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 8 entries in each of the rate and state variable arrays.
% There are a total of 81 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_STATES(:,1) = strpad('PYR in component PYR (millimolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('V_GLYC in component V_GLYC (flux)');
    LEGEND_ALGEBRAIC(:,7) = strpad('V_LDH in component V_LDH (flux)');
    LEGEND_ALGEBRAIC(:,9) = strpad('V_PDH in component V_PDH (flux)');
    LEGEND_ALGEBRAIC(:,21) = strpad('V_ALS in component V_ALS (flux)');
    LEGEND_STATES(:,2) = strpad('ACP in component ACP (millimolar)');
    LEGEND_ALGEBRAIC(:,11) = strpad('V_PTA in component V_PTA (flux)');
    LEGEND_ALGEBRAIC(:,15) = strpad('V_ACK in component V_ACK (flux)');
    LEGEND_STATES(:,3) = strpad('ACAL in component ACAL (millimolar)');
    LEGEND_ALGEBRAIC(:,14) = strpad('V_ACALDH in component V_ACALDH (flux)');
    LEGEND_ALGEBRAIC(:,18) = strpad('V_ADH in component V_ADH (flux)');
    LEGEND_STATES(:,4) = strpad('ACLAC in component ACLAC (millimolar)');
    LEGEND_ALGEBRAIC(:,23) = strpad('V_ALDC in component V_ALDC (flux)');
    LEGEND_ALGEBRAIC(:,28) = strpad('V_NEALC in component V_NEALC (flux)');
    LEGEND_STATES(:,5) = strpad('ACET in component ACET (millimolar)');
    LEGEND_ALGEBRAIC(:,27) = strpad('V_ACETDH in component V_ACETDH (flux)');
    LEGEND_ALGEBRAIC(:,25) = strpad('V_ACETEFF in component V_ACETEFF (flux)');
    LEGEND_STATES(:,6) = strpad('ATP in component ATP (millimolar)');
    LEGEND_ALGEBRAIC(:,19) = strpad('V_ATPase in component V_ATPase (flux)');
    LEGEND_ALGEBRAIC(:,1) = strpad('ADP in component ADP (millimolar)');
    LEGEND_CONSTANTS(:,1) = strpad('A_tot in component ADP (millimolar)');
    LEGEND_STATES(:,7) = strpad('NADH in component NADH (millimolar)');
    LEGEND_ALGEBRAIC(:,30) = strpad('V_NOX in component V_NOX (flux)');
    LEGEND_ALGEBRAIC(:,2) = strpad('NAD in component NAD (millimolar)');
    LEGEND_CONSTANTS(:,2) = strpad('NAD_tot in component NAD (millimolar)');
    LEGEND_STATES(:,8) = strpad('ACCOA in component ACCOA (millimolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('COA in component COA (millimolar)');
    LEGEND_CONSTANTS(:,3) = strpad('C_tot in component COA (millimolar)');
    LEGEND_CONSTANTS(:,4) = strpad('AC in component AC (millimolar)');
    LEGEND_CONSTANTS(:,5) = strpad('BUT in component BUT (millimolar)');
    LEGEND_CONSTANTS(:,6) = strpad('ETOH in component ETOH (millimolar)');
    LEGEND_CONSTANTS(:,7) = strpad('GLC in component GLC (millimolar)');
    LEGEND_CONSTANTS(:,8) = strpad('LAC in component LAC (millimolar)');
    LEGEND_CONSTANTS(:,9) = strpad('O in component O (millimolar)');
    LEGEND_CONSTANTS(:,10) = strpad('P in component P (millimolar)');
    LEGEND_ALGEBRAIC(:,4) = strpad('V_GLYC_temp in component V_GLYC (flux)');
    LEGEND_CONSTANTS(:,11) = strpad('Km_GLC in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,12) = strpad('Km_NAD in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,13) = strpad('Km_ADP in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,14) = strpad('Km_PYR in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,15) = strpad('Km_NADH in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,16) = strpad('Km_ATP in component V_GLYC (millimolar)');
    LEGEND_CONSTANTS(:,17) = strpad('V_GLYC_max in component V_GLYC (flux)');
    LEGEND_ALGEBRAIC(:,6) = strpad('V_LDH_temp in component V_LDH (flux)');
    LEGEND_CONSTANTS(:,18) = strpad('Keq in component V_LDH (dimensionless)');
    LEGEND_CONSTANTS(:,19) = strpad('Km_LAC in component V_LDH (millimolar)');
    LEGEND_CONSTANTS(:,20) = strpad('Km_NAD in component V_LDH (millimolar)');
    LEGEND_CONSTANTS(:,21) = strpad('Km_PYR in component V_LDH (millimolar)');
    LEGEND_CONSTANTS(:,22) = strpad('Km_NADH in component V_LDH (millimolar)');
    LEGEND_CONSTANTS(:,23) = strpad('V_LDH_max in component V_LDH (flux)');
    LEGEND_ALGEBRAIC(:,8) = strpad('V_PDH_temp in component V_PDH (flux)');
    LEGEND_CONSTANTS(:,24) = strpad('Ki in component V_PDH (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('Km_NAD in component V_PDH (millimolar)');
    LEGEND_CONSTANTS(:,26) = strpad('Km_COA in component V_PDH (millimolar)');
    LEGEND_CONSTANTS(:,27) = strpad('Km_PYR in component V_PDH (millimolar)');
    LEGEND_CONSTANTS(:,28) = strpad('Km_NADH in component V_PDH (millimolar)');
    LEGEND_CONSTANTS(:,29) = strpad('Km_ACCOA in component V_PDH (millimolar)');
    LEGEND_CONSTANTS(:,30) = strpad('V_PDH_max in component V_PDH (flux)');
    LEGEND_ALGEBRAIC(:,10) = strpad('V_PTA_temp in component V_PTA (flux)');
    LEGEND_CONSTANTS(:,31) = strpad('Keq in component V_PTA (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('Km_P in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,33) = strpad('Ki_P in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,34) = strpad('Ki_COA in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,35) = strpad('Km_ACP in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,36) = strpad('Ki_ACP in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,37) = strpad('Ki_ACCOA in component V_PTA (millimolar)');
    LEGEND_CONSTANTS(:,38) = strpad('V_PTA_max in component V_PTA (flux)');
    LEGEND_ALGEBRAIC(:,13) = strpad('V_ACK_temp in component V_ACK (flux)');
    LEGEND_CONSTANTS(:,39) = strpad('Keq in component V_ACK (dimensionless)');
    LEGEND_CONSTANTS(:,40) = strpad('Km_AC in component V_ACK (millimolar)');
    LEGEND_CONSTANTS(:,41) = strpad('Km_ATP in component V_ACK (millimolar)');
    LEGEND_CONSTANTS(:,42) = strpad('Km_ADP in component V_ACK (millimolar)');
    LEGEND_CONSTANTS(:,43) = strpad('Km_ACP in component V_ACK (millimolar)');
    LEGEND_CONSTANTS(:,44) = strpad('V_ACK_max in component V_ACK (flux)');
    LEGEND_ALGEBRAIC(:,12) = strpad('V_ACALDH_temp in component V_ACALDH (flux)');
    LEGEND_CONSTANTS(:,45) = strpad('Keq in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,46) = strpad('Km_NAD in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,47) = strpad('Km_NADH in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,48) = strpad('Km_COA in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,49) = strpad('Km_ACCOA in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,50) = strpad('Km_ACAL in component V_ACALDH (millimolar)');
    LEGEND_CONSTANTS(:,51) = strpad('V_ACALDH_max in component V_ACALDH (flux)');
    LEGEND_ALGEBRAIC(:,16) = strpad('V_ADH_temp in component V_ADH (flux)');
    LEGEND_CONSTANTS(:,52) = strpad('Keq in component V_ADH (dimensionless)');
    LEGEND_CONSTANTS(:,53) = strpad('Km_NAD in component V_ADH (millimolar)');
    LEGEND_CONSTANTS(:,54) = strpad('Km_NADH in component V_ADH (millimolar)');
    LEGEND_CONSTANTS(:,55) = strpad('Km_ETOH in component V_ADH (millimolar)');
    LEGEND_CONSTANTS(:,56) = strpad('Km_ACAL in component V_ADH (millimolar)');
    LEGEND_CONSTANTS(:,57) = strpad('V_ADH_max in component V_ADH (flux)');
    LEGEND_ALGEBRAIC(:,20) = strpad('V_ALS_temp in component V_ALS (flux)');
    LEGEND_CONSTANTS(:,58) = strpad('N in component V_ALS (dimensionless)');
    LEGEND_CONSTANTS(:,59) = strpad('Keq in component V_ALS (dimensionless)');
    LEGEND_CONSTANTS(:,60) = strpad('Km_ACLAC in component V_ALS (millimolar)');
    LEGEND_CONSTANTS(:,61) = strpad('Km_PYR in component V_ALS (millimolar)');
    LEGEND_CONSTANTS(:,62) = strpad('V_ALS_max in component V_ALS (flux)');
    LEGEND_ALGEBRAIC(:,22) = strpad('V_ALDC_temp in component V_ALDC (flux)');
    LEGEND_CONSTANTS(:,63) = strpad('Km_ACLAC in component V_ALDC (millimolar)');
    LEGEND_CONSTANTS(:,64) = strpad('Km_ACET in component V_ALDC (millimolar)');
    LEGEND_CONSTANTS(:,65) = strpad('V_ALDC_max in component V_ALDC (flux)');
    LEGEND_ALGEBRAIC(:,24) = strpad('V_ACETEFF_temp in component V_ACETEFF (flux)');
    LEGEND_CONSTANTS(:,66) = strpad('Km_ACET in component V_ACETEFF (millimolar)');
    LEGEND_CONSTANTS(:,67) = strpad('V_ACETEFF_max in component V_ACETEFF (flux)');
    LEGEND_ALGEBRAIC(:,26) = strpad('V_ACETDH_temp in component V_ACETDH (flux)');
    LEGEND_CONSTANTS(:,68) = strpad('Keq in component V_ACETDH (dimensionless)');
    LEGEND_CONSTANTS(:,69) = strpad('Km_NAD in component V_ACETDH (millimolar)');
    LEGEND_CONSTANTS(:,70) = strpad('Km_NADH in component V_ACETDH (millimolar)');
    LEGEND_CONSTANTS(:,71) = strpad('Km_BUT in component V_ACETDH (millimolar)');
    LEGEND_CONSTANTS(:,72) = strpad('Km_ACET in component V_ACETDH (millimolar)');
    LEGEND_CONSTANTS(:,73) = strpad('V_ACETDH_max in component V_ACETDH (flux)');
    LEGEND_ALGEBRAIC(:,17) = strpad('V_ATPase_temp in component V_ATPase (flux)');
    LEGEND_CONSTANTS(:,74) = strpad('N in component V_ATPase (dimensionless)');
    LEGEND_CONSTANTS(:,75) = strpad('Km_ATP in component V_ATPase (dimensionless)');
    LEGEND_CONSTANTS(:,76) = strpad('V_ATPase_max in component V_ATPase (flux)');
    LEGEND_ALGEBRAIC(:,29) = strpad('V_NOX_temp in component V_NOX (flux)');
    LEGEND_CONSTANTS(:,77) = strpad('Km_NAD in component V_NOX (millimolar)');
    LEGEND_CONSTANTS(:,78) = strpad('Km_NADH in component V_NOX (millimolar)');
    LEGEND_CONSTANTS(:,79) = strpad('Km_O in component V_NOX (millimolar)');
    LEGEND_CONSTANTS(:,80) = strpad('V_NOX_max in component V_NOX (flux)');
    LEGEND_CONSTANTS(:,81) = strpad('k in component V_NEALC (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt PYR in component PYR (millimolar)');
    LEGEND_RATES(:,2) = strpad('d/dt ACP in component ACP (millimolar)');
    LEGEND_RATES(:,3) = strpad('d/dt ACAL in component ACAL (millimolar)');
    LEGEND_RATES(:,4) = strpad('d/dt ACLAC in component ACLAC (millimolar)');
    LEGEND_RATES(:,5) = strpad('d/dt ACET in component ACET (millimolar)');
    LEGEND_RATES(:,6) = strpad('d/dt ATP in component ATP (millimolar)');
    LEGEND_RATES(:,7) = strpad('d/dt NADH in component NADH (millimolar)');
    LEGEND_RATES(:,8) = strpad('d/dt ACCOA in component ACCOA (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 = [];
    STATES(:,1) = 1;
    STATES(:,2) = 0.03145;
    STATES(:,3) = 0.11;
    STATES(:,4) = 1e-5;
    STATES(:,5) = 1e-5;
    STATES(:,6) = 0.1;
    CONSTANTS(:,1) = 5;
    STATES(:,7) = 3.67;
    CONSTANTS(:,2) = 10;
    STATES(:,8) = 0.11;
    CONSTANTS(:,3) = 1;
    CONSTANTS(:,4) = 0.01;
    CONSTANTS(:,5) = 0.01;
    CONSTANTS(:,6) = 0.1;
    CONSTANTS(:,7) = 15;
    CONSTANTS(:,8) = 0.1;
    CONSTANTS(:,9) = 0.2;
    CONSTANTS(:,10) = 10;
    CONSTANTS(:,11) = 0.1;
    CONSTANTS(:,12) = 0.1412;
    CONSTANTS(:,13) = 0.04699;
    CONSTANTS(:,14) = 2.5;
    CONSTANTS(:,15) = 0.08999;
    CONSTANTS(:,16) = 0.01867;
    CONSTANTS(:,17) = 2397;
    CONSTANTS(:,18) = 21120.69;
    CONSTANTS(:,19) = 100;
    CONSTANTS(:,20) = 2.4;
    CONSTANTS(:,21) = 1.5;
    CONSTANTS(:,22) = 0.08;
    CONSTANTS(:,23) = 5118;
    CONSTANTS(:,24) = 46.4159;
    CONSTANTS(:,25) = 0.4;
    CONSTANTS(:,26) = 0.014;
    CONSTANTS(:,27) = 1;
    CONSTANTS(:,28) = 0.1;
    CONSTANTS(:,29) = 0.008;
    CONSTANTS(:,30) = 259;
    CONSTANTS(:,31) = 0.0065;
    CONSTANTS(:,32) = 2.6;
    CONSTANTS(:,33) = 2.6;
    CONSTANTS(:,34) = 0.029;
    CONSTANTS(:,35) = 0.7;
    CONSTANTS(:,36) = 0.2;
    CONSTANTS(:,37) = 0.2;
    CONSTANTS(:,38) = 42;
    CONSTANTS(:,39) = 174.217;
    CONSTANTS(:,40) = 7;
    CONSTANTS(:,41) = 0.07;
    CONSTANTS(:,42) = 0.5;
    CONSTANTS(:,43) = 0.16;
    CONSTANTS(:,44) = 2700;
    CONSTANTS(:,45) = 1;
    CONSTANTS(:,46) = 0.08;
    CONSTANTS(:,47) = 0.025;
    CONSTANTS(:,48) = 0.008;
    CONSTANTS(:,49) = 0.007;
    CONSTANTS(:,50) = 10;
    CONSTANTS(:,51) = 97;
    CONSTANTS(:,52) = 12354.9;
    CONSTANTS(:,53) = 0.08;
    CONSTANTS(:,54) = 0.05;
    CONSTANTS(:,55) = 1;
    CONSTANTS(:,56) = 0.03;
    CONSTANTS(:,57) = 162;
    CONSTANTS(:,58) = 2.4;
    CONSTANTS(:,59) = 9e12;
    CONSTANTS(:,60) = 100;
    CONSTANTS(:,61) = 50;
    CONSTANTS(:,62) = 600;
    CONSTANTS(:,63) = 10;
    CONSTANTS(:,64) = 100;
    CONSTANTS(:,65) = 106;
    CONSTANTS(:,66) = 5;
    CONSTANTS(:,67) = 200;
    CONSTANTS(:,68) = 1400;
    CONSTANTS(:,69) = 0.16;
    CONSTANTS(:,70) = 0.02;
    CONSTANTS(:,71) = 2.6;
    CONSTANTS(:,72) = 0.06;
    CONSTANTS(:,73) = 105;
    CONSTANTS(:,74) = 2.58;
    CONSTANTS(:,75) = 6.196;
    CONSTANTS(:,76) = 900;
    CONSTANTS(:,77) = 1;
    CONSTANTS(:,78) = 0.041;
    CONSTANTS(:,79) = 0.2;
    CONSTANTS(:,80) = 118;
    CONSTANTS(:,81) = 0.0003;
    if (isempty(STATES)), warning('Initial values for states not set');, end
end

function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
    global algebraicVariableCount;
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        ALGEBRAIC = zeros(1, algebraicVariableCount);
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
        utilOnes = ones(statesRowCount, 1);
    end
    ALGEBRAIC(:,3) = CONSTANTS(:,3) - STATES(:,8);
    ALGEBRAIC(:,10) = ( (CONSTANTS(:,38)./( CONSTANTS(:,37).*CONSTANTS(:,32))).*( STATES(:,8).*CONSTANTS(:,10) - ( STATES(:,2).*ALGEBRAIC(:,3))./CONSTANTS(:,31)))./(1.00000+STATES(:,8)./CONSTANTS(:,37)+CONSTANTS(:,10)./CONSTANTS(:,33)+STATES(:,2)./CONSTANTS(:,36)+ALGEBRAIC(:,3)./CONSTANTS(:,34)+( STATES(:,8).*CONSTANTS(:,10))./( CONSTANTS(:,37).*CONSTANTS(:,32))+( STATES(:,2).*ALGEBRAIC(:,3))./( CONSTANTS(:,35).*CONSTANTS(:,34)));
    ALGEBRAIC(:,11) = piecewise({ALGEBRAIC(:,10)>=0.00000, ALGEBRAIC(:,10) }, ALGEBRAIC(:,10));
    ALGEBRAIC(:,1) = CONSTANTS(:,1) - STATES(:,6);
    ALGEBRAIC(:,13) = ( (CONSTANTS(:,44)./( CONSTANTS(:,42).*CONSTANTS(:,43))).*( STATES(:,2).*ALGEBRAIC(:,1) - ( CONSTANTS(:,4).*STATES(:,6))./CONSTANTS(:,39)))./( (1.00000+STATES(:,2)./CONSTANTS(:,43)+CONSTANTS(:,4)./CONSTANTS(:,40)).*(1.00000+ALGEBRAIC(:,1)./CONSTANTS(:,42)+STATES(:,6)./CONSTANTS(:,41)));
    ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,13)>=0.00000, ALGEBRAIC(:,13) }, ALGEBRAIC(:,13));
    RATES(:,2) = ALGEBRAIC(:,11) - ALGEBRAIC(:,15);
    ALGEBRAIC(:,2) = CONSTANTS(:,2) - STATES(:,7);
    ALGEBRAIC(:,8) = (( (( (( (CONSTANTS(:,30)./(1.00000+( CONSTANTS(:,24).*STATES(:,7))./ALGEBRAIC(:,2))).*STATES(:,1))./CONSTANTS(:,27)).*ALGEBRAIC(:,2))./CONSTANTS(:,25)).*ALGEBRAIC(:,3))./CONSTANTS(:,26))./( (1.00000+STATES(:,1)./CONSTANTS(:,27)).*(1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,25)+STATES(:,7)./CONSTANTS(:,28)).*(1.00000+ALGEBRAIC(:,3)./CONSTANTS(:,26)+STATES(:,8)./CONSTANTS(:,29)));
    ALGEBRAIC(:,9) = piecewise({ALGEBRAIC(:,8)>=0.00000, ALGEBRAIC(:,8) }, ALGEBRAIC(:,8));
    ALGEBRAIC(:,12) = ( (CONSTANTS(:,51)./( CONSTANTS(:,49).*CONSTANTS(:,47))).*( STATES(:,8).*STATES(:,7) - ( ALGEBRAIC(:,2).*ALGEBRAIC(:,3).*STATES(:,3))./CONSTANTS(:,45)))./( (1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,46)+STATES(:,7)./CONSTANTS(:,47)).*(1.00000+STATES(:,8)./CONSTANTS(:,49)+ALGEBRAIC(:,3)./CONSTANTS(:,48)).*(1.00000+STATES(:,3)./CONSTANTS(:,50)));
    ALGEBRAIC(:,14) = piecewise({ALGEBRAIC(:,12)>=0.00000, ALGEBRAIC(:,12) }, ALGEBRAIC(:,12));
    RATES(:,8) = ALGEBRAIC(:,9) - (ALGEBRAIC(:,14)+ALGEBRAIC(:,11));
    ALGEBRAIC(:,16) = ( (CONSTANTS(:,57)./( CONSTANTS(:,56).*CONSTANTS(:,54))).*( STATES(:,3).*STATES(:,7) - ( CONSTANTS(:,6).*ALGEBRAIC(:,2))./CONSTANTS(:,52)))./( (1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,53)+STATES(:,7)./CONSTANTS(:,54)).*(1.00000+STATES(:,3)./CONSTANTS(:,56)+CONSTANTS(:,6)./CONSTANTS(:,55)));
    ALGEBRAIC(:,18) = piecewise({ALGEBRAIC(:,16)>=0.00000, ALGEBRAIC(:,16) }, ALGEBRAIC(:,16));
    RATES(:,3) = ALGEBRAIC(:,14) - ALGEBRAIC(:,18);
    ALGEBRAIC(:,4) = (( (( (( CONSTANTS(:,17).*CONSTANTS(:,7))./CONSTANTS(:,11)).*ALGEBRAIC(:,2))./CONSTANTS(:,12)).*ALGEBRAIC(:,1))./CONSTANTS(:,13))./( (1.00000+CONSTANTS(:,7)./CONSTANTS(:,11)+STATES(:,1)./CONSTANTS(:,14)).*(1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,12)+STATES(:,7)./CONSTANTS(:,15)).*(1.00000+ALGEBRAIC(:,1)./CONSTANTS(:,13)+STATES(:,6)./CONSTANTS(:,16)));
    ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,4)>=0.00000, ALGEBRAIC(:,4) }, ALGEBRAIC(:,4));
    ALGEBRAIC(:,17) = ( CONSTANTS(:,76).*power(STATES(:,6)./ALGEBRAIC(:,1), CONSTANTS(:,74)))./(power(CONSTANTS(:,75), CONSTANTS(:,74))+power(STATES(:,6)./ALGEBRAIC(:,1), CONSTANTS(:,74)));
    ALGEBRAIC(:,19) = piecewise({ALGEBRAIC(:,17)>=0.00000, ALGEBRAIC(:,17) }, ALGEBRAIC(:,17));
    RATES(:,6) = (ALGEBRAIC(:,5)+ALGEBRAIC(:,15)) - ALGEBRAIC(:,19);
    ALGEBRAIC(:,6) = ( (CONSTANTS(:,23)./( CONSTANTS(:,21).*CONSTANTS(:,22))).*( STATES(:,1).*STATES(:,7) - ( CONSTANTS(:,8).*ALGEBRAIC(:,2))./CONSTANTS(:,18)))./( (1.00000+STATES(:,1)./CONSTANTS(:,21)+CONSTANTS(:,8)./CONSTANTS(:,19)).*(1.00000+STATES(:,7)./CONSTANTS(:,22)+ALGEBRAIC(:,2)./CONSTANTS(:,20)));
    ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,6)>=0.00000, ALGEBRAIC(:,6) }, ALGEBRAIC(:,6));
    ALGEBRAIC(:,20) = ( (( CONSTANTS(:,62).*STATES(:,1))./CONSTANTS(:,61)).*(1.00000 - STATES(:,4)./( STATES(:,1).*CONSTANTS(:,59))).*power(STATES(:,1)./CONSTANTS(:,61)+STATES(:,4)./CONSTANTS(:,60), CONSTANTS(:,58) - 1.00000))./(1.00000+power(STATES(:,1)./CONSTANTS(:,61)+STATES(:,4)./CONSTANTS(:,60), CONSTANTS(:,58)));
    ALGEBRAIC(:,21) = piecewise({ALGEBRAIC(:,20)>=0.00000, ALGEBRAIC(:,20) }, ALGEBRAIC(:,20));
    RATES(:,1) = ALGEBRAIC(:,5) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,9)+ALGEBRAIC(:,21));
    ALGEBRAIC(:,22) = (( CONSTANTS(:,65).*STATES(:,4))./CONSTANTS(:,63))./(1.00000+STATES(:,4)./CONSTANTS(:,63)+STATES(:,5)./CONSTANTS(:,64));
    ALGEBRAIC(:,23) = piecewise({ALGEBRAIC(:,22)>=0.00000, ALGEBRAIC(:,22) }, ALGEBRAIC(:,22));
    ALGEBRAIC(:,28) =  CONSTANTS(:,81).*STATES(:,4);
    RATES(:,4) =  0.500000.*ALGEBRAIC(:,21) - (ALGEBRAIC(:,23)+ALGEBRAIC(:,28));
    ALGEBRAIC(:,26) = ( (CONSTANTS(:,73)./( CONSTANTS(:,72).*CONSTANTS(:,70))).*( STATES(:,5).*STATES(:,7) - ( CONSTANTS(:,5).*ALGEBRAIC(:,2))./CONSTANTS(:,68)))./( (1.00000+STATES(:,5)./CONSTANTS(:,72)+CONSTANTS(:,5)./CONSTANTS(:,71)).*(1.00000+STATES(:,7)./CONSTANTS(:,70)+ALGEBRAIC(:,2)./CONSTANTS(:,69)));
    ALGEBRAIC(:,27) = piecewise({ALGEBRAIC(:,26)>=0.00000, ALGEBRAIC(:,26) }, ALGEBRAIC(:,26));
    ALGEBRAIC(:,24) = (( CONSTANTS(:,67).*STATES(:,5))./CONSTANTS(:,66))./(1.00000+STATES(:,5)./CONSTANTS(:,66));
    ALGEBRAIC(:,25) = piecewise({ALGEBRAIC(:,24)>=0.00000, ALGEBRAIC(:,24) }, ALGEBRAIC(:,24));
    RATES(:,5) = (ALGEBRAIC(:,23)+ALGEBRAIC(:,28)) - (ALGEBRAIC(:,27)+ALGEBRAIC(:,25));
    ALGEBRAIC(:,29) = (( CONSTANTS(:,80).*STATES(:,7).*CONSTANTS(:,9))./( CONSTANTS(:,78).*CONSTANTS(:,79)))./( (1.00000+STATES(:,7)./CONSTANTS(:,78)+ALGEBRAIC(:,2)./CONSTANTS(:,77)).*(1.00000+CONSTANTS(:,9)./CONSTANTS(:,79)));
    ALGEBRAIC(:,30) = piecewise({ALGEBRAIC(:,29)>=0.00000, ALGEBRAIC(:,29) }, ALGEBRAIC(:,29));
    RATES(:,7) = (ALGEBRAIC(:,5)+ALGEBRAIC(:,9)) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,14)+ALGEBRAIC(:,18)+ALGEBRAIC(:,27)+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(:,3) = CONSTANTS(:,3) - STATES(:,8);
    ALGEBRAIC(:,10) = ( (CONSTANTS(:,38)./( CONSTANTS(:,37).*CONSTANTS(:,32))).*( STATES(:,8).*CONSTANTS(:,10) - ( STATES(:,2).*ALGEBRAIC(:,3))./CONSTANTS(:,31)))./(1.00000+STATES(:,8)./CONSTANTS(:,37)+CONSTANTS(:,10)./CONSTANTS(:,33)+STATES(:,2)./CONSTANTS(:,36)+ALGEBRAIC(:,3)./CONSTANTS(:,34)+( STATES(:,8).*CONSTANTS(:,10))./( CONSTANTS(:,37).*CONSTANTS(:,32))+( STATES(:,2).*ALGEBRAIC(:,3))./( CONSTANTS(:,35).*CONSTANTS(:,34)));
    ALGEBRAIC(:,11) = piecewise({ALGEBRAIC(:,10)>=0.00000, ALGEBRAIC(:,10) }, ALGEBRAIC(:,10));
    ALGEBRAIC(:,1) = CONSTANTS(:,1) - STATES(:,6);
    ALGEBRAIC(:,13) = ( (CONSTANTS(:,44)./( CONSTANTS(:,42).*CONSTANTS(:,43))).*( STATES(:,2).*ALGEBRAIC(:,1) - ( CONSTANTS(:,4).*STATES(:,6))./CONSTANTS(:,39)))./( (1.00000+STATES(:,2)./CONSTANTS(:,43)+CONSTANTS(:,4)./CONSTANTS(:,40)).*(1.00000+ALGEBRAIC(:,1)./CONSTANTS(:,42)+STATES(:,6)./CONSTANTS(:,41)));
    ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,13)>=0.00000, ALGEBRAIC(:,13) }, ALGEBRAIC(:,13));
    ALGEBRAIC(:,2) = CONSTANTS(:,2) - STATES(:,7);
    ALGEBRAIC(:,8) = (( (( (( (CONSTANTS(:,30)./(1.00000+( CONSTANTS(:,24).*STATES(:,7))./ALGEBRAIC(:,2))).*STATES(:,1))./CONSTANTS(:,27)).*ALGEBRAIC(:,2))./CONSTANTS(:,25)).*ALGEBRAIC(:,3))./CONSTANTS(:,26))./( (1.00000+STATES(:,1)./CONSTANTS(:,27)).*(1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,25)+STATES(:,7)./CONSTANTS(:,28)).*(1.00000+ALGEBRAIC(:,3)./CONSTANTS(:,26)+STATES(:,8)./CONSTANTS(:,29)));
    ALGEBRAIC(:,9) = piecewise({ALGEBRAIC(:,8)>=0.00000, ALGEBRAIC(:,8) }, ALGEBRAIC(:,8));
    ALGEBRAIC(:,12) = ( (CONSTANTS(:,51)./( CONSTANTS(:,49).*CONSTANTS(:,47))).*( STATES(:,8).*STATES(:,7) - ( ALGEBRAIC(:,2).*ALGEBRAIC(:,3).*STATES(:,3))./CONSTANTS(:,45)))./( (1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,46)+STATES(:,7)./CONSTANTS(:,47)).*(1.00000+STATES(:,8)./CONSTANTS(:,49)+ALGEBRAIC(:,3)./CONSTANTS(:,48)).*(1.00000+STATES(:,3)./CONSTANTS(:,50)));
    ALGEBRAIC(:,14) = piecewise({ALGEBRAIC(:,12)>=0.00000, ALGEBRAIC(:,12) }, ALGEBRAIC(:,12));
    ALGEBRAIC(:,16) = ( (CONSTANTS(:,57)./( CONSTANTS(:,56).*CONSTANTS(:,54))).*( STATES(:,3).*STATES(:,7) - ( CONSTANTS(:,6).*ALGEBRAIC(:,2))./CONSTANTS(:,52)))./( (1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,53)+STATES(:,7)./CONSTANTS(:,54)).*(1.00000+STATES(:,3)./CONSTANTS(:,56)+CONSTANTS(:,6)./CONSTANTS(:,55)));
    ALGEBRAIC(:,18) = piecewise({ALGEBRAIC(:,16)>=0.00000, ALGEBRAIC(:,16) }, ALGEBRAIC(:,16));
    ALGEBRAIC(:,4) = (( (( (( CONSTANTS(:,17).*CONSTANTS(:,7))./CONSTANTS(:,11)).*ALGEBRAIC(:,2))./CONSTANTS(:,12)).*ALGEBRAIC(:,1))./CONSTANTS(:,13))./( (1.00000+CONSTANTS(:,7)./CONSTANTS(:,11)+STATES(:,1)./CONSTANTS(:,14)).*(1.00000+ALGEBRAIC(:,2)./CONSTANTS(:,12)+STATES(:,7)./CONSTANTS(:,15)).*(1.00000+ALGEBRAIC(:,1)./CONSTANTS(:,13)+STATES(:,6)./CONSTANTS(:,16)));
    ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,4)>=0.00000, ALGEBRAIC(:,4) }, ALGEBRAIC(:,4));
    ALGEBRAIC(:,17) = ( CONSTANTS(:,76).*power(STATES(:,6)./ALGEBRAIC(:,1), CONSTANTS(:,74)))./(power(CONSTANTS(:,75), CONSTANTS(:,74))+power(STATES(:,6)./ALGEBRAIC(:,1), CONSTANTS(:,74)));
    ALGEBRAIC(:,19) = piecewise({ALGEBRAIC(:,17)>=0.00000, ALGEBRAIC(:,17) }, ALGEBRAIC(:,17));
    ALGEBRAIC(:,6) = ( (CONSTANTS(:,23)./( CONSTANTS(:,21).*CONSTANTS(:,22))).*( STATES(:,1).*STATES(:,7) - ( CONSTANTS(:,8).*ALGEBRAIC(:,2))./CONSTANTS(:,18)))./( (1.00000+STATES(:,1)./CONSTANTS(:,21)+CONSTANTS(:,8)./CONSTANTS(:,19)).*(1.00000+STATES(:,7)./CONSTANTS(:,22)+ALGEBRAIC(:,2)./CONSTANTS(:,20)));
    ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,6)>=0.00000, ALGEBRAIC(:,6) }, ALGEBRAIC(:,6));
    ALGEBRAIC(:,20) = ( (( CONSTANTS(:,62).*STATES(:,1))./CONSTANTS(:,61)).*(1.00000 - STATES(:,4)./( STATES(:,1).*CONSTANTS(:,59))).*power(STATES(:,1)./CONSTANTS(:,61)+STATES(:,4)./CONSTANTS(:,60), CONSTANTS(:,58) - 1.00000))./(1.00000+power(STATES(:,1)./CONSTANTS(:,61)+STATES(:,4)./CONSTANTS(:,60), CONSTANTS(:,58)));
    ALGEBRAIC(:,21) = piecewise({ALGEBRAIC(:,20)>=0.00000, ALGEBRAIC(:,20) }, ALGEBRAIC(:,20));
    ALGEBRAIC(:,22) = (( CONSTANTS(:,65).*STATES(:,4))./CONSTANTS(:,63))./(1.00000+STATES(:,4)./CONSTANTS(:,63)+STATES(:,5)./CONSTANTS(:,64));
    ALGEBRAIC(:,23) = piecewise({ALGEBRAIC(:,22)>=0.00000, ALGEBRAIC(:,22) }, ALGEBRAIC(:,22));
    ALGEBRAIC(:,28) =  CONSTANTS(:,81).*STATES(:,4);
    ALGEBRAIC(:,26) = ( (CONSTANTS(:,73)./( CONSTANTS(:,72).*CONSTANTS(:,70))).*( STATES(:,5).*STATES(:,7) - ( CONSTANTS(:,5).*ALGEBRAIC(:,2))./CONSTANTS(:,68)))./( (1.00000+STATES(:,5)./CONSTANTS(:,72)+CONSTANTS(:,5)./CONSTANTS(:,71)).*(1.00000+STATES(:,7)./CONSTANTS(:,70)+ALGEBRAIC(:,2)./CONSTANTS(:,69)));
    ALGEBRAIC(:,27) = piecewise({ALGEBRAIC(:,26)>=0.00000, ALGEBRAIC(:,26) }, ALGEBRAIC(:,26));
    ALGEBRAIC(:,24) = (( CONSTANTS(:,67).*STATES(:,5))./CONSTANTS(:,66))./(1.00000+STATES(:,5)./CONSTANTS(:,66));
    ALGEBRAIC(:,25) = piecewise({ALGEBRAIC(:,24)>=0.00000, ALGEBRAIC(:,24) }, ALGEBRAIC(:,24));
    ALGEBRAIC(:,29) = (( CONSTANTS(:,80).*STATES(:,7).*CONSTANTS(:,9))./( CONSTANTS(:,78).*CONSTANTS(:,79)))./( (1.00000+STATES(:,7)./CONSTANTS(:,78)+ALGEBRAIC(:,2)./CONSTANTS(:,77)).*(1.00000+CONSTANTS(:,9)./CONSTANTS(:,79)));
    ALGEBRAIC(:,30) = piecewise({ALGEBRAIC(:,29)>=0.00000, ALGEBRAIC(:,29) }, ALGEBRAIC(:,29));
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