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 =23;
end
% There are a total of 14 entries in each of the rate and state variable arrays.
% There are a total of 90 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('GLCo in component GLCo (millimolar)');
    LEGEND_STATES(:,1) = strpad('GLCi in component GLCi (millimolar)');
    LEGEND_ALGEBRAIC(:,10) = strpad('v_GLT in component v_GLT (flux)');
    LEGEND_ALGEBRAIC(:,9) = strpad('v_GLK in component v_GLK (flux)');
    LEGEND_STATES(:,2) = strpad('G6P in component G6P (millimolar)');
    LEGEND_ALGEBRAIC(:,6) = strpad('v_PGI in component v_PGI (flux)');
    LEGEND_CONSTANTS(:,2) = strpad('v_trehalose in component v_trehalose (flux)');
    LEGEND_CONSTANTS(:,3) = strpad('v_glycogen in component v_glycogen (flux)');
    LEGEND_STATES(:,3) = strpad('F6P in component F6P (millimolar)');
    LEGEND_ALGEBRAIC(:,21) = strpad('v_PFK in component v_PFK (flux)');
    LEGEND_STATES(:,4) = strpad('F16P in component F16P (millimolar)');
    LEGEND_ALGEBRAIC(:,14) = strpad('v_ALD in component v_ALD (flux)');
    LEGEND_CONSTANTS(:,4) = strpad('F26P in component F26P (millimolar)');
    LEGEND_STATES(:,5) = strpad('TRIO in component TRIO (millimolar)');
    LEGEND_ALGEBRAIC(:,11) = strpad('v_GAPDH in component v_GAPDH (flux)');
    LEGEND_ALGEBRAIC(:,22) = strpad('v_G3PDH in component v_G3PDH (flux)');
    LEGEND_STATES(:,6) = strpad('BPG in component BPG (millimolar)');
    LEGEND_ALGEBRAIC(:,12) = strpad('v_PGK in component v_PGK (flux)');
    LEGEND_STATES(:,7) = strpad('P3G in component P3G (millimolar)');
    LEGEND_ALGEBRAIC(:,7) = strpad('v_PGM in component v_PGM (flux)');
    LEGEND_STATES(:,8) = strpad('P2G in component P2G (millimolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('v_ENO in component v_ENO (flux)');
    LEGEND_STATES(:,9) = strpad('PEP in component PEP (millimolar)');
    LEGEND_ALGEBRAIC(:,13) = strpad('v_PYK in component v_PYK (flux)');
    LEGEND_STATES(:,10) = strpad('PYR in component PYR (millimolar)');
    LEGEND_ALGEBRAIC(:,15) = strpad('v_PDC in component v_PDC (flux)');
    LEGEND_STATES(:,11) = strpad('ACE in component ACE (millimolar)');
    LEGEND_ALGEBRAIC(:,16) = strpad('v_ADH in component v_ADH (flux)');
    LEGEND_ALGEBRAIC(:,23) = strpad('v_succinate in component v_succinate (flux)');
    LEGEND_STATES(:,12) = strpad('P in component P (millimolar)');
    LEGEND_ALGEBRAIC(:,17) = strpad('v_ATP in component v_ATP (flux)');
    LEGEND_STATES(:,13) = strpad('NADH in component NADH (millimolar)');
    LEGEND_STATES(:,14) = strpad('NAD in component NAD (millimolar)');
    LEGEND_ALGEBRAIC(:,1) = strpad('DHAP in component DHAP (millimolar)');
    LEGEND_CONSTANTS(:,5) = strpad('Keq_TPI in component DHAP (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('GAP in component GAP (millimolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('ADP in component ADP (millimolar)');
    LEGEND_CONSTANTS(:,6) = strpad('SUM_P in component ADP (millimolar)');
    LEGEND_CONSTANTS(:,7) = strpad('Keq_AK in component ADP (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('ATP in component ATP (millimolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('AMP in component AMP (millimolar)');
    LEGEND_CONSTANTS(:,8) = strpad('ETOH in component ETOH (millimolar)');
    LEGEND_CONSTANTS(:,9) = strpad('GLY in component GLY (millimolar)');
    LEGEND_CONSTANTS(:,10) = strpad('Km_G6P in component v_PGI (millimolar)');
    LEGEND_CONSTANTS(:,11) = strpad('Km_F6P in component v_PGI (millimolar)');
    LEGEND_CONSTANTS(:,12) = strpad('Keq_PGI in component v_PGI (dimensionless)');
    LEGEND_CONSTANTS(:,13) = strpad('v_max in component v_PGI (flux)');
    LEGEND_CONSTANTS(:,14) = strpad('Km_P3G in component v_PGM (millimolar)');
    LEGEND_CONSTANTS(:,15) = strpad('Km_P2G in component v_PGM (millimolar)');
    LEGEND_CONSTANTS(:,16) = strpad('Keq_PGM in component v_PGM (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('v_max in component v_PGM (flux)');
    LEGEND_CONSTANTS(:,18) = strpad('Km_P2G in component v_ENO (millimolar)');
    LEGEND_CONSTANTS(:,19) = strpad('Km_PEP in component v_ENO (millimolar)');
    LEGEND_CONSTANTS(:,20) = strpad('Keq_ENO in component v_ENO (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('v_max in component v_ENO (flux)');
    LEGEND_CONSTANTS(:,22) = strpad('Km_GLCi in component v_GLK (millimolar)');
    LEGEND_CONSTANTS(:,23) = strpad('Km_G6P in component v_GLK (millimolar)');
    LEGEND_CONSTANTS(:,24) = strpad('Km_ATP in component v_GLK (millimolar)');
    LEGEND_CONSTANTS(:,25) = strpad('Km_ADP in component v_GLK (millimolar)');
    LEGEND_CONSTANTS(:,26) = strpad('Keq_GLK in component v_GLK (dimensionless)');
    LEGEND_CONSTANTS(:,27) = strpad('v_max in component v_GLK (flux)');
    LEGEND_CONSTANTS(:,28) = strpad('Km_GAP in component v_GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,29) = strpad('Km_BPG in component v_GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,30) = strpad('Km_NAD in component v_GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,31) = strpad('Km_NADH in component v_GAPDH (millimolar)');
    LEGEND_CONSTANTS(:,32) = strpad('v_max_f in component v_GAPDH (flux)');
    LEGEND_CONSTANTS(:,33) = strpad('v_max_r in component v_GAPDH (flux)');
    LEGEND_CONSTANTS(:,34) = strpad('Km_BPG in component v_PGK (millimolar)');
    LEGEND_CONSTANTS(:,35) = strpad('Km_P3G in component v_PGK (millimolar)');
    LEGEND_CONSTANTS(:,36) = strpad('Km_ADP in component v_PGK (millimolar)');
    LEGEND_CONSTANTS(:,37) = strpad('Km_ATP in component v_PGK (millimolar)');
    LEGEND_CONSTANTS(:,38) = strpad('Keq_PGK in component v_PGK (dimensionless)');
    LEGEND_CONSTANTS(:,39) = strpad('v_max in component v_PGK (flux)');
    LEGEND_CONSTANTS(:,40) = strpad('Km_PEP in component v_PYK (millimolar)');
    LEGEND_CONSTANTS(:,41) = strpad('Km_PYR in component v_PYK (millimolar)');
    LEGEND_CONSTANTS(:,42) = strpad('Km_ADP in component v_PYK (millimolar)');
    LEGEND_CONSTANTS(:,43) = strpad('Km_ATP in component v_PYK (millimolar)');
    LEGEND_CONSTANTS(:,44) = strpad('Keq_PYK in component v_PYK (dimensionless)');
    LEGEND_CONSTANTS(:,45) = strpad('v_max in component v_PYK (flux)');
    LEGEND_CONSTANTS(:,46) = strpad('Km_Glco in component v_GLT (millimolar)');
    LEGEND_CONSTANTS(:,47) = strpad('Km_Glci in component v_GLT (millimolar)');
    LEGEND_CONSTANTS(:,48) = strpad('Keq_Glc in component v_GLT (dimensionless)');
    LEGEND_CONSTANTS(:,49) = strpad('v_max in component v_GLT (flux)');
    LEGEND_CONSTANTS(:,50) = strpad('Km_F16P in component v_ALD (millimolar)');
    LEGEND_CONSTANTS(:,51) = strpad('Km_GAP in component v_ALD (millimolar)');
    LEGEND_CONSTANTS(:,52) = strpad('Km_GAPi in component v_ALD (millimolar)');
    LEGEND_CONSTANTS(:,53) = strpad('Km_DHAP in component v_ALD (millimolar)');
    LEGEND_CONSTANTS(:,54) = strpad('Keq_ALD in component v_ALD (millimolar)');
    LEGEND_CONSTANTS(:,55) = strpad('v_max in component v_ALD (flux)');
    LEGEND_CONSTANTS(:,56) = strpad('nPDC in component v_PDC (dimensionless)');
    LEGEND_CONSTANTS(:,57) = strpad('Km_PYR in component v_PDC (millimolar)');
    LEGEND_CONSTANTS(:,58) = strpad('v_max in component v_PDC (flux)');
    LEGEND_CONSTANTS(:,59) = strpad('Km_NAD in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,60) = strpad('Km_NADH in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,61) = strpad('Km_ACE in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,62) = strpad('Km_ETOH in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,63) = strpad('Ki_NADH in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,64) = strpad('Ki_NAD in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,65) = strpad('Ki_ACE in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,66) = strpad('Ki_ETOH in component v_ADH (millimolar)');
    LEGEND_CONSTANTS(:,67) = strpad('v_max in component v_ADH (flux)');
    LEGEND_CONSTANTS(:,68) = strpad('Keq_ADH in component v_ADH (dimensionless)');
    LEGEND_CONSTANTS(:,69) = strpad('Km_ATPase in component v_ATP (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,70) = strpad('v_max in component v_PFK (flux)');
    LEGEND_CONSTANTS(:,71) = strpad('gR in component v_PFK (dimensionless)');
    LEGEND_CONSTANTS(:,72) = strpad('L0 in component v_PFK (per_millimolar2)');
    LEGEND_CONSTANTS(:,73) = strpad('Km_F6P in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,74) = strpad('Km_ATP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,75) = strpad('CATP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,76) = strpad('Km_AMP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,77) = strpad('CAMP in component v_PFK (dimensionless)');
    LEGEND_CONSTANTS(:,78) = strpad('Ki_ATP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,79) = strpad('Ci_ATP in component v_PFK (dimensionless)');
    LEGEND_CONSTANTS(:,80) = strpad('Km_F26BP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,81) = strpad('CF26BP in component v_PFK (dimensionless)');
    LEGEND_CONSTANTS(:,82) = strpad('Km_F16BP in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,83) = strpad('CF16BP in component v_PFK (dimensionless)');
    LEGEND_ALGEBRAIC(:,19) = strpad('L in component v_PFK (per_millimolar2)');
    LEGEND_ALGEBRAIC(:,18) = strpad('R in component v_PFK (dimensionless)');
    LEGEND_ALGEBRAIC(:,20) = strpad('T in component v_PFK (millimolar)');
    LEGEND_CONSTANTS(:,84) = strpad('Km_DHAP in component v_G3PDH (millimolar)');
    LEGEND_CONSTANTS(:,85) = strpad('Km_GLY in component v_G3PDH (millimolar)');
    LEGEND_CONSTANTS(:,86) = strpad('Km_NADH in component v_G3PDH (millimolar)');
    LEGEND_CONSTANTS(:,87) = strpad('Km_NAD in component v_G3PDH (millimolar)');
    LEGEND_CONSTANTS(:,88) = strpad('Keq_G3PDH in component v_G3PDH (dimensionless)');
    LEGEND_CONSTANTS(:,89) = strpad('v_max in component v_G3PDH (flux)');
    LEGEND_CONSTANTS(:,90) = strpad('Km_succinate in component v_succinate (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt GLCi in component GLCi (millimolar)');
    LEGEND_RATES(:,2) = strpad('d/dt G6P in component G6P (millimolar)');
    LEGEND_RATES(:,3) = strpad('d/dt F6P in component F6P (millimolar)');
    LEGEND_RATES(:,4) = strpad('d/dt F16P in component F16P (millimolar)');
    LEGEND_RATES(:,5) = strpad('d/dt TRIO in component TRIO (millimolar)');
    LEGEND_RATES(:,6) = strpad('d/dt BPG in component BPG (millimolar)');
    LEGEND_RATES(:,7) = strpad('d/dt P3G in component P3G (millimolar)');
    LEGEND_RATES(:,8) = strpad('d/dt P2G in component P2G (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 ACE in component ACE (millimolar)');
    LEGEND_RATES(:,12) = strpad('d/dt P in component P (millimolar)');
    LEGEND_RATES(:,13) = strpad('d/dt NADH in component NADH (millimolar)');
    LEGEND_RATES(:,14) = 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) = 50.0;
    STATES(:,1) = 0.087;
    STATES(:,2) = 2.45;
    CONSTANTS(:,2) = 2.4;
    CONSTANTS(:,3) = 6.0;
    STATES(:,3) = 0.62;
    STATES(:,4) = 5.51;
    CONSTANTS(:,4) = 0.02;
    STATES(:,5) = 0.96;
    STATES(:,6) = 0.0;
    STATES(:,7) = 0.9;
    STATES(:,8) = 0.12;
    STATES(:,9) = 0.07;
    STATES(:,10) = 1.85;
    STATES(:,11) = 0.17;
    STATES(:,12) = 6.31;
    STATES(:,13) = 0.39;
    STATES(:,14) = 1.20;
    CONSTANTS(:,5) = 0.045;
    CONSTANTS(:,6) = 4.1;
    CONSTANTS(:,7) = 0.450;
    CONSTANTS(:,8) = 50.0;
    CONSTANTS(:,9) = 0.15;
    CONSTANTS(:,10) = 1.4;
    CONSTANTS(:,11) = 0.3;
    CONSTANTS(:,12) = 0.314;
    CONSTANTS(:,13) = 339.677;
    CONSTANTS(:,14) = 1.2;
    CONSTANTS(:,15) = 0.08;
    CONSTANTS(:,16) = 0.19;
    CONSTANTS(:,17) = 2525.81;
    CONSTANTS(:,18) = 0.04;
    CONSTANTS(:,19) = 0.5;
    CONSTANTS(:,20) = 6.7;
    CONSTANTS(:,21) = 365.806;
    CONSTANTS(:,22) = 0.08;
    CONSTANTS(:,23) = 30.0;
    CONSTANTS(:,24) = 0.15;
    CONSTANTS(:,25) = 0.23;
    CONSTANTS(:,26) = 3800;
    CONSTANTS(:,27) = 226.452;
    CONSTANTS(:,28) = 0.21;
    CONSTANTS(:,29) = 0.0098;
    CONSTANTS(:,30) = 0.09;
    CONSTANTS(:,31) = 0.06;
    CONSTANTS(:,32) = 1184.52;
    CONSTANTS(:,33) = 6549.68;
    CONSTANTS(:,34) = 0.003;
    CONSTANTS(:,35) = 0.53;
    CONSTANTS(:,36) = 0.2;
    CONSTANTS(:,37) = 0.3;
    CONSTANTS(:,38) = 3200;
    CONSTANTS(:,39) = 1306.45;
    CONSTANTS(:,40) = 0.14;
    CONSTANTS(:,41) = 21.0;
    CONSTANTS(:,42) = 0.53;
    CONSTANTS(:,43) = 1.5;
    CONSTANTS(:,44) = 6500;
    CONSTANTS(:,45) = 1088.71;
    CONSTANTS(:,46) = 1.1918;
    CONSTANTS(:,47) = 1.1918;
    CONSTANTS(:,48) = 1;
    CONSTANTS(:,49) = 97.264;
    CONSTANTS(:,50) = 0.3;
    CONSTANTS(:,51) = 2.0;
    CONSTANTS(:,52) = 10.0;
    CONSTANTS(:,53) = 2.4;
    CONSTANTS(:,54) = 0.069;
    CONSTANTS(:,55) = 322.258;
    CONSTANTS(:,56) = 1.9;
    CONSTANTS(:,57) = 4.33;
    CONSTANTS(:,58) = 174.194;
    CONSTANTS(:,59) = 0.17;
    CONSTANTS(:,60) = 0.11;
    CONSTANTS(:,61) = 1.11;
    CONSTANTS(:,62) = 17.0;
    CONSTANTS(:,63) = 0.031;
    CONSTANTS(:,64) = 0.92;
    CONSTANTS(:,65) = 1.1;
    CONSTANTS(:,66) = 90.0;
    CONSTANTS(:,67) = 810.0;
    CONSTANTS(:,68) = 0.000069;
    CONSTANTS(:,69) = 33.7;
    CONSTANTS(:,70) = 182.903;
    CONSTANTS(:,71) = 5.12;
    CONSTANTS(:,72) = 0.66;
    CONSTANTS(:,73) = 0.1;
    CONSTANTS(:,74) = 0.71;
    CONSTANTS(:,75) = 3.0;
    CONSTANTS(:,76) = 0.0995;
    CONSTANTS(:,77) = 0.0845;
    CONSTANTS(:,78) = 0.65;
    CONSTANTS(:,79) = 100.0;
    CONSTANTS(:,80) = 0.000682;
    CONSTANTS(:,81) = 0.0174;
    CONSTANTS(:,82) = 0.111;
    CONSTANTS(:,83) = 0.397;
    CONSTANTS(:,84) = 0.4;
    CONSTANTS(:,85) = 1;
    CONSTANTS(:,86) = 0.023;
    CONSTANTS(:,87) = 0.93;
    CONSTANTS(:,88) = 4300;
    CONSTANTS(:,89) = 70.15;
    CONSTANTS(:,90) = 21.4;
    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(:,7) = ( (CONSTANTS(:,17)./CONSTANTS(:,14)).*(STATES(:,7) - STATES(:,8)./CONSTANTS(:,16)))./(1.00000+STATES(:,7)./CONSTANTS(:,14)+STATES(:,8)./CONSTANTS(:,15));
    ALGEBRAIC(:,8) = ( (CONSTANTS(:,21)./CONSTANTS(:,18)).*(STATES(:,8) - STATES(:,9)./CONSTANTS(:,20)))./(1.00000+STATES(:,8)./CONSTANTS(:,18)+STATES(:,9)./CONSTANTS(:,19));
    RATES(:,8) = ALGEBRAIC(:,7) - ALGEBRAIC(:,8);
    ALGEBRAIC(:,3) = (CONSTANTS(:,6) - power(( power(STATES(:,12), 2.00000).*(1.00000 -  4.00000.*CONSTANTS(:,7))+ 2.00000.*CONSTANTS(:,6).*STATES(:,12).*( 4.00000.*CONSTANTS(:,7) - 1.00000)+power(CONSTANTS(:,6), 2.00000)), 1.0 ./ 2))./(1.00000 -  4.00000.*CONSTANTS(:,7));
    ALGEBRAIC(:,4) = (STATES(:,12) - ALGEBRAIC(:,3))./2.00000;
    ALGEBRAIC(:,9) = ( (CONSTANTS(:,27)./( CONSTANTS(:,22).*CONSTANTS(:,24))).*( STATES(:,1).*ALGEBRAIC(:,4) - ( STATES(:,2).*ALGEBRAIC(:,3))./CONSTANTS(:,26)))./( (1.00000+STATES(:,1)./CONSTANTS(:,22)+STATES(:,2)./CONSTANTS(:,23)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,24)+ALGEBRAIC(:,3)./CONSTANTS(:,25)));
    ALGEBRAIC(:,6) = ( (CONSTANTS(:,13)./CONSTANTS(:,10)).*(STATES(:,2) - STATES(:,3)./CONSTANTS(:,12)))./(1.00000+STATES(:,2)./CONSTANTS(:,10)+STATES(:,3)./CONSTANTS(:,11));
    RATES(:,2) = ALGEBRAIC(:,9) - (ALGEBRAIC(:,6)+ 2.00000.*CONSTANTS(:,2)+CONSTANTS(:,3));
    ALGEBRAIC(:,10) = ( CONSTANTS(:,49).*(CONSTANTS(:,1) - STATES(:,1)./CONSTANTS(:,48)))./( CONSTANTS(:,46).*(1.00000+CONSTANTS(:,1)./CONSTANTS(:,46)+STATES(:,1)./CONSTANTS(:,47)+( 0.910000.*CONSTANTS(:,1).*STATES(:,1))./( CONSTANTS(:,47).*CONSTANTS(:,46))));
    RATES(:,1) = ALGEBRAIC(:,10) - ALGEBRAIC(:,9);
    ALGEBRAIC(:,11) = (( CONSTANTS(:,32).*(CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*STATES(:,14))./( CONSTANTS(:,28).*CONSTANTS(:,30)) - ( CONSTANTS(:,33).*STATES(:,6).*STATES(:,13))./( CONSTANTS(:,29).*CONSTANTS(:,31)))./( (1.00000+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,28)+STATES(:,6)./CONSTANTS(:,29)).*(1.00000+STATES(:,14)./CONSTANTS(:,30)+STATES(:,13)./CONSTANTS(:,31)));
    ALGEBRAIC(:,12) = ( (CONSTANTS(:,39)./( CONSTANTS(:,35).*CONSTANTS(:,37))).*( CONSTANTS(:,38).*STATES(:,6).*ALGEBRAIC(:,3) -  STATES(:,7).*ALGEBRAIC(:,4)))./( (1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,7)./CONSTANTS(:,35)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,37)+ALGEBRAIC(:,3)./CONSTANTS(:,36)));
    RATES(:,6) = ALGEBRAIC(:,11) - ALGEBRAIC(:,12);
    RATES(:,7) = ALGEBRAIC(:,12) - ALGEBRAIC(:,7);
    ALGEBRAIC(:,13) = ( (CONSTANTS(:,45)./( CONSTANTS(:,40).*CONSTANTS(:,42))).*( STATES(:,9).*ALGEBRAIC(:,3) - ( STATES(:,10).*ALGEBRAIC(:,4))./CONSTANTS(:,44)))./( (1.00000+STATES(:,9)./CONSTANTS(:,40)+STATES(:,10)./CONSTANTS(:,41)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,43)+ALGEBRAIC(:,3)./CONSTANTS(:,42)));
    RATES(:,9) = ALGEBRAIC(:,8) - ALGEBRAIC(:,13);
    ALGEBRAIC(:,15) = ( CONSTANTS(:,58).*(power(STATES(:,10), CONSTANTS(:,56))./power(CONSTANTS(:,57), CONSTANTS(:,56))))./(1.00000+power(STATES(:,10), CONSTANTS(:,56))./power(CONSTANTS(:,57), CONSTANTS(:,56)));
    RATES(:,10) = ALGEBRAIC(:,13) - ALGEBRAIC(:,15);
    ALGEBRAIC(:,5) = CONSTANTS(:,6) - (ALGEBRAIC(:,4)+ALGEBRAIC(:,3));
    ALGEBRAIC(:,19) =  CONSTANTS(:,72).*power((1.00000+ CONSTANTS(:,79).*(ALGEBRAIC(:,4)./CONSTANTS(:,78)))./(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,78)), 2.00000).*power((1.00000+ CONSTANTS(:,77).*(ALGEBRAIC(:,5)./CONSTANTS(:,76)))./(1.00000+ALGEBRAIC(:,5)./CONSTANTS(:,76)), 2.00000).*power((1.00000+ CONSTANTS(:,81).*(CONSTANTS(:,4)./CONSTANTS(:,80))+ CONSTANTS(:,83).*(STATES(:,4)./CONSTANTS(:,82)))./(1.00000+CONSTANTS(:,4)./CONSTANTS(:,80)+STATES(:,4)./CONSTANTS(:,82)), 2.00000);
    ALGEBRAIC(:,18) = 1.00000+STATES(:,3)./CONSTANTS(:,73)+ALGEBRAIC(:,4)./CONSTANTS(:,74)+ CONSTANTS(:,71).*(STATES(:,3)./CONSTANTS(:,73)).*(ALGEBRAIC(:,4)./CONSTANTS(:,74));
    ALGEBRAIC(:,20) = 1.00000+ CONSTANTS(:,75).*(ALGEBRAIC(:,4)./CONSTANTS(:,74));
    ALGEBRAIC(:,21) =  CONSTANTS(:,70).*CONSTANTS(:,71).*(STATES(:,3)./CONSTANTS(:,73)).*(ALGEBRAIC(:,4)./CONSTANTS(:,74)).*(ALGEBRAIC(:,18)./(power(ALGEBRAIC(:,18), 2.00000)+ ALGEBRAIC(:,19).*power(ALGEBRAIC(:,20), 2.00000)));
    RATES(:,3) = ALGEBRAIC(:,6) - ALGEBRAIC(:,21);
    ALGEBRAIC(:,14) = ( (CONSTANTS(:,55)./CONSTANTS(:,50)).*(STATES(:,4) - ( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,54)))./(1.00000+STATES(:,4)./CONSTANTS(:,50)+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,51)+( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,53)+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./( CONSTANTS(:,51).*CONSTANTS(:,53))+( STATES(:,4).*(CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./( CONSTANTS(:,52).*CONSTANTS(:,50)));
    RATES(:,4) = ALGEBRAIC(:,21) - ALGEBRAIC(:,14);
    ALGEBRAIC(:,22) = ( (CONSTANTS(:,89)./( CONSTANTS(:,84).*CONSTANTS(:,86))).*( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*STATES(:,13) - ( CONSTANTS(:,9).*STATES(:,14))./CONSTANTS(:,88)))./( (1.00000+( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,84)+CONSTANTS(:,9)./CONSTANTS(:,85)).*(1.00000+STATES(:,13)./CONSTANTS(:,86)+STATES(:,14)./CONSTANTS(:,87)));
    RATES(:,5) =  2.00000.*ALGEBRAIC(:,14) - (ALGEBRAIC(:,11)+ALGEBRAIC(:,22));
    ALGEBRAIC(:,16) =  - ( (CONSTANTS(:,67)./( CONSTANTS(:,64).*CONSTANTS(:,62))).*(( STATES(:,14).*CONSTANTS(:,8) - ( STATES(:,13).*STATES(:,11))./CONSTANTS(:,68))./(1.00000+STATES(:,14)./CONSTANTS(:,64)+( CONSTANTS(:,59).*CONSTANTS(:,8))./( CONSTANTS(:,64).*CONSTANTS(:,62))+( CONSTANTS(:,60).*STATES(:,11))./( CONSTANTS(:,63).*CONSTANTS(:,61))+STATES(:,13)./CONSTANTS(:,63)+( STATES(:,14).*CONSTANTS(:,8))./( CONSTANTS(:,64).*CONSTANTS(:,62))+( CONSTANTS(:,60).*STATES(:,14).*STATES(:,11))./( CONSTANTS(:,64).*CONSTANTS(:,63).*CONSTANTS(:,61))+( CONSTANTS(:,59).*CONSTANTS(:,8).*STATES(:,13))./( CONSTANTS(:,64).*CONSTANTS(:,62).*CONSTANTS(:,63))+( STATES(:,13).*STATES(:,11))./( CONSTANTS(:,63).*CONSTANTS(:,61))+( STATES(:,14).*CONSTANTS(:,8).*STATES(:,11))./( CONSTANTS(:,64).*CONSTANTS(:,62).*CONSTANTS(:,65))+( CONSTANTS(:,8).*STATES(:,13).*STATES(:,11))./( CONSTANTS(:,66).*CONSTANTS(:,63).*CONSTANTS(:,61)))));
    ALGEBRAIC(:,23) =  CONSTANTS(:,90).*STATES(:,11);
    RATES(:,11) = ALGEBRAIC(:,15) - (ALGEBRAIC(:,16)+ 2.00000.*ALGEBRAIC(:,23));
    ALGEBRAIC(:,17) =  CONSTANTS(:,69).*ALGEBRAIC(:,4);
    RATES(:,12) = (ALGEBRAIC(:,12)+ALGEBRAIC(:,13)) - (ALGEBRAIC(:,9)+ALGEBRAIC(:,21)+ALGEBRAIC(:,17)+CONSTANTS(:,2)+CONSTANTS(:,3)+ 4.00000.*ALGEBRAIC(:,23));
    RATES(:,13) = (ALGEBRAIC(:,11)+ 3.00000.*ALGEBRAIC(:,23)) - (ALGEBRAIC(:,16)+ALGEBRAIC(:,22));
    RATES(:,14) = (ALGEBRAIC(:,16)+ALGEBRAIC(:,22)) - (ALGEBRAIC(:,11)+ 3.00000.*ALGEBRAIC(:,23));
   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(:,7) = ( (CONSTANTS(:,17)./CONSTANTS(:,14)).*(STATES(:,7) - STATES(:,8)./CONSTANTS(:,16)))./(1.00000+STATES(:,7)./CONSTANTS(:,14)+STATES(:,8)./CONSTANTS(:,15));
    ALGEBRAIC(:,8) = ( (CONSTANTS(:,21)./CONSTANTS(:,18)).*(STATES(:,8) - STATES(:,9)./CONSTANTS(:,20)))./(1.00000+STATES(:,8)./CONSTANTS(:,18)+STATES(:,9)./CONSTANTS(:,19));
    ALGEBRAIC(:,3) = (CONSTANTS(:,6) - power(( power(STATES(:,12), 2.00000).*(1.00000 -  4.00000.*CONSTANTS(:,7))+ 2.00000.*CONSTANTS(:,6).*STATES(:,12).*( 4.00000.*CONSTANTS(:,7) - 1.00000)+power(CONSTANTS(:,6), 2.00000)), 1.0 ./ 2))./(1.00000 -  4.00000.*CONSTANTS(:,7));
    ALGEBRAIC(:,4) = (STATES(:,12) - ALGEBRAIC(:,3))./2.00000;
    ALGEBRAIC(:,9) = ( (CONSTANTS(:,27)./( CONSTANTS(:,22).*CONSTANTS(:,24))).*( STATES(:,1).*ALGEBRAIC(:,4) - ( STATES(:,2).*ALGEBRAIC(:,3))./CONSTANTS(:,26)))./( (1.00000+STATES(:,1)./CONSTANTS(:,22)+STATES(:,2)./CONSTANTS(:,23)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,24)+ALGEBRAIC(:,3)./CONSTANTS(:,25)));
    ALGEBRAIC(:,6) = ( (CONSTANTS(:,13)./CONSTANTS(:,10)).*(STATES(:,2) - STATES(:,3)./CONSTANTS(:,12)))./(1.00000+STATES(:,2)./CONSTANTS(:,10)+STATES(:,3)./CONSTANTS(:,11));
    ALGEBRAIC(:,10) = ( CONSTANTS(:,49).*(CONSTANTS(:,1) - STATES(:,1)./CONSTANTS(:,48)))./( CONSTANTS(:,46).*(1.00000+CONSTANTS(:,1)./CONSTANTS(:,46)+STATES(:,1)./CONSTANTS(:,47)+( 0.910000.*CONSTANTS(:,1).*STATES(:,1))./( CONSTANTS(:,47).*CONSTANTS(:,46))));
    ALGEBRAIC(:,11) = (( CONSTANTS(:,32).*(CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*STATES(:,14))./( CONSTANTS(:,28).*CONSTANTS(:,30)) - ( CONSTANTS(:,33).*STATES(:,6).*STATES(:,13))./( CONSTANTS(:,29).*CONSTANTS(:,31)))./( (1.00000+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,28)+STATES(:,6)./CONSTANTS(:,29)).*(1.00000+STATES(:,14)./CONSTANTS(:,30)+STATES(:,13)./CONSTANTS(:,31)));
    ALGEBRAIC(:,12) = ( (CONSTANTS(:,39)./( CONSTANTS(:,35).*CONSTANTS(:,37))).*( CONSTANTS(:,38).*STATES(:,6).*ALGEBRAIC(:,3) -  STATES(:,7).*ALGEBRAIC(:,4)))./( (1.00000+STATES(:,6)./CONSTANTS(:,34)+STATES(:,7)./CONSTANTS(:,35)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,37)+ALGEBRAIC(:,3)./CONSTANTS(:,36)));
    ALGEBRAIC(:,13) = ( (CONSTANTS(:,45)./( CONSTANTS(:,40).*CONSTANTS(:,42))).*( STATES(:,9).*ALGEBRAIC(:,3) - ( STATES(:,10).*ALGEBRAIC(:,4))./CONSTANTS(:,44)))./( (1.00000+STATES(:,9)./CONSTANTS(:,40)+STATES(:,10)./CONSTANTS(:,41)).*(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,43)+ALGEBRAIC(:,3)./CONSTANTS(:,42)));
    ALGEBRAIC(:,15) = ( CONSTANTS(:,58).*(power(STATES(:,10), CONSTANTS(:,56))./power(CONSTANTS(:,57), CONSTANTS(:,56))))./(1.00000+power(STATES(:,10), CONSTANTS(:,56))./power(CONSTANTS(:,57), CONSTANTS(:,56)));
    ALGEBRAIC(:,5) = CONSTANTS(:,6) - (ALGEBRAIC(:,4)+ALGEBRAIC(:,3));
    ALGEBRAIC(:,19) =  CONSTANTS(:,72).*power((1.00000+ CONSTANTS(:,79).*(ALGEBRAIC(:,4)./CONSTANTS(:,78)))./(1.00000+ALGEBRAIC(:,4)./CONSTANTS(:,78)), 2.00000).*power((1.00000+ CONSTANTS(:,77).*(ALGEBRAIC(:,5)./CONSTANTS(:,76)))./(1.00000+ALGEBRAIC(:,5)./CONSTANTS(:,76)), 2.00000).*power((1.00000+ CONSTANTS(:,81).*(CONSTANTS(:,4)./CONSTANTS(:,80))+ CONSTANTS(:,83).*(STATES(:,4)./CONSTANTS(:,82)))./(1.00000+CONSTANTS(:,4)./CONSTANTS(:,80)+STATES(:,4)./CONSTANTS(:,82)), 2.00000);
    ALGEBRAIC(:,18) = 1.00000+STATES(:,3)./CONSTANTS(:,73)+ALGEBRAIC(:,4)./CONSTANTS(:,74)+ CONSTANTS(:,71).*(STATES(:,3)./CONSTANTS(:,73)).*(ALGEBRAIC(:,4)./CONSTANTS(:,74));
    ALGEBRAIC(:,20) = 1.00000+ CONSTANTS(:,75).*(ALGEBRAIC(:,4)./CONSTANTS(:,74));
    ALGEBRAIC(:,21) =  CONSTANTS(:,70).*CONSTANTS(:,71).*(STATES(:,3)./CONSTANTS(:,73)).*(ALGEBRAIC(:,4)./CONSTANTS(:,74)).*(ALGEBRAIC(:,18)./(power(ALGEBRAIC(:,18), 2.00000)+ ALGEBRAIC(:,19).*power(ALGEBRAIC(:,20), 2.00000)));
    ALGEBRAIC(:,14) = ( (CONSTANTS(:,55)./CONSTANTS(:,50)).*(STATES(:,4) - ( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,54)))./(1.00000+STATES(:,4)./CONSTANTS(:,50)+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,51)+( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,53)+( (CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*(1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./( CONSTANTS(:,51).*CONSTANTS(:,53))+( STATES(:,4).*(CONSTANTS(:,5)./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./( CONSTANTS(:,52).*CONSTANTS(:,50)));
    ALGEBRAIC(:,22) = ( (CONSTANTS(:,89)./( CONSTANTS(:,84).*CONSTANTS(:,86))).*( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5).*STATES(:,13) - ( CONSTANTS(:,9).*STATES(:,14))./CONSTANTS(:,88)))./( (1.00000+( (1.00000./(1.00000+CONSTANTS(:,5))).*STATES(:,5))./CONSTANTS(:,84)+CONSTANTS(:,9)./CONSTANTS(:,85)).*(1.00000+STATES(:,13)./CONSTANTS(:,86)+STATES(:,14)./CONSTANTS(:,87)));
    ALGEBRAIC(:,16) =  - ( (CONSTANTS(:,67)./( CONSTANTS(:,64).*CONSTANTS(:,62))).*(( STATES(:,14).*CONSTANTS(:,8) - ( STATES(:,13).*STATES(:,11))./CONSTANTS(:,68))./(1.00000+STATES(:,14)./CONSTANTS(:,64)+( CONSTANTS(:,59).*CONSTANTS(:,8))./( CONSTANTS(:,64).*CONSTANTS(:,62))+( CONSTANTS(:,60).*STATES(:,11))./( CONSTANTS(:,63).*CONSTANTS(:,61))+STATES(:,13)./CONSTANTS(:,63)+( STATES(:,14).*CONSTANTS(:,8))./( CONSTANTS(:,64).*CONSTANTS(:,62))+( CONSTANTS(:,60).*STATES(:,14).*STATES(:,11))./( CONSTANTS(:,64).*CONSTANTS(:,63).*CONSTANTS(:,61))+( CONSTANTS(:,59).*CONSTANTS(:,8).*STATES(:,13))./( CONSTANTS(:,64).*CONSTANTS(:,62).*CONSTANTS(:,63))+( STATES(:,13).*STATES(:,11))./( CONSTANTS(:,63).*CONSTANTS(:,61))+( STATES(:,14).*CONSTANTS(:,8).*STATES(:,11))./( CONSTANTS(:,64).*CONSTANTS(:,62).*CONSTANTS(:,65))+( CONSTANTS(:,8).*STATES(:,13).*STATES(:,11))./( CONSTANTS(:,66).*CONSTANTS(:,63).*CONSTANTS(:,61)))));
    ALGEBRAIC(:,23) =  CONSTANTS(:,90).*STATES(:,11);
    ALGEBRAIC(:,17) =  CONSTANTS(:,69).*ALGEBRAIC(:,4);
    ALGEBRAIC(:,1) = STATES(:,5)./(1.00000+CONSTANTS(:,5));
    ALGEBRAIC(:,2) = ( STATES(:,5).*CONSTANTS(:,5))./(1.00000+CONSTANTS(:,5));
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