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 =42;
end
% There are a total of 31 entries in each of the rate and state variable arrays.
% There are a total of 57 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 (second)');
    LEGEND_STATES(:,1) = strpad('Casp8 in component Casp8 (micromolar)');
    LEGEND_STATES(:,2) = strpad('Casp8Bid in component Casp8 (micromolar)');
    LEGEND_STATES(:,3) = strpad('Bid in component Bid (micromolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('J_0 in component Casp8 (flux)');
    LEGEND_ALGEBRAIC(:,1) = strpad('J_f0 in component Casp8 (flux)');
    LEGEND_ALGEBRAIC(:,2) = strpad('J_Casp8 in component Casp8 (flux)');
    LEGEND_CONSTANTS(:,1) = strpad('k_f0 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k_10 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k_00 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('u in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,4) = strpad('Apaf_1 in component Apaf_1 (micromolar)');
    LEGEND_STATES(:,5) = strpad('CytcApaf_1 in component CytcApaf_1 (micromolar)');
    LEGEND_STATES(:,6) = strpad('Cytc in component Cytc (micromolar)');
    LEGEND_ALGEBRAIC(:,4) = strpad('J_Apaf_1 in component Apaf_1 (flux)');
    LEGEND_ALGEBRAIC(:,5) = strpad('J_1 in component Apaf_1 (flux)');
    LEGEND_CONSTANTS(:,5) = strpad('P_Apaf_1 in component model_constant (flux)');
    LEGEND_CONSTANTS(:,6) = strpad('k_11 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('k_01 in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,7) = strpad('Apop in component Apop (micromolar)');
    LEGEND_ALGEBRAIC(:,7) = strpad('J_1b in component CytcApaf_1 (flux)');
    LEGEND_CONSTANTS(:,8) = strpad('k_11b in component model_constant (rate)');
    LEGEND_CONSTANTS(:,9) = strpad('k_01b in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('p in component model_constant (dimensionless)');
    LEGEND_ALGEBRAIC(:,10) = strpad('J_14 in component Cytc_mito (flux)');
    LEGEND_ALGEBRAIC(:,6) = strpad('J_Cytc in component Cytc (flux)');
    LEGEND_STATES(:,8) = strpad('Cytc_mito in component Cytc_mito (micromolar)');
    LEGEND_STATES(:,9) = strpad('Bax_2 in component Bax_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('J_Cytc_mito in component Cytc_mito (flux)');
    LEGEND_CONSTANTS(:,11) = strpad('P_Cytc_mito in component model_constant (flux)');
    LEGEND_CONSTANTS(:,12) = strpad('k14 in component model_constant (second_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,16) = strpad('J_12b in component tBidBax (flux)');
    LEGEND_ALGEBRAIC(:,9) = strpad('J_Bax_2 in component Bax_2 (flux)');
    LEGEND_STATES(:,10) = strpad('tBid_mito in component tBid_mito (micromolar)');
    LEGEND_STATES(:,11) = strpad('Bax in component Bax (micromolar)');
    LEGEND_ALGEBRAIC(:,13) = strpad('J_11 in component tBid (flux)');
    LEGEND_ALGEBRAIC(:,12) = strpad('J_12a in component tBid_mito (flux)');
    LEGEND_ALGEBRAIC(:,11) = strpad('J_tBid_mito in component tBid_mito (flux)');
    LEGEND_CONSTANTS(:,13) = strpad('k12a in component model_constant (second_order_rate_constant)');
    LEGEND_STATES(:,12) = strpad('tBid in component tBid (micromolar)');
    LEGEND_ALGEBRAIC(:,24) = strpad('J_f8 in component Casp3Bid (flux)');
    LEGEND_ALGEBRAIC(:,14) = strpad('J_tBid in component tBid (flux)');
    LEGEND_CONSTANTS(:,14) = strpad('k11 in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,13) = strpad('tBidBax in component tBidBax (micromolar)');
    LEGEND_ALGEBRAIC(:,15) = strpad('J_tBidBax in component tBidBax (flux)');
    LEGEND_CONSTANTS(:,15) = strpad('k12b in component model_constant (second_order_rate_constant)');
    LEGEND_STATES(:,14) = strpad('Bcl_2 in component Bcl_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,18) = strpad('J_13 in component Bax (flux)');
    LEGEND_ALGEBRAIC(:,17) = strpad('J_Bax in component Bax (flux)');
    LEGEND_CONSTANTS(:,56) = strpad('P_Bax in component Bax (flux)');
    LEGEND_CONSTANTS(:,16) = strpad('k13 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('P_oBax in component model_constant (flux)');
    LEGEND_CONSTANTS(:,18) = strpad('p53 in component model_constant (micromolar)');
    LEGEND_CONSTANTS(:,19) = strpad('p53_thresh in component model_constant (micromolar)');
    LEGEND_CONSTANTS(:,20) = strpad('u_Bax in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,15) = strpad('Casp3 in component Casp3 (micromolar)');
    LEGEND_STATES(:,16) = strpad('Casp3Bcl_2 in component Casp3Bcl_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,19) = strpad('J_9 in component Bcl_2 (flux)');
    LEGEND_ALGEBRAIC(:,21) = strpad('J_Bcl_2 in component Bcl_2 (flux)');
    LEGEND_CONSTANTS(:,21) = strpad('k_19 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('k_09 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,57) = strpad('P_Bcl_2 in component Bcl_2 (flux)');
    LEGEND_CONSTANTS(:,23) = strpad('P_oBcl_2 in component model_constant (flux)');
    LEGEND_CONSTANTS(:,24) = strpad('u_Bcl_2 in component model_constant (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,20) = strpad('J_f9 in component Casp3Bcl_2 (flux)');
    LEGEND_CONSTANTS(:,25) = strpad('k_f9 in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,17) = strpad('Casp3Bid in component Casp3Bid (micromolar)');
    LEGEND_ALGEBRAIC(:,22) = strpad('J_8 in component Casp3Bid (flux)');
    LEGEND_CONSTANTS(:,26) = strpad('k_18 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('k_08 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('k_f8 in component model_constant (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,23) = strpad('J_Bid in component Bid (flux)');
    LEGEND_CONSTANTS(:,29) = strpad('P_Bid in component model_constant (flux)');
    LEGEND_STATES(:,18) = strpad('IAP in component IAP (micromolar)');
    LEGEND_STATES(:,19) = strpad('Casp3IAP in component Casp3 (micromolar)');
    LEGEND_ALGEBRAIC(:,33) = strpad('J_f6 in component Casp9Pro3 (flux)');
    LEGEND_ALGEBRAIC(:,32) = strpad('J_f6b in component ApopCasp9_2Pro3 (flux)');
    LEGEND_ALGEBRAIC(:,26) = strpad('J_7 in component Casp3 (flux)');
    LEGEND_ALGEBRAIC(:,25) = strpad('J_Casp3 in component Casp3 (flux)');
    LEGEND_CONSTANTS(:,30) = strpad('k_17 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,31) = strpad('k_07 in component model_constant (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,28) = strpad('J_2 in component Pro9 (flux)');
    LEGEND_ALGEBRAIC(:,41) = strpad('J_4b in component ApopCasp9 (flux)');
    LEGEND_STATES(:,20) = strpad('Pro9 in component Pro9 (micromolar)');
    LEGEND_STATES(:,21) = strpad('ApopPro9 in component Pro9 (micromolar)');
    LEGEND_STATES(:,22) = strpad('ApopPro9_2 in component ApopPro9_2 (micromolar)');
    LEGEND_ALGEBRAIC(:,29) = strpad('J_3 in component Pro9 (flux)');
    LEGEND_ALGEBRAIC(:,27) = strpad('J_Pro9 in component Pro9 (flux)');
    LEGEND_CONSTANTS(:,32) = strpad('k_12 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,33) = strpad('k_02 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('k_13 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('k_03 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('P_Pro9 in component model_constant (flux)');
    LEGEND_ALGEBRAIC(:,30) = strpad('J_f3 in component ApopPro9_2 (flux)');
    LEGEND_CONSTANTS(:,37) = strpad('k_f3 in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,23) = strpad('ApopCasp9_2Pro3 in component ApopCasp9_2Pro3 (micromolar)');
    LEGEND_STATES(:,24) = strpad('ApopCasp9_2 in component ApopCasp9_2 (micromolar)');
    LEGEND_STATES(:,25) = strpad('Pro3 in component Pro3 (micromolar)');
    LEGEND_ALGEBRAIC(:,31) = strpad('J_6b in component ApopCasp9_2Pro3 (flux)');
    LEGEND_CONSTANTS(:,38) = strpad('k_16b in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('k_06b in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('k_f6b in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,26) = strpad('Casp9Pro3 in component Casp9Pro3 (micromolar)');
    LEGEND_ALGEBRAIC(:,34) = strpad('J_6 in component Pro3 (flux)');
    LEGEND_CONSTANTS(:,41) = strpad('k_f6 in component model_constant (first_order_rate_constant)');
    LEGEND_STATES(:,27) = strpad('Casp9 in component Casp9 (micromolar)');
    LEGEND_ALGEBRAIC(:,35) = strpad('J_Pro3 in component Pro3 (flux)');
    LEGEND_CONSTANTS(:,42) = strpad('k_16 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,43) = strpad('k_06 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,44) = strpad('P_Pro3 in component model_constant (flux)');
    LEGEND_STATES(:,28) = strpad('Casp9IAP in component IAP (micromolar)');
    LEGEND_STATES(:,29) = strpad('ApopCasp9IAP in component IAP (micromolar)');
    LEGEND_STATES(:,30) = strpad('ApopCasp9_2IAP in component IAP (micromolar)');
    LEGEND_STATES(:,31) = strpad('ApopCasp9 in component ApopCasp9 (micromolar)');
    LEGEND_ALGEBRAIC(:,36) = strpad('J_5 in component IAP (flux)');
    LEGEND_ALGEBRAIC(:,37) = strpad('J_5b in component IAP (flux)');
    LEGEND_ALGEBRAIC(:,38) = strpad('J_5c in component IAP (flux)');
    LEGEND_ALGEBRAIC(:,40) = strpad('J_IAP in component IAP (flux)');
    LEGEND_CONSTANTS(:,45) = strpad('P_IAP in component model_constant (flux)');
    LEGEND_CONSTANTS(:,46) = strpad('k_15 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,47) = strpad('k_05 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,48) = strpad('k_15b in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,49) = strpad('k_05b in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,50) = strpad('k_15c in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,51) = strpad('k_05c in component model_constant (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,39) = strpad('J_4 in component ApopCasp9 (flux)');
    LEGEND_CONSTANTS(:,52) = strpad('k_14 in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,53) = strpad('k_04 in component model_constant (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,54) = strpad('k_14b in component model_constant (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,55) = strpad('k_04b in component model_constant (second_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,42) = strpad('J_Casp9 in component Casp9 (flux)');
    LEGEND_RATES(:,1) = strpad('d/dt Casp8 in component Casp8 (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt Casp8Bid in component Casp8 (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt Apaf_1 in component Apaf_1 (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt CytcApaf_1 in component CytcApaf_1 (micromolar)');
    LEGEND_RATES(:,6) = strpad('d/dt Cytc in component Cytc (micromolar)');
    LEGEND_RATES(:,8) = strpad('d/dt Cytc_mito in component Cytc_mito (micromolar)');
    LEGEND_RATES(:,9) = strpad('d/dt Bax_2 in component Bax_2 (micromolar)');
    LEGEND_RATES(:,10) = strpad('d/dt tBid_mito in component tBid_mito (micromolar)');
    LEGEND_RATES(:,12) = strpad('d/dt tBid in component tBid (micromolar)');
    LEGEND_RATES(:,13) = strpad('d/dt tBidBax in component tBidBax (micromolar)');
    LEGEND_RATES(:,11) = strpad('d/dt Bax in component Bax (micromolar)');
    LEGEND_RATES(:,14) = strpad('d/dt Bcl_2 in component Bcl_2 (micromolar)');
    LEGEND_RATES(:,16) = strpad('d/dt Casp3Bcl_2 in component Casp3Bcl_2 (micromolar)');
    LEGEND_RATES(:,17) = strpad('d/dt Casp3Bid in component Casp3Bid (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt Bid in component Bid (micromolar)');
    LEGEND_RATES(:,19) = strpad('d/dt Casp3IAP in component Casp3 (micromolar)');
    LEGEND_RATES(:,15) = strpad('d/dt Casp3 in component Casp3 (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt Apop in component Apop (micromolar)');
    LEGEND_RATES(:,20) = strpad('d/dt Pro9 in component Pro9 (micromolar)');
    LEGEND_RATES(:,21) = strpad('d/dt ApopPro9 in component Pro9 (micromolar)');
    LEGEND_RATES(:,22) = strpad('d/dt ApopPro9_2 in component ApopPro9_2 (micromolar)');
    LEGEND_RATES(:,23) = strpad('d/dt ApopCasp9_2Pro3 in component ApopCasp9_2Pro3 (micromolar)');
    LEGEND_RATES(:,26) = strpad('d/dt Casp9Pro3 in component Casp9Pro3 (micromolar)');
    LEGEND_RATES(:,25) = strpad('d/dt Pro3 in component Pro3 (micromolar)');
    LEGEND_RATES(:,28) = strpad('d/dt Casp9IAP in component IAP (micromolar)');
    LEGEND_RATES(:,29) = strpad('d/dt ApopCasp9IAP in component IAP (micromolar)');
    LEGEND_RATES(:,30) = strpad('d/dt ApopCasp9_2IAP in component IAP (micromolar)');
    LEGEND_RATES(:,18) = strpad('d/dt IAP in component IAP (micromolar)');
    LEGEND_RATES(:,31) = strpad('d/dt ApopCasp9 in component ApopCasp9 (micromolar)');
    LEGEND_RATES(:,27) = strpad('d/dt Casp9 in component Casp9 (micromolar)');
    LEGEND_RATES(:,24) = strpad('d/dt ApopCasp9_2 in component ApopCasp9_2 (micromolar)');
    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) = 0;
    STATES(:,2) = 0;
    STATES(:,3) = 0.004;
    CONSTANTS(:,1) = 0.1;
    CONSTANTS(:,2) = 10;
    CONSTANTS(:,3) = 0.5;
    CONSTANTS(:,4) = 0.006;
    STATES(:,4) = 0.004;
    STATES(:,5) = 0;
    STATES(:,6) = 0;
    CONSTANTS(:,5) = 0.0003;
    CONSTANTS(:,6) = 5;
    CONSTANTS(:,7) = 0.5;
    STATES(:,7) = 0;
    CONSTANTS(:,8) = 50000;
    CONSTANTS(:,9) = 0.5;
    CONSTANTS(:,10) = 4;
    STATES(:,8) = 0.004;
    STATES(:,9) = 0;
    CONSTANTS(:,11) = 0.0003;
    CONSTANTS(:,12) = 10;
    STATES(:,10) = 0;
    STATES(:,11) = 0.004;
    CONSTANTS(:,13) = 10;
    STATES(:,12) = 0;
    CONSTANTS(:,14) = 10;
    STATES(:,13) = 0;
    CONSTANTS(:,15) = 10;
    STATES(:,14) = 0.004;
    CONSTANTS(:,16) = 10;
    CONSTANTS(:,17) = 0.00003;
    CONSTANTS(:,18) = 0.0066;
    CONSTANTS(:,19) = 0.004;
    CONSTANTS(:,20) = 0.006;
    STATES(:,15) = 0;
    STATES(:,16) = 0;
    CONSTANTS(:,21) = 10;
    CONSTANTS(:,22) = 0.5;
    CONSTANTS(:,23) = 0.00008;
    CONSTANTS(:,24) = 0.006;
    CONSTANTS(:,25) = 0.1;
    STATES(:,17) = 0;
    CONSTANTS(:,26) = 10;
    CONSTANTS(:,27) = 0.5;
    CONSTANTS(:,28) = 0.1;
    CONSTANTS(:,29) = 0.00003;
    STATES(:,18) = 0.004;
    STATES(:,19) = 0;
    CONSTANTS(:,30) = 5;
    CONSTANTS(:,31) = 0.0035;
    STATES(:,20) = 0.004;
    STATES(:,21) = 0;
    STATES(:,22) = 0;
    CONSTANTS(:,32) = 10;
    CONSTANTS(:,33) = 0.5;
    CONSTANTS(:,34) = 10;
    CONSTANTS(:,35) = 0.5;
    CONSTANTS(:,36) = 0.0003;
    CONSTANTS(:,37) = 0.1;
    STATES(:,23) = 0;
    STATES(:,24) = 0;
    STATES(:,25) = 0.004;
    CONSTANTS(:,38) = 10;
    CONSTANTS(:,39) = 0.5;
    CONSTANTS(:,40) = 0.1;
    STATES(:,26) = 0;
    CONSTANTS(:,41) = 0.001;
    STATES(:,27) = 0;
    CONSTANTS(:,42) = 10;
    CONSTANTS(:,43) = 0.5;
    CONSTANTS(:,44) = 0.0003;
    STATES(:,28) = 0;
    STATES(:,29) = 0;
    STATES(:,30) = 0;
    STATES(:,31) = 0;
    CONSTANTS(:,45) = 0.00003;
    CONSTANTS(:,46) = 5;
    CONSTANTS(:,47) = 0.0035;
    CONSTANTS(:,48) = 5;
    CONSTANTS(:,49) = 0.0035;
    CONSTANTS(:,50) = 5;
    CONSTANTS(:,51) = 0.0035;
    CONSTANTS(:,52) = 5;
    CONSTANTS(:,53) = 0.5;
    CONSTANTS(:,54) = 5;
    CONSTANTS(:,55) = 0.5;
    CONSTANTS(:,56) =  CONSTANTS(:,17).*(1.00000+power(CONSTANTS(:,18), 4.00000)./(power(CONSTANTS(:,18), 4.00000)+power(CONSTANTS(:,19), 4.00000)));
    CONSTANTS(:,57) = ( CONSTANTS(:,23).*power(CONSTANTS(:,19), 4.00000))./(power(CONSTANTS(:,18), 4.00000)+power(CONSTANTS(:,19), 4.00000));
    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(:,3) =  CONSTANTS(:,2).*STATES(:,1).*STATES(:,3) -  CONSTANTS(:,3).*STATES(:,2);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*STATES(:,2);
    ALGEBRAIC(:,2) =   - CONSTANTS(:,4).*STATES(:,1);
    RATES(:,1) =  - ALGEBRAIC(:,3)+ALGEBRAIC(:,1)+ALGEBRAIC(:,2);
    RATES(:,2) = ALGEBRAIC(:,3) - ALGEBRAIC(:,1);
    ALGEBRAIC(:,4) = CONSTANTS(:,5) -  CONSTANTS(:,4).*STATES(:,4);
    ALGEBRAIC(:,5) =  CONSTANTS(:,6).*STATES(:,6).*STATES(:,4) -  CONSTANTS(:,7).*STATES(:,5);
    RATES(:,4) =  - ALGEBRAIC(:,5)+ALGEBRAIC(:,4);
    ALGEBRAIC(:,7) =  CONSTANTS(:,8).*power(STATES(:,5), CONSTANTS(:,10)) -  CONSTANTS(:,9).*STATES(:,7);
    RATES(:,5) = ALGEBRAIC(:,5) -  7.00000.*ALGEBRAIC(:,7);
    ALGEBRAIC(:,10) =  CONSTANTS(:,12).*STATES(:,9).*STATES(:,8);
    ALGEBRAIC(:,6) =   - CONSTANTS(:,4).*STATES(:,6);
    RATES(:,6) = (ALGEBRAIC(:,10) - ALGEBRAIC(:,5))+ALGEBRAIC(:,6);
    ALGEBRAIC(:,8) = CONSTANTS(:,11) -  CONSTANTS(:,4).*STATES(:,8);
    RATES(:,8) =  - ALGEBRAIC(:,10)+ALGEBRAIC(:,8);
    ALGEBRAIC(:,13) =  CONSTANTS(:,14).*STATES(:,12);
    ALGEBRAIC(:,12) =  CONSTANTS(:,13).*STATES(:,10).*STATES(:,11);
    ALGEBRAIC(:,11) =   - CONSTANTS(:,4).*STATES(:,10);
    RATES(:,10) = (ALGEBRAIC(:,13) - ALGEBRAIC(:,12))+ALGEBRAIC(:,11);
    ALGEBRAIC(:,16) =  CONSTANTS(:,15).*STATES(:,13).*STATES(:,11);
    ALGEBRAIC(:,9) =   - CONSTANTS(:,4).*STATES(:,9);
    RATES(:,9) = ALGEBRAIC(:,16)+ALGEBRAIC(:,9);
    ALGEBRAIC(:,15) =   - CONSTANTS(:,4).*STATES(:,13);
    RATES(:,13) = (ALGEBRAIC(:,12) - ALGEBRAIC(:,16))+ALGEBRAIC(:,15);
    ALGEBRAIC(:,18) =  CONSTANTS(:,16).*STATES(:,14).*STATES(:,11);
    ALGEBRAIC(:,17) = CONSTANTS(:,56) -  CONSTANTS(:,20).*STATES(:,11);
    RATES(:,11) = (( - ALGEBRAIC(:,12) - ALGEBRAIC(:,16)) - ALGEBRAIC(:,18))+ALGEBRAIC(:,17);
    ALGEBRAIC(:,19) =  CONSTANTS(:,21).*STATES(:,15).*STATES(:,14) -  CONSTANTS(:,22).*STATES(:,16);
    ALGEBRAIC(:,21) = CONSTANTS(:,57) -  CONSTANTS(:,24).*STATES(:,14);
    RATES(:,14) = ( - ALGEBRAIC(:,19) - ALGEBRAIC(:,18))+ALGEBRAIC(:,21);
    ALGEBRAIC(:,20) =  CONSTANTS(:,25).*STATES(:,16);
    RATES(:,16) = ALGEBRAIC(:,19) - ALGEBRAIC(:,20);
    ALGEBRAIC(:,24) =  CONSTANTS(:,28).*STATES(:,17);
    ALGEBRAIC(:,14) =   - CONSTANTS(:,4).*STATES(:,12);
    RATES(:,12) = ((ALGEBRAIC(:,1)+ALGEBRAIC(:,24)) - ALGEBRAIC(:,13))+ALGEBRAIC(:,16)+ALGEBRAIC(:,14);
    ALGEBRAIC(:,22) =  CONSTANTS(:,26).*STATES(:,15).*STATES(:,3) -  CONSTANTS(:,27).*STATES(:,17);
    RATES(:,17) = ALGEBRAIC(:,22) - ALGEBRAIC(:,24);
    ALGEBRAIC(:,23) = CONSTANTS(:,29) -  CONSTANTS(:,4).*STATES(:,3);
    RATES(:,3) = ( - ALGEBRAIC(:,3) - ALGEBRAIC(:,22))+ALGEBRAIC(:,23);
    ALGEBRAIC(:,26) =  CONSTANTS(:,30).*STATES(:,15).*STATES(:,18) -  CONSTANTS(:,31).*STATES(:,19);
    RATES(:,19) = ALGEBRAIC(:,26);
    ALGEBRAIC(:,28) =  CONSTANTS(:,32).*STATES(:,7).*STATES(:,20) -  CONSTANTS(:,33).*STATES(:,21);
    ALGEBRAIC(:,29) =  CONSTANTS(:,34).*STATES(:,21).*STATES(:,20) -  CONSTANTS(:,35).*STATES(:,22);
    ALGEBRAIC(:,27) = CONSTANTS(:,36) -  CONSTANTS(:,4).*STATES(:,20);
    RATES(:,20) = ( - ALGEBRAIC(:,28) - ALGEBRAIC(:,29))+ALGEBRAIC(:,27);
    RATES(:,21) = ALGEBRAIC(:,28) - ALGEBRAIC(:,29);
    ALGEBRAIC(:,30) =  CONSTANTS(:,37).*STATES(:,22);
    RATES(:,22) = ALGEBRAIC(:,29) - ALGEBRAIC(:,30);
    ALGEBRAIC(:,32) =  CONSTANTS(:,40).*STATES(:,23);
    ALGEBRAIC(:,31) =  CONSTANTS(:,38).*STATES(:,24).*STATES(:,25) -  CONSTANTS(:,39).*STATES(:,23);
    RATES(:,23) = ALGEBRAIC(:,31) - ALGEBRAIC(:,32);
    ALGEBRAIC(:,33) =  CONSTANTS(:,41).*STATES(:,26);
    ALGEBRAIC(:,25) =   - CONSTANTS(:,4).*STATES(:,15);
    RATES(:,15) = (((((ALGEBRAIC(:,33)+ALGEBRAIC(:,32)) - ALGEBRAIC(:,26)) - ALGEBRAIC(:,22))+ALGEBRAIC(:,24)) - ALGEBRAIC(:,19))+ALGEBRAIC(:,20)+ALGEBRAIC(:,25);
    ALGEBRAIC(:,34) =  CONSTANTS(:,42).*STATES(:,27).*STATES(:,25) -  CONSTANTS(:,43).*STATES(:,26);
    RATES(:,26) = ALGEBRAIC(:,34) - ALGEBRAIC(:,33);
    ALGEBRAIC(:,35) = CONSTANTS(:,44) -  CONSTANTS(:,4).*STATES(:,25);
    RATES(:,25) = ( - ALGEBRAIC(:,34) - ALGEBRAIC(:,31))+ALGEBRAIC(:,35);
    ALGEBRAIC(:,36) =  CONSTANTS(:,46).*STATES(:,27).*STATES(:,18) -  CONSTANTS(:,47).*STATES(:,28);
    RATES(:,28) = ALGEBRAIC(:,36);
    ALGEBRAIC(:,37) =  CONSTANTS(:,48).*STATES(:,31).*STATES(:,18) -  CONSTANTS(:,49).*STATES(:,29);
    RATES(:,29) = ALGEBRAIC(:,37);
    ALGEBRAIC(:,38) =  CONSTANTS(:,50).*STATES(:,24).*STATES(:,18) -  CONSTANTS(:,51).*STATES(:,30);
    RATES(:,30) = ALGEBRAIC(:,38);
    ALGEBRAIC(:,40) = CONSTANTS(:,45) -  CONSTANTS(:,4).*STATES(:,18);
    RATES(:,18) = ((( - ALGEBRAIC(:,36) - ALGEBRAIC(:,37)) - ALGEBRAIC(:,38)) - ALGEBRAIC(:,26))+ALGEBRAIC(:,40);
    ALGEBRAIC(:,39) =  CONSTANTS(:,52).*STATES(:,24) -  CONSTANTS(:,53).*STATES(:,31).*STATES(:,27);
    RATES(:,24) = (((ALGEBRAIC(:,30) - ALGEBRAIC(:,39)) - ALGEBRAIC(:,38)) - ALGEBRAIC(:,31))+ALGEBRAIC(:,32);
    ALGEBRAIC(:,41) =  CONSTANTS(:,54).*STATES(:,31) -  CONSTANTS(:,55).*STATES(:,7).*STATES(:,27);
    RATES(:,7) = (ALGEBRAIC(:,7) - ALGEBRAIC(:,28))+ALGEBRAIC(:,41);
    RATES(:,31) = (ALGEBRAIC(:,39) - ALGEBRAIC(:,41)) - ALGEBRAIC(:,37);
    ALGEBRAIC(:,42) =   - CONSTANTS(:,4).*STATES(:,27);
    RATES(:,27) = (((ALGEBRAIC(:,39)+ALGEBRAIC(:,41)) - ALGEBRAIC(:,36)) - ALGEBRAIC(:,34))+ALGEBRAIC(:,33)+ALGEBRAIC(:,42);
   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(:,3) =  CONSTANTS(:,2).*STATES(:,1).*STATES(:,3) -  CONSTANTS(:,3).*STATES(:,2);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*STATES(:,2);
    ALGEBRAIC(:,2) =   - CONSTANTS(:,4).*STATES(:,1);
    ALGEBRAIC(:,4) = CONSTANTS(:,5) -  CONSTANTS(:,4).*STATES(:,4);
    ALGEBRAIC(:,5) =  CONSTANTS(:,6).*STATES(:,6).*STATES(:,4) -  CONSTANTS(:,7).*STATES(:,5);
    ALGEBRAIC(:,7) =  CONSTANTS(:,8).*power(STATES(:,5), CONSTANTS(:,10)) -  CONSTANTS(:,9).*STATES(:,7);
    ALGEBRAIC(:,10) =  CONSTANTS(:,12).*STATES(:,9).*STATES(:,8);
    ALGEBRAIC(:,6) =   - CONSTANTS(:,4).*STATES(:,6);
    ALGEBRAIC(:,8) = CONSTANTS(:,11) -  CONSTANTS(:,4).*STATES(:,8);
    ALGEBRAIC(:,13) =  CONSTANTS(:,14).*STATES(:,12);
    ALGEBRAIC(:,12) =  CONSTANTS(:,13).*STATES(:,10).*STATES(:,11);
    ALGEBRAIC(:,11) =   - CONSTANTS(:,4).*STATES(:,10);
    ALGEBRAIC(:,16) =  CONSTANTS(:,15).*STATES(:,13).*STATES(:,11);
    ALGEBRAIC(:,9) =   - CONSTANTS(:,4).*STATES(:,9);
    ALGEBRAIC(:,15) =   - CONSTANTS(:,4).*STATES(:,13);
    ALGEBRAIC(:,18) =  CONSTANTS(:,16).*STATES(:,14).*STATES(:,11);
    ALGEBRAIC(:,17) = CONSTANTS(:,56) -  CONSTANTS(:,20).*STATES(:,11);
    ALGEBRAIC(:,19) =  CONSTANTS(:,21).*STATES(:,15).*STATES(:,14) -  CONSTANTS(:,22).*STATES(:,16);
    ALGEBRAIC(:,21) = CONSTANTS(:,57) -  CONSTANTS(:,24).*STATES(:,14);
    ALGEBRAIC(:,20) =  CONSTANTS(:,25).*STATES(:,16);
    ALGEBRAIC(:,24) =  CONSTANTS(:,28).*STATES(:,17);
    ALGEBRAIC(:,14) =   - CONSTANTS(:,4).*STATES(:,12);
    ALGEBRAIC(:,22) =  CONSTANTS(:,26).*STATES(:,15).*STATES(:,3) -  CONSTANTS(:,27).*STATES(:,17);
    ALGEBRAIC(:,23) = CONSTANTS(:,29) -  CONSTANTS(:,4).*STATES(:,3);
    ALGEBRAIC(:,26) =  CONSTANTS(:,30).*STATES(:,15).*STATES(:,18) -  CONSTANTS(:,31).*STATES(:,19);
    ALGEBRAIC(:,28) =  CONSTANTS(:,32).*STATES(:,7).*STATES(:,20) -  CONSTANTS(:,33).*STATES(:,21);
    ALGEBRAIC(:,29) =  CONSTANTS(:,34).*STATES(:,21).*STATES(:,20) -  CONSTANTS(:,35).*STATES(:,22);
    ALGEBRAIC(:,27) = CONSTANTS(:,36) -  CONSTANTS(:,4).*STATES(:,20);
    ALGEBRAIC(:,30) =  CONSTANTS(:,37).*STATES(:,22);
    ALGEBRAIC(:,32) =  CONSTANTS(:,40).*STATES(:,23);
    ALGEBRAIC(:,31) =  CONSTANTS(:,38).*STATES(:,24).*STATES(:,25) -  CONSTANTS(:,39).*STATES(:,23);
    ALGEBRAIC(:,33) =  CONSTANTS(:,41).*STATES(:,26);
    ALGEBRAIC(:,25) =   - CONSTANTS(:,4).*STATES(:,15);
    ALGEBRAIC(:,34) =  CONSTANTS(:,42).*STATES(:,27).*STATES(:,25) -  CONSTANTS(:,43).*STATES(:,26);
    ALGEBRAIC(:,35) = CONSTANTS(:,44) -  CONSTANTS(:,4).*STATES(:,25);
    ALGEBRAIC(:,36) =  CONSTANTS(:,46).*STATES(:,27).*STATES(:,18) -  CONSTANTS(:,47).*STATES(:,28);
    ALGEBRAIC(:,37) =  CONSTANTS(:,48).*STATES(:,31).*STATES(:,18) -  CONSTANTS(:,49).*STATES(:,29);
    ALGEBRAIC(:,38) =  CONSTANTS(:,50).*STATES(:,24).*STATES(:,18) -  CONSTANTS(:,51).*STATES(:,30);
    ALGEBRAIC(:,40) = CONSTANTS(:,45) -  CONSTANTS(:,4).*STATES(:,18);
    ALGEBRAIC(:,39) =  CONSTANTS(:,52).*STATES(:,24) -  CONSTANTS(:,53).*STATES(:,31).*STATES(:,27);
    ALGEBRAIC(:,41) =  CONSTANTS(:,54).*STATES(:,31) -  CONSTANTS(:,55).*STATES(:,7).*STATES(:,27);
    ALGEBRAIC(:,42) =   - CONSTANTS(:,4).*STATES(:,27);
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