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 =30;
end
% There are a total of 18 entries in each of the rate and state variable arrays.
% There are a total of 33 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('q_ATP in component environment (fmol)');
    LEGEND_STATES(:,2) = strpad('q_AC in component environment (fmol)');
    LEGEND_STATES(:,3) = strpad('q_cAMP in component environment (fmol)');
    LEGEND_STATES(:,4) = strpad('q_AC_ATP in component environment (fmol)');
    LEGEND_STATES(:,5) = strpad('q_FSK in component environment (fmol)');
    LEGEND_STATES(:,6) = strpad('q_FSK_AC in component environment (fmol)');
    LEGEND_STATES(:,7) = strpad('q_FSK_AC_ATP in component environment (fmol)');
    LEGEND_STATES(:,8) = strpad('q_Gsa_GTP in component environment (fmol)');
    LEGEND_STATES(:,9) = strpad('q_Gsa_GTP_AC in component environment (fmol)');
    LEGEND_STATES(:,10) = strpad('q_Gsa_GTP_AC_ATP in component environment (fmol)');
    LEGEND_STATES(:,11) = strpad('q_PDE in component environment (fmol)');
    LEGEND_STATES(:,12) = strpad('q_PDEinh in component environment (fmol)');
    LEGEND_STATES(:,13) = strpad('q_PDE_cAMP in component environment (fmol)');
    LEGEND_STATES(:,14) = strpad('q_IBMX in component environment (fmol)');
    LEGEND_STATES(:,15) = strpad('q_five_AMP in component environment (fmol)');
    LEGEND_STATES(:,16) = strpad('q_Gia_GTP in component environment (fmol)');
    LEGEND_STATES(:,17) = strpad('q_ACinh in component environment (fmol)');
    LEGEND_STATES(:,18) = strpad('q_PPi in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,19) = strpad('v_1a in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,20) = strpad('v_1b in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,21) = strpad('v_2a in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,22) = strpad('v_2b in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,23) = strpad('v_3a in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,24) = strpad('v_3b in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,25) = strpad('v_4a in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,27) = strpad('v_4b in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,29) = strpad('v_5 in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,26) = strpad('v_6 in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,28) = strpad('v_7 in component cAMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,30) = strpad('v_GiAC in component cAMP (fmol_per_sec)');
    LEGEND_CONSTANTS(:,1) = strpad('kappa_1a in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,2) = strpad('kappa_1b in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,3) = strpad('kappa_2a in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,4) = strpad('kappa_2b in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,5) = strpad('kappa_3a in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,6) = strpad('kappa_3b in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,7) = strpad('kappa_4a in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,8) = strpad('kappa_4b in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,9) = strpad('kappa_5 in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,10) = strpad('kappa_6 in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,11) = strpad('kappa_7 in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,12) = strpad('kappa_GiAC in component cAMP_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,13) = strpad('K_ATP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,14) = strpad('K_cAMP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,15) = strpad('K_AC in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,16) = strpad('K_AC_ATP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,17) = strpad('K_Gsa_GTP_AC in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,18) = strpad('K_Gsa_GTP_AC_ATP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,19) = strpad('K_FSK_AC in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,20) = strpad('K_FSK_AC_ATP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,21) = strpad('K_PDE in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,22) = strpad('K_PDE_cAMP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,23) = strpad('K_five_AMP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,24) = strpad('K_IBMX in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,25) = strpad('K_PDEinh in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,26) = strpad('K_Gsa_GTP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,27) = strpad('K_FSK in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,28) = strpad('K_Gia_GTP in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,29) = strpad('K_ACinh in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,30) = strpad('K_PPi in component cAMP_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,31) = strpad('R in component constants (J_per_K_per_mol)');
    LEGEND_CONSTANTS(:,32) = strpad('T in component constants (kelvin)');
    LEGEND_ALGEBRAIC(:,1) = strpad('mu_ATP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,2) = strpad('mu_cAMP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,3) = strpad('mu_AC in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,4) = strpad('mu_AC_ATP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,5) = strpad('mu_Gsa_GTP_AC in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,6) = strpad('mu_Gsa_GTP_AC_ATP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,7) = strpad('mu_FSK_AC in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,8) = strpad('mu_FSK_AC_ATP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,9) = strpad('mu_PDE in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,10) = strpad('mu_PDE_cAMP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,11) = strpad('mu_five_AMP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,12) = strpad('mu_IBMX in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,13) = strpad('mu_PDEinh in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,14) = strpad('mu_Gsa_GTP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,15) = strpad('mu_FSK in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,16) = strpad('mu_Gia_GTP in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,17) = strpad('mu_ACinh in component cAMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,18) = strpad('mu_PPi in component cAMP (J_per_mol)');
    LEGEND_CONSTANTS(:,33) = strpad('F in component constants (C_per_mol)');
    LEGEND_RATES(:,1) = strpad('d/dt q_ATP in component environment (fmol)');
    LEGEND_RATES(:,2) = strpad('d/dt q_AC in component environment (fmol)');
    LEGEND_RATES(:,4) = strpad('d/dt q_AC_ATP in component environment (fmol)');
    LEGEND_RATES(:,3) = strpad('d/dt q_cAMP in component environment (fmol)');
    LEGEND_RATES(:,5) = strpad('d/dt q_FSK in component environment (fmol)');
    LEGEND_RATES(:,6) = strpad('d/dt q_FSK_AC in component environment (fmol)');
    LEGEND_RATES(:,7) = strpad('d/dt q_FSK_AC_ATP in component environment (fmol)');
    LEGEND_RATES(:,8) = strpad('d/dt q_Gsa_GTP in component environment (fmol)');
    LEGEND_RATES(:,9) = strpad('d/dt q_Gsa_GTP_AC in component environment (fmol)');
    LEGEND_RATES(:,10) = strpad('d/dt q_Gsa_GTP_AC_ATP in component environment (fmol)');
    LEGEND_RATES(:,13) = strpad('d/dt q_PDE_cAMP in component environment (fmol)');
    LEGEND_RATES(:,11) = strpad('d/dt q_PDE in component environment (fmol)');
    LEGEND_RATES(:,14) = strpad('d/dt q_IBMX in component environment (fmol)');
    LEGEND_RATES(:,12) = strpad('d/dt q_PDEinh in component environment (fmol)');
    LEGEND_RATES(:,15) = strpad('d/dt q_five_AMP in component environment (fmol)');
    LEGEND_RATES(:,16) = strpad('d/dt q_Gia_GTP in component environment (fmol)');
    LEGEND_RATES(:,17) = strpad('d/dt q_ACinh in component environment (fmol)');
    LEGEND_RATES(:,18) = strpad('d/dt q_PPi in component environment (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 = [];
    STATES(:,1) = 190;
    STATES(:,2) = 1.889E-03;
    STATES(:,3) = 3.212E-02;
    STATES(:,4) = 1e-18;
    STATES(:,5) = 3.8e-5;
    STATES(:,6) = 1e-18;
    STATES(:,7) = 1e-18;
    STATES(:,8) = 9.519E-04;
    STATES(:,9) = 1e-18;
    STATES(:,10) = 1e-18;
    STATES(:,11) = 1.482E-03;
    STATES(:,12) = 1e-18;
    STATES(:,13) = 1e-18;
    STATES(:,14) = 3.80E-06;
    STATES(:,15) = 1e-18;
    STATES(:,16) = 4.81E-04;
    STATES(:,17) = 1e-18;
    STATES(:,18) = 1e-18;
    CONSTANTS(:,1) = 9.47329e+06;
    CONSTANTS(:,2) = 0.00197793;
    CONSTANTS(:,3) = 176000;
    CONSTANTS(:,4) = 0.047492;
    CONSTANTS(:,5) = 5.07667e+08;
    CONSTANTS(:,6) = 5.9031e-17;
    CONSTANTS(:,7) = 36084.5;
    CONSTANTS(:,8) = 0.138787;
    CONSTANTS(:,9) = 751.564;
    CONSTANTS(:,10) = 556.617;
    CONSTANTS(:,11) = 160555;
    CONSTANTS(:,12) = 685.521;
    CONSTANTS(:,13) = 9.19362e-06;
    CONSTANTS(:,14) = 0.0102598;
    CONSTANTS(:,15) = 9.02358;
    CONSTANTS(:,16) = 2.93942;
    CONSTANTS(:,17) = 52.2258;
    CONSTANTS(:,18) = 5.20284;
    CONSTANTS(:,19) = 0.181058;
    CONSTANTS(:,20) = 0.0492449;
    CONSTANTS(:,21) = 2.28256;
    CONSTANTS(:,22) = 1.04728;
    CONSTANTS(:,23) = 0.0102598;
    CONSTANTS(:,24) = 0.01642;
    CONSTANTS(:,25) = 38.679;
    CONSTANTS(:,26) = 0.420618;
    CONSTANTS(:,27) = 1.32565e-05;
    CONSTANTS(:,28) = 0.013661;
    CONSTANTS(:,29) = 42.4053;
    CONSTANTS(:,30) = 2.60488e-05;
    CONSTANTS(:,31) = 8.31;
    CONSTANTS(:,32) = 310;
    CONSTANTS(:,33) = 96485;
    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(:,1) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,13).*STATES(:,1));
    ALGEBRAIC(:,3) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,15).*STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,16).*STATES(:,4));
    ALGEBRAIC(:,19) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,4)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,2) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,14).*STATES(:,3));
    ALGEBRAIC(:,18) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,30).*STATES(:,18));
    ALGEBRAIC(:,20) =  CONSTANTS(:,2).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,4) = ALGEBRAIC(:,19) - ALGEBRAIC(:,20);
    ALGEBRAIC(:,5) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,17).*STATES(:,9));
    ALGEBRAIC(:,6) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,18).*STATES(:,10));
    ALGEBRAIC(:,21) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,22) =  CONSTANTS(:,4).*(exp(ALGEBRAIC(:,6)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,10) = ALGEBRAIC(:,21) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,7) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,19).*STATES(:,6));
    ALGEBRAIC(:,8) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,20).*STATES(:,7));
    ALGEBRAIC(:,23) =  CONSTANTS(:,5).*(exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,8)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,1) = ( - ALGEBRAIC(:,19) - ALGEBRAIC(:,23)) - ALGEBRAIC(:,21);
    ALGEBRAIC(:,24) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,7) = ALGEBRAIC(:,23) - ALGEBRAIC(:,24);
    ALGEBRAIC(:,9) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,21).*STATES(:,11));
    ALGEBRAIC(:,10) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,22).*STATES(:,13));
    ALGEBRAIC(:,25) =  CONSTANTS(:,7).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,2))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,10)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,3) = (ALGEBRAIC(:,20)+ALGEBRAIC(:,24)+ALGEBRAIC(:,22)) - ALGEBRAIC(:,25);
    ALGEBRAIC(:,14) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,26).*STATES(:,8));
    ALGEBRAIC(:,26) =  CONSTANTS(:,10).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,14))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,8) =  - ALGEBRAIC(:,26);
    RATES(:,9) = (ALGEBRAIC(:,26) - ALGEBRAIC(:,21))+ALGEBRAIC(:,22);
    ALGEBRAIC(:,15) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,27).*STATES(:,5));
    ALGEBRAIC(:,28) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,3))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,5) =  - ALGEBRAIC(:,28);
    RATES(:,6) = (ALGEBRAIC(:,28)+ALGEBRAIC(:,24)) - ALGEBRAIC(:,23);
    ALGEBRAIC(:,11) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,23).*STATES(:,15));
    ALGEBRAIC(:,27) =  CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,11))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,13) = ALGEBRAIC(:,25) - ALGEBRAIC(:,27);
    RATES(:,15) = ALGEBRAIC(:,27);
    ALGEBRAIC(:,16) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,28).*STATES(:,16));
    ALGEBRAIC(:,17) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,29).*STATES(:,17));
    ALGEBRAIC(:,30) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,16))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,2) = (((ALGEBRAIC(:,20) - ALGEBRAIC(:,19)) - ALGEBRAIC(:,26)) - ALGEBRAIC(:,28)) - ALGEBRAIC(:,30);
    ALGEBRAIC(:,12) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,24).*STATES(:,14));
    ALGEBRAIC(:,13) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,25).*STATES(:,12));
    ALGEBRAIC(:,29) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,12))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    RATES(:,11) = (ALGEBRAIC(:,27) - ALGEBRAIC(:,25)) - ALGEBRAIC(:,29);
    RATES(:,14) =  - ALGEBRAIC(:,29);
    RATES(:,12) = ALGEBRAIC(:,29);
    RATES(:,16) =  - ALGEBRAIC(:,30);
    RATES(:,17) = ALGEBRAIC(:,30);
    RATES(:,18) = ALGEBRAIC(:,30);
   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(:,1) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,13).*STATES(:,1));
    ALGEBRAIC(:,3) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,15).*STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,16).*STATES(:,4));
    ALGEBRAIC(:,19) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,4)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,2) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,14).*STATES(:,3));
    ALGEBRAIC(:,18) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,30).*STATES(:,18));
    ALGEBRAIC(:,20) =  CONSTANTS(:,2).*(exp(ALGEBRAIC(:,4)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,5) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,17).*STATES(:,9));
    ALGEBRAIC(:,6) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,18).*STATES(:,10));
    ALGEBRAIC(:,21) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,22) =  CONSTANTS(:,4).*(exp(ALGEBRAIC(:,6)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,7) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,19).*STATES(:,6));
    ALGEBRAIC(:,8) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,20).*STATES(:,7));
    ALGEBRAIC(:,23) =  CONSTANTS(:,5).*(exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,1))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,8)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,24) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,8)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,7)+ALGEBRAIC(:,2)+ALGEBRAIC(:,18))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,9) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,21).*STATES(:,11));
    ALGEBRAIC(:,10) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,22).*STATES(:,13));
    ALGEBRAIC(:,25) =  CONSTANTS(:,7).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,2))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,10)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,14) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,26).*STATES(:,8));
    ALGEBRAIC(:,26) =  CONSTANTS(:,10).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,14))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,5)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,15) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,27).*STATES(:,5));
    ALGEBRAIC(:,28) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,15)+ALGEBRAIC(:,3))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,7)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,11) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,23).*STATES(:,15));
    ALGEBRAIC(:,27) =  CONSTANTS(:,8).*(exp(ALGEBRAIC(:,10)./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,11))./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,16) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,28).*STATES(:,16));
    ALGEBRAIC(:,17) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,29).*STATES(:,17));
    ALGEBRAIC(:,30) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,16))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,17)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
    ALGEBRAIC(:,12) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,24).*STATES(:,14));
    ALGEBRAIC(:,13) =  CONSTANTS(:,31).*CONSTANTS(:,32).*log( CONSTANTS(:,25).*STATES(:,12));
    ALGEBRAIC(:,29) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,12))./( CONSTANTS(:,31).*CONSTANTS(:,32))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,31).*CONSTANTS(:,32))));
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