES(:,3));
ALGEBRAIC(:,9) = ALGEBRAIC(:,3);
ALGEBRAIC(:,10) = CONSTANTS(:,14).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,20) = ALGEBRAIC(:,15) - ALGEBRAIC(:,10);
ALGEBRAIC(:,12) = ALGEBRAIC(:,3);
ALGEBRAIC(:,14) = CONSTANTS(:,26)+ALGEBRAIC(:,4);
ALGEBRAIC(:,16) = CONSTANTS(:,16).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
ALGEBRAIC(:,21) = ALGEBRAIC(:,10) - ALGEBRAIC(:,16);
ALGEBRAIC(:,22) = ALGEBRAIC(:,16) - ALGEBRAIC(:,7);
ALGEBRAIC(:,17) = ALGEBRAIC(:,16);
ALGEBRAIC(:,18) = - ALGEBRAIC(:,15);
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end