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 =35;
end
% There are a total of 19 entries in each of the rate and state variable arrays.
% There are a total of 40 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_RB1_inactive in component environment (fmol)');
    LEGEND_STATES(:,2) = strpad('q_L_RB1_inactive in component environment (fmol)');
    LEGEND_STATES(:,3) = strpad('q_LB1_ode in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,1) = strpad('q_LB1_stim in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,4) = strpad('q_LB1 in component environment (fmol)');
    LEGEND_STATES(:,4) = strpad('q_RB1 in component environment (fmol)');
    LEGEND_STATES(:,5) = strpad('q_Gs in component environment (fmol)');
    LEGEND_STATES(:,6) = strpad('q_RB1_Gs in component environment (fmol)');
    LEGEND_STATES(:,7) = strpad('q_L_RB1 in component environment (fmol)');
    LEGEND_STATES(:,8) = strpad('q_L_RB1_Gs in component environment (fmol)');
    LEGEND_STATES(:,9) = strpad('q_Gsa_GTP in component environment (fmol)');
    LEGEND_STATES(:,10) = strpad('q_Gsbetagamma in component environment (fmol)');
    LEGEND_STATES(:,11) = strpad('q_Gsa_GDP in component environment (fmol)');
    LEGEND_STATES(:,12) = strpad('q_GTP in component environment (fmol)');
    LEGEND_STATES(:,13) = strpad('q_GDP in component environment (fmol)');
    LEGEND_STATES(:,14) = strpad('q_Pi in component environment (fmol)');
    LEGEND_STATES(:,15) = strpad('q_RB1_tag in component environment (fmol)');
    LEGEND_STATES(:,16) = strpad('q_L_RB1_tag in component environment (fmol)');
    LEGEND_STATES(:,17) = strpad('q_RB1_GRKArr in component environment (fmol)');
    LEGEND_STATES(:,18) = strpad('q_L_RB1_GRKArr in component environment (fmol)');
    LEGEND_STATES(:,19) = strpad('q_GRKArr in component environment (fmol)');
    LEGEND_CONSTANTS(:,1) = strpad('stimSt in component environment (second)');
    LEGEND_CONSTANTS(:,2) = strpad('stimDur in component environment (second)');
    LEGEND_CONSTANTS(:,3) = strpad('tR in component environment (second)');
    LEGEND_CONSTANTS(:,4) = strpad('stimMag in component environment (fmol)');
    LEGEND_CONSTANTS(:,5) = strpad('stimHolding in component environment (fmol)');
    LEGEND_CONSTANTS(:,39) = strpad('m in component environment (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,25) = strpad('v_Rswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,26) = strpad('v_LRswitch_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,27) = strpad('v_C_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,28) = strpad('v_R_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,29) = strpad('v_L_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,30) = strpad('v_Act1_Gs in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,31) = strpad('v_Act2_Gs in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,32) = strpad('v_Hyd_Gs in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,34) = strpad('v_Reassoc_Gs in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,33) = strpad('v_InternR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,35) = strpad('v_InternLR_B1 in component GPCR_B1AR_reduced (fmol_per_sec)');
    LEGEND_CONSTANTS(:,40) = strpad('v_Rsynthesis in component environment (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,2) = strpad('conserv_R_T in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,6) = strpad('conserv_L_T in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,3) = strpad('conserv_G_T in component environment (fmol)');
    LEGEND_CONSTANTS(:,6) = strpad('kappa_Rswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,7) = strpad('kappa_LRswitch_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,8) = strpad('kappa_C_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,9) = strpad('kappa_R_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,10) = strpad('kappa_L_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,11) = strpad('kappa_Act1_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,12) = strpad('kappa_Act2_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,13) = strpad('kappa_Hyd_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,14) = strpad('kappa_Reassoc_Gs in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,15) = strpad('kappa_InternR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,16) = strpad('kappa_InternLR_B1 in component GPCR_B1AR_reduced_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,17) = strpad('K_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,18) = strpad('K_L_RB1_inactive in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,19) = strpad('K_LB1 in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,20) = strpad('K_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,21) = strpad('K_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,22) = strpad('K_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,23) = strpad('K_L_RB1 in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,24) = strpad('K_L_RB1_Gs in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,25) = strpad('K_Gsa_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,26) = strpad('K_Gsbetagamma in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,27) = strpad('K_Gsa_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,28) = strpad('K_GTP in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,29) = strpad('K_GDP in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,30) = strpad('K_Pi in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,31) = strpad('K_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,32) = strpad('K_L_RB1_tag in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,33) = strpad('K_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,34) = strpad('K_L_RB1_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,35) = strpad('K_GRKArr in component GPCR_B1AR_reduced_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,36) = strpad('R in component constants (J_per_K_per_mol)');
    LEGEND_CONSTANTS(:,37) = strpad('T in component constants (kelvin)');
    LEGEND_ALGEBRAIC(:,5) = strpad('mu_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,7) = strpad('mu_L_RB1_inactive in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,8) = strpad('mu_LB1 in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,9) = strpad('mu_RB1 in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,10) = strpad('mu_Gs in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,11) = strpad('mu_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,12) = strpad('mu_L_RB1 in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,13) = strpad('mu_L_RB1_Gs in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,14) = strpad('mu_Gsa_GTP in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,15) = strpad('mu_Gsbetagamma in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,16) = strpad('mu_Gsa_GDP in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,17) = strpad('mu_GTP in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,18) = strpad('mu_GDP in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,19) = strpad('mu_Pi in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,20) = strpad('mu_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,21) = strpad('mu_L_RB1_tag in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,22) = strpad('mu_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,23) = strpad('mu_L_RB1_GRKArr in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_ALGEBRAIC(:,24) = strpad('mu_GRKArr in component GPCR_B1AR_reduced (J_per_mol)');
    LEGEND_CONSTANTS(:,38) = strpad('F in component constants (C_per_mol)');
    LEGEND_RATES(:,1) = strpad('d/dt q_RB1_inactive in component environment (fmol)');
    LEGEND_RATES(:,2) = strpad('d/dt q_L_RB1_inactive in component environment (fmol)');
    LEGEND_RATES(:,3) = strpad('d/dt q_LB1_ode in component environment (fmol)');
    LEGEND_RATES(:,4) = strpad('d/dt q_RB1 in component environment (fmol)');
    LEGEND_RATES(:,5) = strpad('d/dt q_Gs in component environment (fmol)');
    LEGEND_RATES(:,6) = strpad('d/dt q_RB1_Gs in component environment (fmol)');
    LEGEND_RATES(:,7) = strpad('d/dt q_L_RB1 in component environment (fmol)');
    LEGEND_RATES(:,8) = strpad('d/dt q_L_RB1_Gs in component environment (fmol)');
    LEGEND_RATES(:,9) = strpad('d/dt q_Gsa_GTP in component environment (fmol)');
    LEGEND_RATES(:,10) = strpad('d/dt q_Gsbetagamma in component environment (fmol)');
    LEGEND_RATES(:,11) = strpad('d/dt q_Gsa_GDP in component environment (fmol)');
    LEGEND_RATES(:,12) = strpad('d/dt q_GTP in component environment (fmol)');
    LEGEND_RATES(:,13) = strpad('d/dt q_GDP in component environment (fmol)');
    LEGEND_RATES(:,14) = strpad('d/dt q_Pi in component environment (fmol)');
    LEGEND_RATES(:,15) = strpad('d/dt q_RB1_tag in component environment (fmol)');
    LEGEND_RATES(:,16) = strpad('d/dt q_L_RB1_tag in component environment (fmol)');
    LEGEND_RATES(:,17) = strpad('d/dt q_RB1_GRKArr in component environment (fmol)');
    LEGEND_RATES(:,18) = strpad('d/dt q_L_RB1_GRKArr in component environment (fmol)');
    LEGEND_RATES(:,19) = strpad('d/dt q_GRKArr 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) = 0.0004579000e0;
    STATES(:,2) = 1e-18;
    STATES(:,3) = 0;
    STATES(:,4) = 1e-18;
    STATES(:,5) = 0.1455400000;
    STATES(:,6) = 1e-18;
    STATES(:,7) = 1e-18;
    STATES(:,8) = 1e-18;
    STATES(:,9) = 0.01;
    STATES(:,10) = 0.02;
    STATES(:,11) = 0.01;
    STATES(:,12) = 2.2;
    STATES(:,13) = 1.1;
    STATES(:,14) = 570;
    STATES(:,15) = 1e-18;
    STATES(:,16) = 1e-18;
    STATES(:,17) = 1e-18;
    STATES(:,18) = 1e-18;
    STATES(:,19) = 1e-3;
    CONSTANTS(:,1) = 0.5e1;
    CONSTANTS(:,2) = 5e-1;
    CONSTANTS(:,3) = 5e-1;
    CONSTANTS(:,4) = 1e1;
    CONSTANTS(:,5) = 1e-8;
    CONSTANTS(:,6) = 1036.38;
    CONSTANTS(:,7) = 1.83921e-07;
    CONSTANTS(:,8) = 891573;
    CONSTANTS(:,9) = 1.58222e+06;
    CONSTANTS(:,10) = 52417.5;
    CONSTANTS(:,11) = 0.000610519;
    CONSTANTS(:,12) = 0.576677;
    CONSTANTS(:,13) = 0.0661821;
    CONSTANTS(:,14) = 8.60273e-06;
    CONSTANTS(:,15) = 0.00230556;
    CONSTANTS(:,16) = 2.17775;
    CONSTANTS(:,17) = 28.0492;
    CONSTANTS(:,18) = 1.58056e+11;
    CONSTANTS(:,19) = 0.0574759;
    CONSTANTS(:,20) = 0.280492;
    CONSTANTS(:,21) = 0.00337913;
    CONSTANTS(:,22) = 1.07597;
    CONSTANTS(:,23) = 0.158056;
    CONSTANTS(:,24) = 0.00113911;
    CONSTANTS(:,25) = 0.00878478;
    CONSTANTS(:,26) = 736.699;
    CONSTANTS(:,27) = 161.34;
    CONSTANTS(:,28) = 823.314;
    CONSTANTS(:,29) = 3.61368e-10;
    CONSTANTS(:,30) = 7.91408e-11;
    CONSTANTS(:,31) = 0.500146;
    CONSTANTS(:,32) = 0.000529497;
    CONSTANTS(:,33) = 1.26086e-05;
    CONSTANTS(:,34) = 1.33485e-08;
    CONSTANTS(:,35) = 732843;
    CONSTANTS(:,36) = 8.31;
    CONSTANTS(:,37) = 310;
    CONSTANTS(:,38) = 96485;
    CONSTANTS(:,39) = CONSTANTS(:,4)./CONSTANTS(:,3);
    CONSTANTS(:,40) = 0.000100000;
    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(:,5) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,17).*STATES(:,1));
    ALGEBRAIC(:,9) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,20).*STATES(:,4));
    ALGEBRAIC(:,25) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,1) =  - ALGEBRAIC(:,25)+ 0.00000.*CONSTANTS(:,40);
    ALGEBRAIC(:,7) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,18).*STATES(:,2));
    ALGEBRAIC(:,12) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,23).*STATES(:,7));
    ALGEBRAIC(:,26) =  CONSTANTS(:,7).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,12)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,2) =  - ALGEBRAIC(:,26);
    ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,1)&VOI>CONSTANTS(:,1) - CONSTANTS(:,3), CONSTANTS(:,5)+ CONSTANTS(:,39).*((VOI - CONSTANTS(:,1))+CONSTANTS(:,3)) , VOI>=CONSTANTS(:,1)&VOI<CONSTANTS(:,1)+CONSTANTS(:,2), CONSTANTS(:,4)+CONSTANTS(:,5) , VOI<=CONSTANTS(:,1)+CONSTANTS(:,3)+CONSTANTS(:,2)&VOI>=CONSTANTS(:,1)+CONSTANTS(:,2), CONSTANTS(:,5)+  - CONSTANTS(:,39).*(((VOI - CONSTANTS(:,1)) - CONSTANTS(:,3)) - CONSTANTS(:,2)) }, CONSTANTS(:,5));
    ALGEBRAIC(:,4) = ALGEBRAIC(:,1)+STATES(:,3);
    ALGEBRAIC(:,8) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,19).*ALGEBRAIC(:,4));
    ALGEBRAIC(:,29) =  CONSTANTS(:,10).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,8))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,12)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,3) =  - ALGEBRAIC(:,29);
    ALGEBRAIC(:,10) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,21).*STATES(:,5));
    ALGEBRAIC(:,11) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,22).*STATES(:,6));
    ALGEBRAIC(:,27) =  CONSTANTS(:,8).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,10))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,4) = (ALGEBRAIC(:,25) - ALGEBRAIC(:,27)) - ALGEBRAIC(:,29);
    ALGEBRAIC(:,14) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,25).*STATES(:,9));
    ALGEBRAIC(:,15) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,26).*STATES(:,10));
    ALGEBRAIC(:,17) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,28).*STATES(:,12));
    ALGEBRAIC(:,18) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,29).*STATES(:,13));
    ALGEBRAIC(:,20) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,31).*STATES(:,15));
    ALGEBRAIC(:,30) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,11)+ALGEBRAIC(:,17))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15)+ALGEBRAIC(:,20)+ALGEBRAIC(:,18))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,6) = ALGEBRAIC(:,27) - ALGEBRAIC(:,30);
    ALGEBRAIC(:,13) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,24).*STATES(:,8));
    ALGEBRAIC(:,28) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,10))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,7) = (ALGEBRAIC(:,26) - ALGEBRAIC(:,28))+ALGEBRAIC(:,29);
    ALGEBRAIC(:,21) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,32).*STATES(:,16));
    ALGEBRAIC(:,31) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,13)+ALGEBRAIC(:,17))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15)+ALGEBRAIC(:,21)+ALGEBRAIC(:,18))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,8) = ALGEBRAIC(:,28) - ALGEBRAIC(:,31);
    RATES(:,12) =  - ALGEBRAIC(:,30) - ALGEBRAIC(:,31);
    RATES(:,13) = ALGEBRAIC(:,30)+ALGEBRAIC(:,31);
    ALGEBRAIC(:,16) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,27).*STATES(:,11));
    ALGEBRAIC(:,19) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,30).*STATES(:,14));
    ALGEBRAIC(:,32) =  CONSTANTS(:,13).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,19))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,9) = (ALGEBRAIC(:,30)+ALGEBRAIC(:,31)) - ALGEBRAIC(:,32);
    RATES(:,14) = ALGEBRAIC(:,32);
    ALGEBRAIC(:,22) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,33).*STATES(:,17));
    ALGEBRAIC(:,24) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,35).*STATES(:,19));
    ALGEBRAIC(:,33) =  CONSTANTS(:,15).*(exp((ALGEBRAIC(:,20)+ALGEBRAIC(:,24))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,22)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,15) = ALGEBRAIC(:,30) - ALGEBRAIC(:,33);
    RATES(:,17) = ALGEBRAIC(:,33);
    ALGEBRAIC(:,34) =  CONSTANTS(:,14).*(exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,15))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,10)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,5) = ( - ALGEBRAIC(:,27) - ALGEBRAIC(:,28))+ALGEBRAIC(:,34);
    RATES(:,10) = (ALGEBRAIC(:,30)+ALGEBRAIC(:,31)) - ALGEBRAIC(:,34);
    RATES(:,11) = ALGEBRAIC(:,32) - ALGEBRAIC(:,34);
    ALGEBRAIC(:,23) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,34).*STATES(:,18));
    ALGEBRAIC(:,35) =  CONSTANTS(:,16).*(exp((ALGEBRAIC(:,21)+ALGEBRAIC(:,24))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,23)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    RATES(:,16) = ALGEBRAIC(:,31) - ALGEBRAIC(:,35);
    RATES(:,18) = ALGEBRAIC(:,35);
    RATES(:,19) =  - ALGEBRAIC(:,33) - ALGEBRAIC(:,35);
   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(:,5) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,17).*STATES(:,1));
    ALGEBRAIC(:,9) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,20).*STATES(:,4));
    ALGEBRAIC(:,25) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,9)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,7) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,18).*STATES(:,2));
    ALGEBRAIC(:,12) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,23).*STATES(:,7));
    ALGEBRAIC(:,26) =  CONSTANTS(:,7).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,12)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,1)&VOI>CONSTANTS(:,1) - CONSTANTS(:,3), CONSTANTS(:,5)+ CONSTANTS(:,39).*((VOI - CONSTANTS(:,1))+CONSTANTS(:,3)) , VOI>=CONSTANTS(:,1)&VOI<CONSTANTS(:,1)+CONSTANTS(:,2), CONSTANTS(:,4)+CONSTANTS(:,5) , VOI<=CONSTANTS(:,1)+CONSTANTS(:,3)+CONSTANTS(:,2)&VOI>=CONSTANTS(:,1)+CONSTANTS(:,2), CONSTANTS(:,5)+  - CONSTANTS(:,39).*(((VOI - CONSTANTS(:,1)) - CONSTANTS(:,3)) - CONSTANTS(:,2)) }, CONSTANTS(:,5));
    ALGEBRAIC(:,4) = ALGEBRAIC(:,1)+STATES(:,3);
    ALGEBRAIC(:,8) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,19).*ALGEBRAIC(:,4));
    ALGEBRAIC(:,29) =  CONSTANTS(:,10).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,8))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,12)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,10) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,21).*STATES(:,5));
    ALGEBRAIC(:,11) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,22).*STATES(:,6));
    ALGEBRAIC(:,27) =  CONSTANTS(:,8).*(exp((ALGEBRAIC(:,9)+ALGEBRAIC(:,10))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,14) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,25).*STATES(:,9));
    ALGEBRAIC(:,15) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,26).*STATES(:,10));
    ALGEBRAIC(:,17) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,28).*STATES(:,12));
    ALGEBRAIC(:,18) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,29).*STATES(:,13));
    ALGEBRAIC(:,20) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,31).*STATES(:,15));
    ALGEBRAIC(:,30) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,11)+ALGEBRAIC(:,17))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15)+ALGEBRAIC(:,20)+ALGEBRAIC(:,18))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,13) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,24).*STATES(:,8));
    ALGEBRAIC(:,28) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,12)+ALGEBRAIC(:,10))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,13)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,21) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,32).*STATES(:,16));
    ALGEBRAIC(:,31) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,13)+ALGEBRAIC(:,17))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15)+ALGEBRAIC(:,21)+ALGEBRAIC(:,18))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,16) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,27).*STATES(:,11));
    ALGEBRAIC(:,19) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,30).*STATES(:,14));
    ALGEBRAIC(:,32) =  CONSTANTS(:,13).*(exp(ALGEBRAIC(:,14)./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,19))./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,22) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,33).*STATES(:,17));
    ALGEBRAIC(:,24) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,35).*STATES(:,19));
    ALGEBRAIC(:,33) =  CONSTANTS(:,15).*(exp((ALGEBRAIC(:,20)+ALGEBRAIC(:,24))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,22)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,34) =  CONSTANTS(:,14).*(exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,15))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,10)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,23) =  CONSTANTS(:,36).*CONSTANTS(:,37).*log( CONSTANTS(:,34).*STATES(:,18));
    ALGEBRAIC(:,35) =  CONSTANTS(:,16).*(exp((ALGEBRAIC(:,21)+ALGEBRAIC(:,24))./( CONSTANTS(:,36).*CONSTANTS(:,37))) - exp(ALGEBRAIC(:,23)./( CONSTANTS(:,36).*CONSTANTS(:,37))));
    ALGEBRAIC(:,2) = STATES(:,1)+STATES(:,2)+STATES(:,4)+STATES(:,6)+STATES(:,7)+STATES(:,8)+STATES(:,15)+STATES(:,16)+STATES(:,17)+STATES(:,18);
    ALGEBRAIC(:,3) = STATES(:,5)+STATES(:,6)+STATES(:,8)+STATES(:,9)+STATES(:,11);
    ALGEBRAIC(:,6) = STATES(:,2)+ALGEBRAIC(:,4)+STATES(:,7)+STATES(:,8)+STATES(:,16)+STATES(:,18);
end

% Compute result of a piecewise function
function x = piecewise(cases, default)
    set = [0];
    for i = 1:2:length(cases)
        if (length(cases{i+1}) == 1)
            x(cases{i} & ~set,:) = cases{i+1};
        else
            x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
        end
        set = set | cases{i};
        if(set), break, end
    end
    if (length(default) == 1)
        x(~set,:) = default;
    else
        x(~set,:) = default(~set);
    end
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