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 =0;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 15 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('time in component environment (hour)');
    LEGEND_STATES(:,1) = strpad('c11 in component c11 (per_millilitre)');
    LEGEND_CONSTANTS(:,1) = strpad('p1 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,2) = strpad('p2 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,3) = strpad('p5 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,4) = strpad('p6 in component model_parameters (per_hour)');
    LEGEND_STATES(:,2) = strpad('c12 in component c12 (per_millilitre)');
    LEGEND_STATES(:,3) = strpad('c21 in component c21 (per_millilitre)');
    LEGEND_CONSTANTS(:,5) = strpad('p4 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,6) = strpad('p11 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,7) = strpad('p12 in component model_parameters (per_hour)');
    LEGEND_STATES(:,4) = strpad('c22 in component c22 (per_millilitre)');
    LEGEND_STATES(:,5) = strpad('c31 in component c31 (per_millilitre)');
    LEGEND_CONSTANTS(:,8) = strpad('p3 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,9) = strpad('p7 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,10) = strpad('p8 in component model_parameters (per_hour)');
    LEGEND_STATES(:,6) = strpad('c32 in component c32 (per_millilitre)');
    LEGEND_STATES(:,7) = strpad('c41 in component c41 (per_millilitre)');
    LEGEND_CONSTANTS(:,11) = strpad('p9 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,12) = strpad('p10 in component model_parameters (per_hour)');
    LEGEND_STATES(:,8) = strpad('c42 in component c42 (per_millilitre)');
    LEGEND_STATES(:,9) = strpad('c51 in component c51 (per_millilitre)');
    LEGEND_CONSTANTS(:,13) = strpad('p13 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,14) = strpad('p14 in component model_parameters (per_hour)');
    LEGEND_CONSTANTS(:,15) = strpad('p15 in component model_parameters (per_hour)');
    LEGEND_STATES(:,10) = strpad('c52 in component c52 (per_millilitre)');
    LEGEND_RATES(:,1) = strpad('d/dt c11 in component c11 (per_millilitre)');
    LEGEND_RATES(:,3) = strpad('d/dt c21 in component c21 (per_millilitre)');
    LEGEND_RATES(:,5) = strpad('d/dt c31 in component c31 (per_millilitre)');
    LEGEND_RATES(:,7) = strpad('d/dt c41 in component c41 (per_millilitre)');
    LEGEND_RATES(:,9) = strpad('d/dt c51 in component c51 (per_millilitre)');
    LEGEND_RATES(:,2) = strpad('d/dt c12 in component c12 (per_millilitre)');
    LEGEND_RATES(:,4) = strpad('d/dt c22 in component c22 (per_millilitre)');
    LEGEND_RATES(:,6) = strpad('d/dt c32 in component c32 (per_millilitre)');
    LEGEND_RATES(:,8) = strpad('d/dt c42 in component c42 (per_millilitre)');
    LEGEND_RATES(:,10) = strpad('d/dt c52 in component c52 (per_millilitre)');
    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 = [];
    STATES(:,1) = 9000;
    CONSTANTS(:,1) = 0.032044;
    CONSTANTS(:,2) = 0.016630;
    CONSTANTS(:,3) = 6.363016;
    CONSTANTS(:,4) = 7.574118;
    STATES(:,2) = 12000;
    STATES(:,3) = 0;
    CONSTANTS(:,5) = 0.019571;
    CONSTANTS(:,6) = 4.881967;
    CONSTANTS(:,7) = 5.356513;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    CONSTANTS(:,8) = 0.001885;
    CONSTANTS(:,9) = 1.140535;
    CONSTANTS(:,10) = 1.429125;
    STATES(:,6) = 0;
    STATES(:,7) = 0;
    CONSTANTS(:,11) = 9.768637;
    CONSTANTS(:,12) = 5.3640806;
    STATES(:,8) = 0;
    STATES(:,9) = 0;
    CONSTANTS(:,13) = 0.052968;
    CONSTANTS(:,14) = 0.443166;
    CONSTANTS(:,15) = 0.103700;
    STATES(:,10) = 0;
    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);
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
    end
    RATES(:,1) =   - CONSTANTS(:,1).*STATES(:,1) -  CONSTANTS(:,2).*STATES(:,1) -  CONSTANTS(:,3).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,2);
    RATES(:,3) =  CONSTANTS(:,1).*STATES(:,1) -  CONSTANTS(:,5).*STATES(:,3) -  CONSTANTS(:,6).*STATES(:,3)+ CONSTANTS(:,7).*STATES(:,4);
    RATES(:,5) =  CONSTANTS(:,2).*STATES(:,1) -  CONSTANTS(:,8).*STATES(:,5) -  CONSTANTS(:,9).*STATES(:,5)+ CONSTANTS(:,10).*STATES(:,6);
    RATES(:,7) =  CONSTANTS(:,8).*STATES(:,5)+ CONSTANTS(:,5).*STATES(:,3) -  CONSTANTS(:,11).*STATES(:,7)+ CONSTANTS(:,12).*STATES(:,8);
    RATES(:,9) =  CONSTANTS(:,13).*STATES(:,1) -  CONSTANTS(:,14).*STATES(:,9)+ CONSTANTS(:,15).*STATES(:,10);
    RATES(:,2) =  CONSTANTS(:,3).*STATES(:,1) -  CONSTANTS(:,4).*STATES(:,2);
    RATES(:,4) =  CONSTANTS(:,6).*STATES(:,3) -  CONSTANTS(:,7).*STATES(:,4);
    RATES(:,6) =  CONSTANTS(:,9).*STATES(:,5) -  CONSTANTS(:,10).*STATES(:,6);
    RATES(:,8) =  CONSTANTS(:,11).*STATES(:,7) -  CONSTANTS(:,12).*STATES(:,8);
    RATES(:,10) =  CONSTANTS(:,14).*STATES(:,9) -  CONSTANTS(:,15).*STATES(:,10);
   RATES = RATES';
end

% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
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