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 29 entries in each of the rate and state variable arrays.
% There are a total of 45 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('BMK1 in component BMK1 (micromolar)');
    LEGEND_ALGEBRAIC(:,10) = strpad('v10a in component v10 (flux)');
    LEGEND_ALGEBRAIC(:,11) = strpad('v10b in component v10 (flux)');
    LEGEND_STATES(:,2) = strpad('MRNA in component MRNA (micromolar)');
    LEGEND_ALGEBRAIC(:,29) = strpad('v18 in component v18 (flux)');
    LEGEND_ALGEBRAIC(:,31) = strpad('v19 in component v19 (flux)');
    LEGEND_STATES(:,3) = strpad('NFATc in component NFATc (micromolar)');
    LEGEND_ALGEBRAIC(:,1) = strpad('v1 in component v1 (flux)');
    LEGEND_ALGEBRAIC(:,32) = strpad('v14 in component v14 (flux)');
    LEGEND_ALGEBRAIC(:,35) = strpad('v15 in component v15 (flux)');
    LEGEND_STATES(:,4) = strpad('NFATn in component NFATn (micromolar)');
    LEGEND_ALGEBRAIC(:,20) = strpad('v16 in component v16 (flux)');
    LEGEND_ALGEBRAIC(:,26) = strpad('v17 in component v17 (flux)');
    LEGEND_STATES(:,5) = strpad('NFATpc in component NFATpc (micromolar)');
    LEGEND_ALGEBRAIC(:,2) = strpad('v2 in component v2 (flux)');
    LEGEND_ALGEBRAIC(:,9) = strpad('v9 in component v9 (flux)');
    LEGEND_STATES(:,6) = strpad('NFATpn in component NFATpn (micromolar)');
    LEGEND_STATES(:,7) = strpad('GSK3betac in component GSK3betac (micromolar)');
    LEGEND_ALGEBRAIC(:,3) = strpad('v3 in component v3 (flux)');
    LEGEND_ALGEBRAIC(:,17) = strpad('v12a in component v12 (flux)');
    LEGEND_ALGEBRAIC(:,19) = strpad('v12b in component v12 (flux)');
    LEGEND_ALGEBRAIC(:,33) = strpad('v15a in component v15 (flux)');
    LEGEND_ALGEBRAIC(:,34) = strpad('v15b in component v15 (flux)');
    LEGEND_STATES(:,8) = strpad('GSK3betan in component GSK3betan (micromolar)');
    LEGEND_ALGEBRAIC(:,22) = strpad('v17a in component v17 (flux)');
    LEGEND_ALGEBRAIC(:,24) = strpad('v17b in component v17 (flux)');
    LEGEND_STATES(:,9) = strpad('CaNc in component CaNc (micromolar)');
    LEGEND_ALGEBRAIC(:,6) = strpad('v6 in component v6 (flux)');
    LEGEND_STATES(:,10) = strpad('CaNc_star in component CaNc_star (micromolar)');
    LEGEND_ALGEBRAIC(:,4) = strpad('v4 in component v4 (flux)');
    LEGEND_ALGEBRAIC(:,7) = strpad('v7 in component v7 (flux)');
    LEGEND_ALGEBRAIC(:,13) = strpad('v11a in component v11 (flux)');
    LEGEND_ALGEBRAIC(:,14) = strpad('v11b in component v11 (flux)');
    LEGEND_ALGEBRAIC(:,23) = strpad('v13a in component v13 (flux)');
    LEGEND_ALGEBRAIC(:,25) = strpad('v13b in component v13 (flux)');
    LEGEND_ALGEBRAIC(:,27) = strpad('v14a in component v14 (flux)');
    LEGEND_ALGEBRAIC(:,30) = strpad('v14b in component v14 (flux)');
    LEGEND_STATES(:,11) = strpad('CaNn_star in component CaNn_star (micromolar)');
    LEGEND_ALGEBRAIC(:,16) = strpad('v16a in component v16 (flux)');
    LEGEND_ALGEBRAIC(:,18) = strpad('v16b in component v16 (flux)');
    LEGEND_STATES(:,12) = strpad('CaNn in component CaNn (micromolar)');
    LEGEND_STATES(:,13) = strpad('CaM in component CaM (micromolar)');
    LEGEND_ALGEBRAIC(:,5) = strpad('v5 in component v5 (flux)');
    LEGEND_STATES(:,14) = strpad('CaMCa in component CaMCa (micromolar)');
    LEGEND_STATES(:,15) = strpad('MCIP in component MCIP (micromolar)');
    LEGEND_ALGEBRAIC(:,12) = strpad('v10 in component v10 (flux)');
    LEGEND_ALGEBRAIC(:,15) = strpad('v11 in component v11 (flux)');
    LEGEND_STATES(:,16) = strpad('MCIPp in component MCIPp (micromolar)');
    LEGEND_ALGEBRAIC(:,21) = strpad('v12 in component v12 (flux)');
    LEGEND_ALGEBRAIC(:,28) = strpad('v13 in component v13 (flux)');
    LEGEND_STATES(:,17) = strpad('MCIPpp in component MCIPpp (micromolar)');
    LEGEND_ALGEBRAIC(:,8) = strpad('v8 in component v8 (flux)');
    LEGEND_STATES(:,18) = strpad('Comp1 in component Comp1 (micromolar)');
    LEGEND_STATES(:,19) = strpad('Comp2 in component Comp2 (micromolar)');
    LEGEND_STATES(:,20) = strpad('Comp3 in component Comp3 (micromolar)');
    LEGEND_STATES(:,21) = strpad('P1433 in component P1433 (micromolar)');
    LEGEND_STATES(:,22) = strpad('MCIP_BMK1 in component MCIP_BMK1 (micromolar)');
    LEGEND_STATES(:,23) = strpad('MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)');
    LEGEND_STATES(:,24) = strpad('MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)');
    LEGEND_STATES(:,25) = strpad('MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)');
    LEGEND_STATES(:,26) = strpad('NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)');
    LEGEND_STATES(:,27) = strpad('NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)');
    LEGEND_STATES(:,28) = strpad('NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)');
    LEGEND_STATES(:,29) = strpad('NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)');
    LEGEND_CONSTANTS(:,1) = strpad('k29 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k30 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k31 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k32 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,5) = strpad('k33 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k34 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,7) = strpad('Ca in component model_parameters (micromolar)');
    LEGEND_CONSTANTS(:,8) = strpad('k1 in component model_parameters (fifth_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('k2 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k3 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,11) = strpad('k4 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,12) = strpad('k5 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('k6 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('k19 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,15) = strpad('k20 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,16) = strpad('k27 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,17) = strpad('k28 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('k7 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('k8 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,20) = strpad('k9 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,21) = strpad('k10 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('k11 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('k12 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,24) = strpad('k13 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,25) = strpad('k14 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('k15 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('k16 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('k17 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,29) = strpad('k18 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,30) = strpad('k21 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,31) = strpad('k22 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,32) = strpad('k23 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,33) = strpad('k24 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,34) = strpad('k25 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('k26 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('k35 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('k36 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('k37 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('k38 in component model_parameters (second_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('k39 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,41) = strpad('k40 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,42) = strpad('k41 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,43) = strpad('k42 in component model_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,44) = strpad('t_half in component model_parameters (minute)');
    LEGEND_CONSTANTS(:,45) = strpad('k43 in component model_parameters (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt BMK1 in component BMK1 (micromolar)');
    LEGEND_RATES(:,2) = strpad('d/dt MRNA in component MRNA (micromolar)');
    LEGEND_RATES(:,3) = strpad('d/dt NFATc in component NFATc (micromolar)');
    LEGEND_RATES(:,4) = strpad('d/dt NFATn in component NFATn (micromolar)');
    LEGEND_RATES(:,5) = strpad('d/dt NFATpc in component NFATpc (micromolar)');
    LEGEND_RATES(:,6) = strpad('d/dt NFATpn in component NFATpn (micromolar)');
    LEGEND_RATES(:,7) = strpad('d/dt GSK3betac in component GSK3betac (micromolar)');
    LEGEND_RATES(:,8) = strpad('d/dt GSK3betan in component GSK3betan (micromolar)');
    LEGEND_RATES(:,9) = strpad('d/dt CaNc in component CaNc (micromolar)');
    LEGEND_RATES(:,10) = strpad('d/dt CaNc_star in component CaNc_star (micromolar)');
    LEGEND_RATES(:,11) = strpad('d/dt CaNn_star in component CaNn_star (micromolar)');
    LEGEND_RATES(:,12) = strpad('d/dt CaNn in component CaNn (micromolar)');
    LEGEND_RATES(:,13) = strpad('d/dt CaM in component CaM (micromolar)');
    LEGEND_RATES(:,14) = strpad('d/dt CaMCa in component CaMCa (micromolar)');
    LEGEND_RATES(:,15) = strpad('d/dt MCIP in component MCIP (micromolar)');
    LEGEND_RATES(:,16) = strpad('d/dt MCIPp in component MCIPp (micromolar)');
    LEGEND_RATES(:,17) = strpad('d/dt MCIPpp in component MCIPpp (micromolar)');
    LEGEND_RATES(:,18) = strpad('d/dt Comp1 in component Comp1 (micromolar)');
    LEGEND_RATES(:,19) = strpad('d/dt Comp2 in component Comp2 (micromolar)');
    LEGEND_RATES(:,20) = strpad('d/dt Comp3 in component Comp3 (micromolar)');
    LEGEND_RATES(:,21) = strpad('d/dt P1433 in component P1433 (micromolar)');
    LEGEND_RATES(:,22) = strpad('d/dt MCIP_BMK1 in component MCIP_BMK1 (micromolar)');
    LEGEND_RATES(:,23) = strpad('d/dt MCIPp_CaNc_star in component MCIPp_CaNc_star (micromolar)');
    LEGEND_RATES(:,24) = strpad('d/dt MCIPp_GSK3betac in component MCIPp_GSK3betac (micromolar)');
    LEGEND_RATES(:,25) = strpad('d/dt MCIPpp_CaNc_star in component MCIPpp_CaNc_star (micromolar)');
    LEGEND_RATES(:,26) = strpad('d/dt NFATpc_CaNc_star in component NFATpc_CaNc_star (micromolar)');
    LEGEND_RATES(:,27) = strpad('d/dt NFATc_GSK3betac in component NFATc_GSK3betac (micromolar)');
    LEGEND_RATES(:,28) = strpad('d/dt NFATpn_CaNn_star in component NFATpn_CaNn_star (micromolar)');
    LEGEND_RATES(:,29) = strpad('d/dt NFATn_GSK3betan in component NFATn_GSK3betan (micromolar)');
    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) = 0.012;
    STATES(:,2) = 3.33E-4;
    STATES(:,3) = 2E-5;
    STATES(:,4) = 4.99E-4;
    STATES(:,5) = 4.94E-3;
    STATES(:,6) = 8.01E-5;
    STATES(:,7) = 0.17;
    STATES(:,8) = 0.339;
    STATES(:,9) = 0.91;
    STATES(:,10) = 0.0275;
    STATES(:,11) = 0.0568;
    STATES(:,12) = 0.0057;
    STATES(:,13) = 25.2;
    STATES(:,14) = 7.88E-7;
    STATES(:,15) = 2.15E-4;
    STATES(:,16) = 7.76E-3;
    STATES(:,17) = 0.0798;
    STATES(:,18) = 5.21E-3;
    STATES(:,19) = 0.283;
    STATES(:,20) = 0.014;
    STATES(:,21) = 0.708;
    STATES(:,22) = 2.14E-5;
    STATES(:,23) = 1.07E-4;
    STATES(:,24) = 1.1E-3;
    STATES(:,25) = 1.1E-3;
    STATES(:,26) = 8.15E-5;
    STATES(:,27) = 1.36E-6;
    STATES(:,28) = 2.27E-6;
    STATES(:,29) = 8.46E-5;
    CONSTANTS(:,1) = 0.4;
    CONSTANTS(:,2) = 0.1;
    CONSTANTS(:,3) = 0.1;
    CONSTANTS(:,4) = 0.05;
    CONSTANTS(:,5) = 0.114;
    CONSTANTS(:,6) = 0.0552;
    CONSTANTS(:,7) = 0.2;
    CONSTANTS(:,8) = 5;
    CONSTANTS(:,9) = 100;
    CONSTANTS(:,10) = 2760;
    CONSTANTS(:,11) = 0.072;
    CONSTANTS(:,12) = 50;
    CONSTANTS(:,13) = 0.0567;
    CONSTANTS(:,14) = 0.5;
    CONSTANTS(:,15) = 0.1;
    CONSTANTS(:,16) = 0.4;
    CONSTANTS(:,17) = 0.1;
    CONSTANTS(:,18) = 5;
    CONSTANTS(:,19) = 0.1;
    CONSTANTS(:,20) = 0.5;
    CONSTANTS(:,21) = 0.1;
    CONSTANTS(:,22) = 0.1;
    CONSTANTS(:,23) = 0.1;
    CONSTANTS(:,24) = 0.5;
    CONSTANTS(:,25) = 0.5;
    CONSTANTS(:,26) = 0.1;
    CONSTANTS(:,27) = 0.1;
    CONSTANTS(:,28) = 0.1;
    CONSTANTS(:,29) = 0.1;
    CONSTANTS(:,30) = 0.15;
    CONSTANTS(:,31) = 0.15;
    CONSTANTS(:,32) = 0.15;
    CONSTANTS(:,33) = 0.1;
    CONSTANTS(:,34) = 0.15;
    CONSTANTS(:,35) = 0.1;
    CONSTANTS(:,36) = 0.15;
    CONSTANTS(:,37) = 0.1;
    CONSTANTS(:,38) = 0.2;
    CONSTANTS(:,39) = 0.1;
    CONSTANTS(:,40) = 0.1;
    CONSTANTS(:,41) = 0.1;
    CONSTANTS(:,42) = 0.02;
    CONSTANTS(:,43) = 0.03;
    CONSTANTS(:,44) = 15;
    CONSTANTS(:,45) = 0.03;
    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(:,8).*STATES(:,13).*power(CONSTANTS(:,7), 4.00000) -  CONSTANTS(:,9).*STATES(:,14);
    RATES(:,13) =  - ALGEBRAIC(:,5);
    ALGEBRAIC(:,6) =  CONSTANTS(:,10).*STATES(:,14).*STATES(:,9) -  CONSTANTS(:,11).*STATES(:,10);
    RATES(:,9) =  - ALGEBRAIC(:,6);
    RATES(:,12) =  - ALGEBRAIC(:,6);
    RATES(:,14) = ALGEBRAIC(:,5) - ALGEBRAIC(:,6);
    ALGEBRAIC(:,7) =  CONSTANTS(:,12).*STATES(:,10).*STATES(:,15) -  CONSTANTS(:,13).*STATES(:,18);
    RATES(:,18) = ALGEBRAIC(:,7);
    ALGEBRAIC(:,8) =  CONSTANTS(:,14).*STATES(:,21).*STATES(:,17) -  CONSTANTS(:,15).*STATES(:,19);
    RATES(:,19) = ALGEBRAIC(:,8);
    ALGEBRAIC(:,9) =  CONSTANTS(:,16).*STATES(:,5).*STATES(:,21) -  CONSTANTS(:,17).*STATES(:,20);
    RATES(:,20) = ALGEBRAIC(:,9);
    RATES(:,21) =  - (ALGEBRAIC(:,8)+ALGEBRAIC(:,9));
    ALGEBRAIC(:,10) =  CONSTANTS(:,18).*STATES(:,15).*STATES(:,1) -  CONSTANTS(:,19).*STATES(:,22);
    ALGEBRAIC(:,11) =  CONSTANTS(:,20).*STATES(:,22);
    RATES(:,1) = ALGEBRAIC(:,11) - ALGEBRAIC(:,10);
    RATES(:,22) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
    ALGEBRAIC(:,13) =  CONSTANTS(:,21).*STATES(:,16).*STATES(:,10) -  CONSTANTS(:,22).*STATES(:,23);
    ALGEBRAIC(:,14) =  CONSTANTS(:,23).*STATES(:,23);
    RATES(:,23) = ALGEBRAIC(:,13) - ALGEBRAIC(:,14);
    ALGEBRAIC(:,4) =  CONSTANTS(:,5).*STATES(:,10) -  CONSTANTS(:,6).*STATES(:,11);
    ALGEBRAIC(:,16) =  CONSTANTS(:,36).*STATES(:,6).*STATES(:,11) -  CONSTANTS(:,37).*STATES(:,28);
    ALGEBRAIC(:,18) =  CONSTANTS(:,38).*STATES(:,28);
    RATES(:,11) = (ALGEBRAIC(:,4)+ALGEBRAIC(:,18)) - ALGEBRAIC(:,16);
    ALGEBRAIC(:,17) =  CONSTANTS(:,24).*STATES(:,16).*STATES(:,7) -  CONSTANTS(:,25).*STATES(:,24);
    ALGEBRAIC(:,19) =  CONSTANTS(:,26).*STATES(:,24);
    RATES(:,24) = ALGEBRAIC(:,17) - ALGEBRAIC(:,19);
    RATES(:,28) = ALGEBRAIC(:,16) - ALGEBRAIC(:,18);
    ALGEBRAIC(:,3) =  CONSTANTS(:,3).*STATES(:,7) -  CONSTANTS(:,4).*STATES(:,8);
    ALGEBRAIC(:,22) =  CONSTANTS(:,39).*STATES(:,4).*STATES(:,8) -  CONSTANTS(:,40).*STATES(:,29);
    ALGEBRAIC(:,24) =  CONSTANTS(:,41).*STATES(:,29);
    RATES(:,8) = (ALGEBRAIC(:,3)+ALGEBRAIC(:,24)) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,23) =  CONSTANTS(:,27).*STATES(:,17).*STATES(:,10) -  CONSTANTS(:,28).*STATES(:,25);
    ALGEBRAIC(:,25) =  CONSTANTS(:,29).*STATES(:,25);
    RATES(:,25) = ALGEBRAIC(:,23) - ALGEBRAIC(:,25);
    RATES(:,29) = ALGEBRAIC(:,22) - ALGEBRAIC(:,24);
    ALGEBRAIC(:,20) = ALGEBRAIC(:,16)+ALGEBRAIC(:,18);
    ALGEBRAIC(:,26) = ALGEBRAIC(:,22)+ALGEBRAIC(:,24);
    ALGEBRAIC(:,2) =  CONSTANTS(:,2).*STATES(:,6);
    RATES(:,6) = ALGEBRAIC(:,26) - (ALGEBRAIC(:,2)+ALGEBRAIC(:,20));
    ALGEBRAIC(:,12) = ALGEBRAIC(:,10)+ALGEBRAIC(:,11);
    ALGEBRAIC(:,15) = ALGEBRAIC(:,13)+ALGEBRAIC(:,14);
    ALGEBRAIC(:,21) = ALGEBRAIC(:,17)+ALGEBRAIC(:,19);
    ALGEBRAIC(:,28) = ALGEBRAIC(:,23)+ALGEBRAIC(:,25);
    RATES(:,16) = (ALGEBRAIC(:,12)+ALGEBRAIC(:,28)) - (ALGEBRAIC(:,15)+ALGEBRAIC(:,21));
    RATES(:,17) = ALGEBRAIC(:,21) - (ALGEBRAIC(:,8)+ALGEBRAIC(:,28));
    ALGEBRAIC(:,29) =  CONSTANTS(:,42).*STATES(:,4) -  CONSTANTS(:,43).*STATES(:,2);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*STATES(:,3);
    RATES(:,4) = (ALGEBRAIC(:,1)+ALGEBRAIC(:,20)) - (ALGEBRAIC(:,26)+ALGEBRAIC(:,29));
    ALGEBRAIC(:,27) =  CONSTANTS(:,30).*STATES(:,5).*STATES(:,10) -  CONSTANTS(:,31).*STATES(:,26);
    ALGEBRAIC(:,30) =  CONSTANTS(:,32).*STATES(:,26);
    RATES(:,10) = (ALGEBRAIC(:,6)+ALGEBRAIC(:,14)+ALGEBRAIC(:,25)+ALGEBRAIC(:,30)) - (ALGEBRAIC(:,4)+ALGEBRAIC(:,7)+ALGEBRAIC(:,13)+ALGEBRAIC(:,23)+ALGEBRAIC(:,27));
    RATES(:,26) = ALGEBRAIC(:,27) - ALGEBRAIC(:,30);
    ALGEBRAIC(:,31) =  CONSTANTS(:,45).*STATES(:,2) -  (log(2.00000)./CONSTANTS(:,44)).*STATES(:,15);
    RATES(:,2) = ALGEBRAIC(:,31) - ALGEBRAIC(:,29);
    RATES(:,15) = ALGEBRAIC(:,15) - (ALGEBRAIC(:,7)+ALGEBRAIC(:,12)+ALGEBRAIC(:,31));
    ALGEBRAIC(:,33) =  CONSTANTS(:,33).*STATES(:,3).*STATES(:,7) -  CONSTANTS(:,34).*STATES(:,27);
    ALGEBRAIC(:,34) =  CONSTANTS(:,35).*STATES(:,27);
    RATES(:,7) = (ALGEBRAIC(:,19)+ALGEBRAIC(:,34)) - (ALGEBRAIC(:,3)+ALGEBRAIC(:,17)+ALGEBRAIC(:,33));
    RATES(:,27) = ALGEBRAIC(:,33) - ALGEBRAIC(:,34);
    ALGEBRAIC(:,32) = ALGEBRAIC(:,27)+ALGEBRAIC(:,30);
    ALGEBRAIC(:,35) = ALGEBRAIC(:,33)+ALGEBRAIC(:,34);
    RATES(:,3) = ALGEBRAIC(:,32) - (ALGEBRAIC(:,1)+ALGEBRAIC(:,35));
    RATES(:,5) = (ALGEBRAIC(:,2)+ALGEBRAIC(:,35)) - (ALGEBRAIC(:,9)+ALGEBRAIC(:,32));
   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(:,8).*STATES(:,13).*power(CONSTANTS(:,7), 4.00000) -  CONSTANTS(:,9).*STATES(:,14);
    ALGEBRAIC(:,6) =  CONSTANTS(:,10).*STATES(:,14).*STATES(:,9) -  CONSTANTS(:,11).*STATES(:,10);
    ALGEBRAIC(:,7) =  CONSTANTS(:,12).*STATES(:,10).*STATES(:,15) -  CONSTANTS(:,13).*STATES(:,18);
    ALGEBRAIC(:,8) =  CONSTANTS(:,14).*STATES(:,21).*STATES(:,17) -  CONSTANTS(:,15).*STATES(:,19);
    ALGEBRAIC(:,9) =  CONSTANTS(:,16).*STATES(:,5).*STATES(:,21) -  CONSTANTS(:,17).*STATES(:,20);
    ALGEBRAIC(:,10) =  CONSTANTS(:,18).*STATES(:,15).*STATES(:,1) -  CONSTANTS(:,19).*STATES(:,22);
    ALGEBRAIC(:,11) =  CONSTANTS(:,20).*STATES(:,22);
    ALGEBRAIC(:,13) =  CONSTANTS(:,21).*STATES(:,16).*STATES(:,10) -  CONSTANTS(:,22).*STATES(:,23);
    ALGEBRAIC(:,14) =  CONSTANTS(:,23).*STATES(:,23);
    ALGEBRAIC(:,4) =  CONSTANTS(:,5).*STATES(:,10) -  CONSTANTS(:,6).*STATES(:,11);
    ALGEBRAIC(:,16) =  CONSTANTS(:,36).*STATES(:,6).*STATES(:,11) -  CONSTANTS(:,37).*STATES(:,28);
    ALGEBRAIC(:,18) =  CONSTANTS(:,38).*STATES(:,28);
    ALGEBRAIC(:,17) =  CONSTANTS(:,24).*STATES(:,16).*STATES(:,7) -  CONSTANTS(:,25).*STATES(:,24);
    ALGEBRAIC(:,19) =  CONSTANTS(:,26).*STATES(:,24);
    ALGEBRAIC(:,3) =  CONSTANTS(:,3).*STATES(:,7) -  CONSTANTS(:,4).*STATES(:,8);
    ALGEBRAIC(:,22) =  CONSTANTS(:,39).*STATES(:,4).*STATES(:,8) -  CONSTANTS(:,40).*STATES(:,29);
    ALGEBRAIC(:,24) =  CONSTANTS(:,41).*STATES(:,29);
    ALGEBRAIC(:,23) =  CONSTANTS(:,27).*STATES(:,17).*STATES(:,10) -  CONSTANTS(:,28).*STATES(:,25);
    ALGEBRAIC(:,25) =  CONSTANTS(:,29).*STATES(:,25);
    ALGEBRAIC(:,20) = ALGEBRAIC(:,16)+ALGEBRAIC(:,18);
    ALGEBRAIC(:,26) = ALGEBRAIC(:,22)+ALGEBRAIC(:,24);
    ALGEBRAIC(:,2) =  CONSTANTS(:,2).*STATES(:,6);
    ALGEBRAIC(:,12) = ALGEBRAIC(:,10)+ALGEBRAIC(:,11);
    ALGEBRAIC(:,15) = ALGEBRAIC(:,13)+ALGEBRAIC(:,14);
    ALGEBRAIC(:,21) = ALGEBRAIC(:,17)+ALGEBRAIC(:,19);
    ALGEBRAIC(:,28) = ALGEBRAIC(:,23)+ALGEBRAIC(:,25);
    ALGEBRAIC(:,29) =  CONSTANTS(:,42).*STATES(:,4) -  CONSTANTS(:,43).*STATES(:,2);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*STATES(:,3);
    ALGEBRAIC(:,27) =  CONSTANTS(:,30).*STATES(:,5).*STATES(:,10) -  CONSTANTS(:,31).*STATES(:,26);
    ALGEBRAIC(:,30) =  CONSTANTS(:,32).*STATES(:,26);
    ALGEBRAIC(:,31) =  CONSTANTS(:,45).*STATES(:,2) -  (log(2.00000)./CONSTANTS(:,44)).*STATES(:,15);
    ALGEBRAIC(:,33) =  CONSTANTS(:,33).*STATES(:,3).*STATES(:,7) -  CONSTANTS(:,34).*STATES(:,27);
    ALGEBRAIC(:,34) =  CONSTANTS(:,35).*STATES(:,27);
    ALGEBRAIC(:,32) = ALGEBRAIC(:,27)+ALGEBRAIC(:,30);
    ALGEBRAIC(:,35) = ALGEBRAIC(:,33)+ALGEBRAIC(:,34);
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