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 =24;
end
% There are a total of 22 entries in each of the rate and state variable arrays.
% There are a total of 60 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 (minute)');
    LEGEND_CONSTANTS(:,1) = strpad('Glc_x_0 in component Glc_x_0 (millimolar)');
    LEGEND_STATES(:,1) = strpad('Glc_x in component Glc_x (millimolar)');
    LEGEND_ALGEBRAIC(:,2) = strpad('GlcTrans in component GlcTrans (flux)');
    LEGEND_ALGEBRAIC(:,1) = strpad('inGlc in component inGlc (flux)');
    LEGEND_STATES(:,2) = strpad('Glc in component Glc (millimolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('HK in component HK (flux)');
    LEGEND_STATES(:,3) = strpad('G6P in component G6P (millimolar)');
    LEGEND_ALGEBRAIC(:,4) = strpad('PGI in component PGI (flux)');
    LEGEND_ALGEBRAIC(:,11) = strpad('storage in component storage (flux)');
    LEGEND_STATES(:,4) = strpad('F6P in component F6P (millimolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('PFK in component PFK (flux)');
    LEGEND_STATES(:,5) = strpad('FBP in component FBP (millimolar)');
    LEGEND_ALGEBRAIC(:,6) = strpad('ALD in component ALD (flux)');
    LEGEND_STATES(:,6) = strpad('GAP in component GAP (millimolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('GAPDH in component GAPDH (flux)');
    LEGEND_ALGEBRAIC(:,7) = strpad('TIM in component TIM (flux)');
    LEGEND_STATES(:,7) = strpad('DHAP in component DHAP (millimolar)');
    LEGEND_ALGEBRAIC(:,15) = strpad('lpGlyc in component lpGlyc (flux)');
    LEGEND_STATES(:,8) = strpad('BPG in component BPG (millimolar)');
    LEGEND_ALGEBRAIC(:,9) = strpad('lpPEP in component lpPEP (flux)');
    LEGEND_STATES(:,9) = strpad('PEP in component PEP (millimolar)');
    LEGEND_ALGEBRAIC(:,10) = strpad('PK in component PK (flux)');
    LEGEND_STATES(:,10) = strpad('Pyr in component Pyr (millimolar)');
    LEGEND_ALGEBRAIC(:,12) = strpad('PDC in component PDC (flux)');
    LEGEND_STATES(:,11) = strpad('ATP in component ATP (millimolar)');
    LEGEND_ALGEBRAIC(:,13) = strpad('consum in component consum (flux)');
    LEGEND_ALGEBRAIC(:,16) = strpad('AK in component AK (flux)');
    LEGEND_STATES(:,12) = strpad('ADP in component ADP (millimolar)');
    LEGEND_STATES(:,13) = strpad('AMP in component AMP (millimolar)');
    LEGEND_CONSTANTS(:,2) = strpad('CN_x_0 in component CN_x_0 (millimolar)');
    LEGEND_STATES(:,14) = strpad('CN_x in component CN_x (millimolar)');
    LEGEND_ALGEBRAIC(:,22) = strpad('lacto in component lacto (flux)');
    LEGEND_ALGEBRAIC(:,24) = strpad('inCN in component inCN (flux)');
    LEGEND_STATES(:,15) = strpad('ACA in component ACA (millimolar)');
    LEGEND_ALGEBRAIC(:,19) = strpad('difACA in component difACA (flux)');
    LEGEND_ALGEBRAIC(:,14) = strpad('ADH in component ADH (flux)');
    LEGEND_STATES(:,16) = strpad('ACA_x in component ACA_x (millimolar)');
    LEGEND_ALGEBRAIC(:,17) = strpad('outACA in component outACA (flux)');
    LEGEND_STATES(:,17) = strpad('EtOH in component EtOH (millimolar)');
    LEGEND_ALGEBRAIC(:,20) = strpad('difEtOH in component difEtOH (flux)');
    LEGEND_STATES(:,18) = strpad('EtOH_x in component EtOH_x (millimolar)');
    LEGEND_ALGEBRAIC(:,18) = strpad('outEtOH in component outEtOH (flux)');
    LEGEND_STATES(:,19) = strpad('Glyc in component Glyc (millimolar)');
    LEGEND_ALGEBRAIC(:,23) = strpad('difGlyc in component difGlyc (flux)');
    LEGEND_STATES(:,20) = strpad('Glyc_x in component Glyc_x (millimolar)');
    LEGEND_ALGEBRAIC(:,21) = strpad('outGlyc in component outGlyc (flux)');
    LEGEND_STATES(:,21) = strpad('NADH in component NADH (millimolar)');
    LEGEND_STATES(:,22) = strpad('NAD in component NAD (millimolar)');
    LEGEND_CONSTANTS(:,3) = strpad('k0 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('K2_Glc in component GlcTrans (millimolar)');
    LEGEND_CONSTANTS(:,5) = strpad('K2_IG6P in component GlcTrans (millimolar)');
    LEGEND_CONSTANTS(:,6) = strpad('K2_IIG6P in component GlcTrans (millimolar)');
    LEGEND_CONSTANTS(:,7) = strpad('V_2m in component GlcTrans (flux)');
    LEGEND_CONSTANTS(:,8) = strpad('P2 in component GlcTrans (dimensionless)');
    LEGEND_CONSTANTS(:,9) = strpad('y_vol in component model_parameters (dimensionless)');
    LEGEND_CONSTANTS(:,10) = strpad('K3_DGlc in component HK (millimolar)');
    LEGEND_CONSTANTS(:,11) = strpad('K3_Glc in component HK (millimolar)');
    LEGEND_CONSTANTS(:,12) = strpad('K3_ATP in component HK (millimolar)');
    LEGEND_CONSTANTS(:,13) = strpad('V_3m in component HK (flux)');
    LEGEND_CONSTANTS(:,14) = strpad('V_4m in component PGI (flux)');
    LEGEND_CONSTANTS(:,15) = strpad('K4_G6P in component PGI (millimolar)');
    LEGEND_CONSTANTS(:,16) = strpad('K4_F6P in component PGI (millimolar)');
    LEGEND_CONSTANTS(:,17) = strpad('K4_eq in component PGI (dimensionless)');
    LEGEND_CONSTANTS(:,18) = strpad('K5 in component PFK (millimolar2)');
    LEGEND_CONSTANTS(:,19) = strpad('kappa5 in component PFK (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('V_5m in component PFK (flux)');
    LEGEND_CONSTANTS(:,21) = strpad('K6_eq in component ALD (millimolar)');
    LEGEND_CONSTANTS(:,22) = strpad('K6_FBP in component ALD (millimolar)');
    LEGEND_CONSTANTS(:,23) = strpad('K6_DHAP in component ALD (millimolar)');
    LEGEND_CONSTANTS(:,24) = strpad('K6_GAP in component ALD (millimolar)');
    LEGEND_CONSTANTS(:,25) = strpad('K6_IGAP in component ALD (millimolar)');
    LEGEND_CONSTANTS(:,26) = strpad('V_6r in component ALD (flux)');
    LEGEND_CONSTANTS(:,27) = strpad('V_6f in component ALD (flux)');
    LEGEND_CONSTANTS(:,28) = strpad('K7_eq in component TIM (dimensionless)');
    LEGEND_CONSTANTS(:,29) = strpad('K7_DHAP in component TIM (millimolar)');
    LEGEND_CONSTANTS(:,30) = strpad('K7_GAP in component TIM (millimolar)');
    LEGEND_CONSTANTS(:,31) = strpad('V_7m in component TIM (flux)');
    LEGEND_CONSTANTS(:,32) = strpad('K8_NAD in component GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,33) = strpad('K8_NADH in component GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,34) = strpad('K8_GAP in component GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,35) = strpad('K8_BPG in component GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,36) = strpad('K8_eq in component GAPDH (dimensionless)');
    LEGEND_CONSTANTS(:,37) = strpad('V_8m in component GAPDH (flux)');
    LEGEND_CONSTANTS(:,38) = strpad('k9f in component lpPEP (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('k9r in component lpPEP (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('K10_PEP in component PK (millimolar)');
    LEGEND_CONSTANTS(:,41) = strpad('K10_ADP in component PK (millimolar)');
    LEGEND_CONSTANTS(:,42) = strpad('V_10m in component PK (flux)');
    LEGEND_CONSTANTS(:,43) = strpad('K11 in component PDC (millimolar)');
    LEGEND_CONSTANTS(:,44) = strpad('V_11m in component PDC (flux)');
    LEGEND_CONSTANTS(:,45) = strpad('K12_NADH in component ADH (millimolar)');
    LEGEND_CONSTANTS(:,46) = strpad('K12_ACA in component ADH (millimolar)');
    LEGEND_CONSTANTS(:,47) = strpad('V_12m in component ADH (flux)');
    LEGEND_CONSTANTS(:,48) = strpad('k13 in component difEtOH (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,49) = strpad('K15_NADH in component lpGlyc (millimolar)');
    LEGEND_CONSTANTS(:,50) = strpad('K15_INADH in component lpGlyc (millimolar)');
    LEGEND_CONSTANTS(:,51) = strpad('K15_INAD in component lpGlyc (millimolar)');
    LEGEND_CONSTANTS(:,52) = strpad('K15_DHAP in component lpGlyc (millimolar)');
    LEGEND_CONSTANTS(:,53) = strpad('V_15m in component lpGlyc (flux)');
    LEGEND_CONSTANTS(:,54) = strpad('k16 in component difGlyc (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,55) = strpad('k18 in component difACA (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,56) = strpad('k20 in component lacto (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,57) = strpad('k22 in component storage (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,58) = strpad('k23 in component consum (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,59) = strpad('k24f in component AK (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,60) = strpad('k24r in component AK (second_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt Glc_x in component Glc_x (millimolar)');
    LEGEND_RATES(:,2) = strpad('d/dt Glc in component Glc (millimolar)');
    LEGEND_RATES(:,3) = strpad('d/dt G6P in component G6P (millimolar)');
    LEGEND_RATES(:,4) = strpad('d/dt F6P in component F6P (millimolar)');
    LEGEND_RATES(:,5) = strpad('d/dt FBP in component FBP (millimolar)');
    LEGEND_RATES(:,6) = strpad('d/dt GAP in component GAP (millimolar)');
    LEGEND_RATES(:,7) = strpad('d/dt DHAP in component DHAP (millimolar)');
    LEGEND_RATES(:,8) = strpad('d/dt BPG in component BPG (millimolar)');
    LEGEND_RATES(:,9) = strpad('d/dt PEP in component PEP (millimolar)');
    LEGEND_RATES(:,10) = strpad('d/dt Pyr in component Pyr (millimolar)');
    LEGEND_RATES(:,11) = strpad('d/dt ATP in component ATP (millimolar)');
    LEGEND_RATES(:,12) = strpad('d/dt ADP in component ADP (millimolar)');
    LEGEND_RATES(:,13) = strpad('d/dt AMP in component AMP (millimolar)');
    LEGEND_RATES(:,14) = strpad('d/dt CN_x in component CN_x (millimolar)');
    LEGEND_RATES(:,15) = strpad('d/dt ACA in component ACA (millimolar)');
    LEGEND_RATES(:,16) = strpad('d/dt ACA_x in component ACA_x (millimolar)');
    LEGEND_RATES(:,17) = strpad('d/dt EtOH in component EtOH (millimolar)');
    LEGEND_RATES(:,18) = strpad('d/dt EtOH_x in component EtOH_x (millimolar)');
    LEGEND_RATES(:,19) = strpad('d/dt Glyc in component Glyc (millimolar)');
    LEGEND_RATES(:,20) = strpad('d/dt Glyc_x in component Glyc_x (millimolar)');
    LEGEND_RATES(:,21) = strpad('d/dt NADH in component NADH (millimolar)');
    LEGEND_RATES(:,22) = strpad('d/dt NAD in component NAD (millimolar)');
    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) = 24.0;
    STATES(:,1) = 6.7;
    STATES(:,2) = 0.573074;
    STATES(:,3) = 4.2;
    STATES(:,4) = 0.49;
    STATES(:,5) = 4.64;
    STATES(:,6) = 0.115;
    STATES(:,7) = 2.95;
    STATES(:,8) = 0.00027;
    STATES(:,9) = 0.04;
    STATES(:,10) = 8.7;
    STATES(:,11) = 2.1;
    STATES(:,12) = 1.5;
    STATES(:,13) = 0.33;
    CONSTANTS(:,2) = 5.60;
    STATES(:,14) = 5.20358;
    STATES(:,15) = 1.48153;
    STATES(:,16) = 1.28836;
    STATES(:,17) = 19.2379;
    STATES(:,18) = 16.4514;
    STATES(:,19) = 4.196;
    STATES(:,20) = 1.68478;
    STATES(:,21) = 0.33;
    STATES(:,22) = 0.65;
    CONSTANTS(:,3) = 0.048;
    CONSTANTS(:,4) = 1.7;
    CONSTANTS(:,5) = 1.2;
    CONSTANTS(:,6) = 7.2;
    CONSTANTS(:,7) = 1014.96;
    CONSTANTS(:,8) = 1.0;
    CONSTANTS(:,9) = 59.0;
    CONSTANTS(:,10) = 0.37;
    CONSTANTS(:,11) = 0.0;
    CONSTANTS(:,12) = 0.1;
    CONSTANTS(:,13) = 51.7547;
    CONSTANTS(:,14) = 496.042;
    CONSTANTS(:,15) = 0.8;
    CONSTANTS(:,16) = 0.15;
    CONSTANTS(:,17) = 0.13;
    CONSTANTS(:,18) = 0.021;
    CONSTANTS(:,19) = 0.15;
    CONSTANTS(:,20) = 45.4327;
    CONSTANTS(:,21) = 0.081;
    CONSTANTS(:,22) = 0.3;
    CONSTANTS(:,23) = 2.0;
    CONSTANTS(:,24) = 4.0;
    CONSTANTS(:,25) = 10.0;
    CONSTANTS(:,26) = 1.10391E4;
    CONSTANTS(:,27) = 2.20782E3;
    CONSTANTS(:,28) = 0.055;
    CONSTANTS(:,29) = 1.23;
    CONSTANTS(:,30) = 1.27;
    CONSTANTS(:,31) = 1.16365E2;
    CONSTANTS(:,32) = 0.1;
    CONSTANTS(:,33) = 0.06;
    CONSTANTS(:,34) = 0.6;
    CONSTANTS(:,35) = 0.01;
    CONSTANTS(:,36) = 0.0055;
    CONSTANTS(:,37) = 8.33858E2;
    CONSTANTS(:,38) = 4.43866E5;
    CONSTANTS(:,39) = 1.52862E3;
    CONSTANTS(:,40) = 0.2;
    CONSTANTS(:,41) = 0.17;
    CONSTANTS(:,42) = 3.43096E2;
    CONSTANTS(:,43) = 0.3;
    CONSTANTS(:,44) = 5.31328E1;
    CONSTANTS(:,45) = 0.1;
    CONSTANTS(:,46) = 0.71;
    CONSTANTS(:,47) = 8.98023E1;
    CONSTANTS(:,48) = 16.72;
    CONSTANTS(:,49) = 0.13;
    CONSTANTS(:,50) = 0.034;
    CONSTANTS(:,51) = 0.13;
    CONSTANTS(:,52) = 25.0;
    CONSTANTS(:,53) = 8.14797E1;
    CONSTANTS(:,54) = 1.9;
    CONSTANTS(:,55) = 24.7;
    CONSTANTS(:,56) = 2.83828E-3;
    CONSTANTS(:,57) = 2.25932;
    CONSTANTS(:,58) = 3.20760;
    CONSTANTS(:,59) = 4.32900E2;
    CONSTANTS(:,60) = 1.33333E2;
    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(:,2) =  (CONSTANTS(:,7)./CONSTANTS(:,9)).*((STATES(:,1)./CONSTANTS(:,4))./(1.00000+STATES(:,1)./CONSTANTS(:,4)+ (( CONSTANTS(:,8).*(STATES(:,1)./CONSTANTS(:,4))+1.00000)./( CONSTANTS(:,8).*(STATES(:,2)./CONSTANTS(:,4))+1.00000)).*(1.00000+STATES(:,2)./CONSTANTS(:,4)+STATES(:,3)./CONSTANTS(:,5)+( STATES(:,2).*STATES(:,3))./( CONSTANTS(:,4).*CONSTANTS(:,6))))) -  (CONSTANTS(:,7)./CONSTANTS(:,9)).*((STATES(:,2)./CONSTANTS(:,4))./(1.00000+STATES(:,2)./CONSTANTS(:,4)+ (( CONSTANTS(:,8).*(STATES(:,2)./CONSTANTS(:,4))+1.00000)./( CONSTANTS(:,8).*(STATES(:,1)./CONSTANTS(:,4))+1.00000)).*(1.00000+STATES(:,1)./CONSTANTS(:,4))+STATES(:,3)./CONSTANTS(:,5)+( STATES(:,2).*STATES(:,3))./( CONSTANTS(:,4).*CONSTANTS(:,6))));
    ALGEBRAIC(:,1) =  CONSTANTS(:,3).*(CONSTANTS(:,1) - STATES(:,1));
    RATES(:,1) = ALGEBRAIC(:,1) - ALGEBRAIC(:,2);
    ALGEBRAIC(:,3) = ( CONSTANTS(:,13).*STATES(:,11).*STATES(:,2))./( CONSTANTS(:,10).*CONSTANTS(:,12)+ CONSTANTS(:,11).*STATES(:,11)+ CONSTANTS(:,12).*STATES(:,2)+ STATES(:,2).*STATES(:,11));
    RATES(:,2) =  59.0000.*ALGEBRAIC(:,2) - ALGEBRAIC(:,3);
    ALGEBRAIC(:,4) = ( CONSTANTS(:,14).*STATES(:,3))./(CONSTANTS(:,15)+STATES(:,3)+ (CONSTANTS(:,15)./CONSTANTS(:,16)).*STATES(:,4)) - ( CONSTANTS(:,14).*(STATES(:,4)./CONSTANTS(:,17)))./(CONSTANTS(:,15)+STATES(:,3)+ (CONSTANTS(:,15)./CONSTANTS(:,16)).*STATES(:,4));
    ALGEBRAIC(:,5) = ( CONSTANTS(:,20).*power(STATES(:,4), 2.00000))./( CONSTANTS(:,18).*(1.00000+ CONSTANTS(:,19).*(STATES(:,11)./STATES(:,13)).*(STATES(:,11)./STATES(:,13)))+power(STATES(:,4), 2.00000));
    RATES(:,4) = ALGEBRAIC(:,4) - ALGEBRAIC(:,5);
    ALGEBRAIC(:,6) = ( CONSTANTS(:,27).*STATES(:,5))./(CONSTANTS(:,22)+STATES(:,5)+( STATES(:,6).*CONSTANTS(:,23).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,7).*CONSTANTS(:,24).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,5).*STATES(:,6))./CONSTANTS(:,25)+( STATES(:,6).*STATES(:,7).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))) - ( CONSTANTS(:,27).*(( STATES(:,6).*STATES(:,7))./CONSTANTS(:,21)))./(CONSTANTS(:,22)+STATES(:,5)+( STATES(:,6).*CONSTANTS(:,23).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,7).*CONSTANTS(:,24).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,5).*STATES(:,6))./CONSTANTS(:,25)+( STATES(:,6).*STATES(:,7).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26)));
    RATES(:,5) = ALGEBRAIC(:,5) - ALGEBRAIC(:,6);
    ALGEBRAIC(:,8) = ( CONSTANTS(:,37).*STATES(:,6).*STATES(:,22))./( CONSTANTS(:,34).*CONSTANTS(:,32).*(1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,8)./CONSTANTS(:,35)).*(1.00000+STATES(:,22)./CONSTANTS(:,32)+STATES(:,21)./CONSTANTS(:,33))) - ( CONSTANTS(:,37).*(( STATES(:,8).*STATES(:,21))./CONSTANTS(:,36)))./( CONSTANTS(:,34).*CONSTANTS(:,32).*(1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,8)./CONSTANTS(:,35)).*(1.00000+STATES(:,22)./CONSTANTS(:,32)+STATES(:,21)./CONSTANTS(:,33)));
    ALGEBRAIC(:,7) = ( CONSTANTS(:,31).*STATES(:,7))./(CONSTANTS(:,29)+STATES(:,7)+ (CONSTANTS(:,29)./CONSTANTS(:,30)).*STATES(:,6)) - ( CONSTANTS(:,31).*(STATES(:,6)./CONSTANTS(:,28)))./(CONSTANTS(:,29)+STATES(:,7)+ (CONSTANTS(:,29)./CONSTANTS(:,30)).*STATES(:,6));
    RATES(:,6) = (ALGEBRAIC(:,6)+ALGEBRAIC(:,7)) - ALGEBRAIC(:,8);
    ALGEBRAIC(:,9) =  CONSTANTS(:,38).*STATES(:,8).*STATES(:,12) -  CONSTANTS(:,39).*STATES(:,9).*STATES(:,11);
    RATES(:,8) = ALGEBRAIC(:,8) - ALGEBRAIC(:,9);
    ALGEBRAIC(:,10) = ( CONSTANTS(:,42).*STATES(:,12).*STATES(:,9))./( (CONSTANTS(:,40)+STATES(:,9)).*(CONSTANTS(:,41)+STATES(:,12)));
    RATES(:,9) = ALGEBRAIC(:,9) - ALGEBRAIC(:,10);
    ALGEBRAIC(:,11) =  CONSTANTS(:,57).*STATES(:,11).*STATES(:,3);
    RATES(:,3) = ALGEBRAIC(:,3) - (ALGEBRAIC(:,4)+ALGEBRAIC(:,11));
    ALGEBRAIC(:,12) = ( CONSTANTS(:,44).*STATES(:,10))./(CONSTANTS(:,43)+STATES(:,10));
    RATES(:,10) = ALGEBRAIC(:,10) - ALGEBRAIC(:,12);
    ALGEBRAIC(:,15) = ( CONSTANTS(:,53).*STATES(:,7))./( CONSTANTS(:,52).*(1.00000+ (CONSTANTS(:,50)./STATES(:,21)).*(1.00000+STATES(:,22)./CONSTANTS(:,51)))+ STATES(:,7).*(1.00000+ (CONSTANTS(:,49)./STATES(:,21)).*(1.00000+STATES(:,22)./CONSTANTS(:,51))));
    RATES(:,7) = ALGEBRAIC(:,6) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,15));
    ALGEBRAIC(:,13) =  CONSTANTS(:,58).*STATES(:,11);
    ALGEBRAIC(:,16) =  CONSTANTS(:,59).*STATES(:,13).*STATES(:,11) -  CONSTANTS(:,60).*power(STATES(:,12), 2.00000);
    RATES(:,11) = (ALGEBRAIC(:,10)+ALGEBRAIC(:,9)) - (ALGEBRAIC(:,5)+ALGEBRAIC(:,11)+ALGEBRAIC(:,3)+ALGEBRAIC(:,13)+ALGEBRAIC(:,16));
    RATES(:,12) = (ALGEBRAIC(:,5)+ALGEBRAIC(:,11)+ALGEBRAIC(:,3)+ALGEBRAIC(:,13)+ 2.00000.*ALGEBRAIC(:,16)) - (ALGEBRAIC(:,10)+ALGEBRAIC(:,9));
    RATES(:,13) =  - ALGEBRAIC(:,16);
    ALGEBRAIC(:,14) = ( CONSTANTS(:,47).*STATES(:,15).*STATES(:,21))./( (CONSTANTS(:,45)+STATES(:,21)).*(CONSTANTS(:,46)+STATES(:,15)));
    RATES(:,21) = ALGEBRAIC(:,8) - (ALGEBRAIC(:,14)+ALGEBRAIC(:,15));
    RATES(:,22) = (ALGEBRAIC(:,14)+ALGEBRAIC(:,15)) - ALGEBRAIC(:,8);
    ALGEBRAIC(:,19) =  (CONSTANTS(:,55)./CONSTANTS(:,9)).*(STATES(:,15) - STATES(:,16));
    RATES(:,15) = ALGEBRAIC(:,12) - ( 59.0000.*ALGEBRAIC(:,19)+ALGEBRAIC(:,14));
    ALGEBRAIC(:,20) =  (CONSTANTS(:,48)./CONSTANTS(:,9)).*(STATES(:,17) - STATES(:,18));
    RATES(:,17) = ALGEBRAIC(:,14) -  59.0000.*ALGEBRAIC(:,20);
    ALGEBRAIC(:,18) =  CONSTANTS(:,3).*STATES(:,18);
    RATES(:,18) = ALGEBRAIC(:,20) - ALGEBRAIC(:,18);
    ALGEBRAIC(:,22) =  CONSTANTS(:,56).*STATES(:,16).*STATES(:,14);
    ALGEBRAIC(:,17) =  CONSTANTS(:,3).*STATES(:,16);
    RATES(:,16) = ALGEBRAIC(:,19) - (ALGEBRAIC(:,22)+ALGEBRAIC(:,17));
    ALGEBRAIC(:,23) =  (CONSTANTS(:,54)./CONSTANTS(:,9)).*(STATES(:,19) - STATES(:,20));
    RATES(:,19) = ALGEBRAIC(:,15) -  59.0000.*ALGEBRAIC(:,23);
    ALGEBRAIC(:,21) =  CONSTANTS(:,3).*STATES(:,20);
    RATES(:,20) = ALGEBRAIC(:,23) - ALGEBRAIC(:,21);
    ALGEBRAIC(:,24) =  CONSTANTS(:,3).*(CONSTANTS(:,2) - STATES(:,14));
    RATES(:,14) = ALGEBRAIC(:,24) - 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(:,2) =  (CONSTANTS(:,7)./CONSTANTS(:,9)).*((STATES(:,1)./CONSTANTS(:,4))./(1.00000+STATES(:,1)./CONSTANTS(:,4)+ (( CONSTANTS(:,8).*(STATES(:,1)./CONSTANTS(:,4))+1.00000)./( CONSTANTS(:,8).*(STATES(:,2)./CONSTANTS(:,4))+1.00000)).*(1.00000+STATES(:,2)./CONSTANTS(:,4)+STATES(:,3)./CONSTANTS(:,5)+( STATES(:,2).*STATES(:,3))./( CONSTANTS(:,4).*CONSTANTS(:,6))))) -  (CONSTANTS(:,7)./CONSTANTS(:,9)).*((STATES(:,2)./CONSTANTS(:,4))./(1.00000+STATES(:,2)./CONSTANTS(:,4)+ (( CONSTANTS(:,8).*(STATES(:,2)./CONSTANTS(:,4))+1.00000)./( CONSTANTS(:,8).*(STATES(:,1)./CONSTANTS(:,4))+1.00000)).*(1.00000+STATES(:,1)./CONSTANTS(:,4))+STATES(:,3)./CONSTANTS(:,5)+( STATES(:,2).*STATES(:,3))./( CONSTANTS(:,4).*CONSTANTS(:,6))));
    ALGEBRAIC(:,1) =  CONSTANTS(:,3).*(CONSTANTS(:,1) - STATES(:,1));
    ALGEBRAIC(:,3) = ( CONSTANTS(:,13).*STATES(:,11).*STATES(:,2))./( CONSTANTS(:,10).*CONSTANTS(:,12)+ CONSTANTS(:,11).*STATES(:,11)+ CONSTANTS(:,12).*STATES(:,2)+ STATES(:,2).*STATES(:,11));
    ALGEBRAIC(:,4) = ( CONSTANTS(:,14).*STATES(:,3))./(CONSTANTS(:,15)+STATES(:,3)+ (CONSTANTS(:,15)./CONSTANTS(:,16)).*STATES(:,4)) - ( CONSTANTS(:,14).*(STATES(:,4)./CONSTANTS(:,17)))./(CONSTANTS(:,15)+STATES(:,3)+ (CONSTANTS(:,15)./CONSTANTS(:,16)).*STATES(:,4));
    ALGEBRAIC(:,5) = ( CONSTANTS(:,20).*power(STATES(:,4), 2.00000))./( CONSTANTS(:,18).*(1.00000+ CONSTANTS(:,19).*(STATES(:,11)./STATES(:,13)).*(STATES(:,11)./STATES(:,13)))+power(STATES(:,4), 2.00000));
    ALGEBRAIC(:,6) = ( CONSTANTS(:,27).*STATES(:,5))./(CONSTANTS(:,22)+STATES(:,5)+( STATES(:,6).*CONSTANTS(:,23).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,7).*CONSTANTS(:,24).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,5).*STATES(:,6))./CONSTANTS(:,25)+( STATES(:,6).*STATES(:,7).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))) - ( CONSTANTS(:,27).*(( STATES(:,6).*STATES(:,7))./CONSTANTS(:,21)))./(CONSTANTS(:,22)+STATES(:,5)+( STATES(:,6).*CONSTANTS(:,23).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,7).*CONSTANTS(:,24).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26))+( STATES(:,5).*STATES(:,6))./CONSTANTS(:,25)+( STATES(:,6).*STATES(:,7).*CONSTANTS(:,27))./( CONSTANTS(:,21).*CONSTANTS(:,26)));
    ALGEBRAIC(:,8) = ( CONSTANTS(:,37).*STATES(:,6).*STATES(:,22))./( CONSTANTS(:,34).*CONSTANTS(:,32).*(1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,8)./CONSTANTS(:,35)).*(1.00000+STATES(:,22)./CONSTANTS(:,32)+STATES(:,21)./CONSTANTS(:,33))) - ( CONSTANTS(:,37).*(( STATES(:,8).*STATES(:,21))./CONSTANTS(:,36)))./( CONSTANTS(:,34).*CONSTANTS(:,32).*(1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,8)./CONSTANTS(:,35)).*(1.00000+STATES(:,22)./CONSTANTS(:,32)+STATES(:,21)./CONSTANTS(:,33)));
    ALGEBRAIC(:,7) = ( CONSTANTS(:,31).*STATES(:,7))./(CONSTANTS(:,29)+STATES(:,7)+ (CONSTANTS(:,29)./CONSTANTS(:,30)).*STATES(:,6)) - ( CONSTANTS(:,31).*(STATES(:,6)./CONSTANTS(:,28)))./(CONSTANTS(:,29)+STATES(:,7)+ (CONSTANTS(:,29)./CONSTANTS(:,30)).*STATES(:,6));
    ALGEBRAIC(:,9) =  CONSTANTS(:,38).*STATES(:,8).*STATES(:,12) -  CONSTANTS(:,39).*STATES(:,9).*STATES(:,11);
    ALGEBRAIC(:,10) = ( CONSTANTS(:,42).*STATES(:,12).*STATES(:,9))./( (CONSTANTS(:,40)+STATES(:,9)).*(CONSTANTS(:,41)+STATES(:,12)));
    ALGEBRAIC(:,11) =  CONSTANTS(:,57).*STATES(:,11).*STATES(:,3);
    ALGEBRAIC(:,12) = ( CONSTANTS(:,44).*STATES(:,10))./(CONSTANTS(:,43)+STATES(:,10));
    ALGEBRAIC(:,15) = ( CONSTANTS(:,53).*STATES(:,7))./( CONSTANTS(:,52).*(1.00000+ (CONSTANTS(:,50)./STATES(:,21)).*(1.00000+STATES(:,22)./CONSTANTS(:,51)))+ STATES(:,7).*(1.00000+ (CONSTANTS(:,49)./STATES(:,21)).*(1.00000+STATES(:,22)./CONSTANTS(:,51))));
    ALGEBRAIC(:,13) =  CONSTANTS(:,58).*STATES(:,11);
    ALGEBRAIC(:,16) =  CONSTANTS(:,59).*STATES(:,13).*STATES(:,11) -  CONSTANTS(:,60).*power(STATES(:,12), 2.00000);
    ALGEBRAIC(:,14) = ( CONSTANTS(:,47).*STATES(:,15).*STATES(:,21))./( (CONSTANTS(:,45)+STATES(:,21)).*(CONSTANTS(:,46)+STATES(:,15)));
    ALGEBRAIC(:,19) =  (CONSTANTS(:,55)./CONSTANTS(:,9)).*(STATES(:,15) - STATES(:,16));
    ALGEBRAIC(:,20) =  (CONSTANTS(:,48)./CONSTANTS(:,9)).*(STATES(:,17) - STATES(:,18));
    ALGEBRAIC(:,18) =  CONSTANTS(:,3).*STATES(:,18);
    ALGEBRAIC(:,22) =  CONSTANTS(:,56).*STATES(:,16).*STATES(:,14);
    ALGEBRAIC(:,17) =  CONSTANTS(:,3).*STATES(:,16);
    ALGEBRAIC(:,23) =  (CONSTANTS(:,54)./CONSTANTS(:,9)).*(STATES(:,19) - STATES(:,20));
    ALGEBRAIC(:,21) =  CONSTANTS(:,3).*STATES(:,20);
    ALGEBRAIC(:,24) =  CONSTANTS(:,3).*(CONSTANTS(:,2) - STATES(:,14));
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