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 =49;
end
% There are a total of 7 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('t in component params_BG (second)');
    LEGEND_CONSTANTS(:,1) = strpad('R in component params_BG (J_per_K_mol)');
    LEGEND_CONSTANTS(:,2) = strpad('T in component params_BG (kelvin)');
    LEGEND_CONSTANTS(:,3) = strpad('F in component params_BG (C_per_mol)');
    LEGEND_CONSTANTS(:,4) = strpad('K_Hi in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,56) = strpad('q_Hi in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,5) = strpad('K_Ho in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,58) = strpad('q_Ho in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,6) = strpad('K_Cai in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,46) = strpad('q_Cai in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,7) = strpad('K_Cao in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,48) = strpad('q_Cao in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,8) = strpad('K_Pi in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,50) = strpad('q_Pi in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,9) = strpad('K_ATPi in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,52) = strpad('q_ATPi in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,10) = strpad('K_ADPi in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,54) = strpad('q_ADPi in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,11) = strpad('K_1 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,12) = strpad('q_init_1 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,13) = strpad('K_2 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,14) = strpad('q_init_2 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,15) = strpad('K_3 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,16) = strpad('q_init_3 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,17) = strpad('K_4 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,18) = strpad('q_init_4 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,19) = strpad('K_5 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,20) = strpad('q_init_5 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,21) = strpad('K_6 in component params_BG (per_fmol)');
    LEGEND_CONSTANTS(:,22) = strpad('q_init_6 in component params_BG (fmol)');
    LEGEND_CONSTANTS(:,23) = strpad('kappa_r1 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,24) = strpad('kappa_r2 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,25) = strpad('kappa_r3 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,26) = strpad('kappa_r4 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,27) = strpad('kappa_r5 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,28) = strpad('kappa_r6 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,57) = strpad('mu_Hi in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,59) = strpad('mu_Ho in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,47) = strpad('mu_Cai in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,49) = strpad('mu_Cao in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,51) = strpad('mu_Pi in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,53) = strpad('mu_ATPi in component BG_SERCA (J_per_mol)');
    LEGEND_CONSTANTS(:,55) = strpad('mu_ADPi in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,1) = strpad('mu_1 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,22) = strpad('v_1 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,2) = strpad('mu_2 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,43) = strpad('v_2 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,3) = strpad('mu_3 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,44) = strpad('v_3 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,4) = strpad('mu_4 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,33) = strpad('v_4 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,5) = strpad('mu_5 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,34) = strpad('v_5 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,6) = strpad('mu_6 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,23) = strpad('v_6 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,24) = strpad('V_Vm in component BG_SERCA (volt)');
    LEGEND_ALGEBRAIC(:,21) = strpad('V0_Vm in component params_BG (volt)');
    LEGEND_CONSTANTS(:,29) = strpad('z_zf1 in component params_BG (dimensionless)');
    LEGEND_CONSTANTS(:,30) = strpad('z_zr1 in component params_BG (dimensionless)');
    LEGEND_CONSTANTS(:,31) = strpad('z_zf2 in component params_BG (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('z_zr2 in component params_BG (dimensionless)');
    LEGEND_ALGEBRAIC(:,25) = strpad('Vm_zf1 in component BG_SERCA (volt)');
    LEGEND_ALGEBRAIC(:,36) = strpad('I_zf1 in component BG_SERCA (fA)');
    LEGEND_ALGEBRAIC(:,28) = strpad('mu_zf1 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,35) = strpad('v_zf1 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,27) = strpad('Vm_zr1 in component BG_SERCA (volt)');
    LEGEND_ALGEBRAIC(:,38) = strpad('I_zr1 in component BG_SERCA (fA)');
    LEGEND_ALGEBRAIC(:,30) = strpad('mu_zr1 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,37) = strpad('v_zr1 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,26) = strpad('Vm_zf2 in component BG_SERCA (volt)');
    LEGEND_ALGEBRAIC(:,46) = strpad('I_zf2 in component BG_SERCA (fA)');
    LEGEND_ALGEBRAIC(:,29) = strpad('mu_zf2 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,45) = strpad('v_zf2 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,39) = strpad('Vm_zr2 in component BG_SERCA (volt)');
    LEGEND_ALGEBRAIC(:,48) = strpad('I_zr2 in component BG_SERCA (fA)');
    LEGEND_ALGEBRAIC(:,40) = strpad('mu_zr2 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,47) = strpad('v_zr2 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,7) = strpad('A_f_r1 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,17) = strpad('v_r1 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,8) = strpad('A_r_r1 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,9) = strpad('A_f_r2 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,42) = strpad('v_r2 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,41) = strpad('A_r_r2 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,10) = strpad('A_f_r3 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,18) = strpad('v_r3 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,11) = strpad('A_r_r3 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,12) = strpad('A_f_r4 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,32) = strpad('v_r4 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,31) = strpad('A_r_r4 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,13) = strpad('A_f_r5 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,19) = strpad('v_r5 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,14) = strpad('A_r_r5 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,15) = strpad('A_f_r6 in component BG_SERCA (J_per_mol)');
    LEGEND_ALGEBRAIC(:,20) = strpad('v_r6 in component BG_SERCA (fmol_per_s)');
    LEGEND_ALGEBRAIC(:,16) = strpad('A_r_r6 in component BG_SERCA (J_per_mol)');
    LEGEND_STATES(:,1) = strpad('q_1 in component BG_SERCA (fmol)');
    LEGEND_STATES(:,2) = strpad('q_2 in component BG_SERCA (fmol)');
    LEGEND_STATES(:,3) = strpad('q_3 in component BG_SERCA (fmol)');
    LEGEND_STATES(:,4) = strpad('q_4 in component BG_SERCA (fmol)');
    LEGEND_STATES(:,5) = strpad('q_5 in component BG_SERCA (fmol)');
    LEGEND_STATES(:,6) = strpad('q_6 in component BG_SERCA (fmol)');
    LEGEND_ALGEBRAIC(:,49) = strpad('Ii in component BG_SERCA (fA)');
    LEGEND_CONSTANTS(:,33) = strpad('nH in component BG_SERCA (dimensionless)');
    LEGEND_CONSTANTS(:,34) = strpad('nCa in component BG_SERCA (dimensionless)');
    LEGEND_CONSTANTS(:,35) = strpad('kappa_r7 in component params_BG (fmol_per_s)');
    LEGEND_CONSTANTS(:,36) = strpad('Cai in component params_BG (mM)');
    LEGEND_CONSTANTS(:,37) = strpad('Cao in component params_BG (mM)');
    LEGEND_CONSTANTS(:,38) = strpad('Hi in component params_BG (mM)');
    LEGEND_CONSTANTS(:,39) = strpad('Ho in component params_BG (mM)');
    LEGEND_CONSTANTS(:,40) = strpad('Pi in component params_BG (mM)');
    LEGEND_CONSTANTS(:,41) = strpad('ATPi in component params_BG (mM)');
    LEGEND_CONSTANTS(:,42) = strpad('ADPi in component params_BG (mM)');
    LEGEND_CONSTANTS(:,43) = strpad('V_i in component params_BG (pL)');
    LEGEND_CONSTANTS(:,44) = strpad('V_o in component params_BG (pL)');
    LEGEND_STATES(:,7) = strpad('V_E in component params_BG (volt)');
    LEGEND_CONSTANTS(:,45) = strpad('dt in component params_BG (second)');
    LEGEND_RATES(:,1) = strpad('d/dt q_1 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,2) = strpad('d/dt q_2 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,3) = strpad('d/dt q_3 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,4) = strpad('d/dt q_4 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,5) = strpad('d/dt q_5 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,6) = strpad('d/dt q_6 in component BG_SERCA (fmol)');
    LEGEND_RATES(:,7) = strpad('d/dt V_E in component params_BG (volt)');
    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) = 8.31;
    CONSTANTS(:,2) = 293;
    CONSTANTS(:,3) = 96485;
    CONSTANTS(:,4) = 1e-06;
    CONSTANTS(:,5) = 1e-06;
    CONSTANTS(:,6) = 1e-08;
    CONSTANTS(:,7) = 1e-08;
    CONSTANTS(:,8) = 1e-08;
    CONSTANTS(:,9) = 1e-08;
    CONSTANTS(:,10) = 1e-08;
    CONSTANTS(:,11) = 1;
    CONSTANTS(:,12) = 1;
    CONSTANTS(:,13) = 1;
    CONSTANTS(:,14) = 1;
    CONSTANTS(:,15) = 1;
    CONSTANTS(:,16) = 1;
    CONSTANTS(:,17) = 1;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 1;
    CONSTANTS(:,20) = 1;
    CONSTANTS(:,21) = 1;
    CONSTANTS(:,22) = 1;
    CONSTANTS(:,23) = 1;
    CONSTANTS(:,24) = 1;
    CONSTANTS(:,25) = 1;
    CONSTANTS(:,26) = 1;
    CONSTANTS(:,27) = 1;
    CONSTANTS(:,28) = 1;
    CONSTANTS(:,29) = 1;
    CONSTANTS(:,30) = 1;
    CONSTANTS(:,31) = 1;
    CONSTANTS(:,32) = 1;
    CONSTANTS(:,33) = 1;
    CONSTANTS(:,34) = 2;
    CONSTANTS(:,35) = 1;
    CONSTANTS(:,36) = 20;
    CONSTANTS(:,37) = 100;
    CONSTANTS(:,38) = 10e-3;
    CONSTANTS(:,39) = 1e-12;
    CONSTANTS(:,40) = 1e-12;
    CONSTANTS(:,41) = 1e-12;
    CONSTANTS(:,42) = 1e-12;
    CONSTANTS(:,43) = 8.5e5;
    CONSTANTS(:,44) = 8.5e5;
    STATES(:,7) = -0.05;
    CONSTANTS(:,45) = 1e-3;
    CONSTANTS(:,46) =  CONSTANTS(:,36).*CONSTANTS(:,43);
    CONSTANTS(:,59) = 0.00000;
    CONSTANTS(:,47) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,6).*CONSTANTS(:,46));
    CONSTANTS(:,48) =  CONSTANTS(:,37).*CONSTANTS(:,44);
    CONSTANTS(:,49) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,7).*CONSTANTS(:,48));
    CONSTANTS(:,50) =  CONSTANTS(:,40).*CONSTANTS(:,44);
    CONSTANTS(:,51) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,8).*CONSTANTS(:,50));
    CONSTANTS(:,52) =  CONSTANTS(:,41).*CONSTANTS(:,44);
    CONSTANTS(:,53) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,9).*CONSTANTS(:,52));
    CONSTANTS(:,54) =  CONSTANTS(:,42).*CONSTANTS(:,44);
    CONSTANTS(:,55) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,10).*CONSTANTS(:,54));
    CONSTANTS(:,56) =  CONSTANTS(:,38).*CONSTANTS(:,43);
    CONSTANTS(:,57) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,4).*CONSTANTS(:,56));
    CONSTANTS(:,58) =  CONSTANTS(:,39).*CONSTANTS(:,44);
    CONSTANTS(:,59) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,5).*CONSTANTS(:,58));
    STATES(:,1) = CONSTANTS(:,12);
    STATES(:,2) = CONSTANTS(:,14);
    STATES(:,3) = CONSTANTS(:,16);
    STATES(:,4) = CONSTANTS(:,18);
    STATES(:,5) = CONSTANTS(:,20);
    STATES(:,6) = CONSTANTS(:,22);
    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
    RATES(:,7) = CONSTANTS(:,59);
    ALGEBRAIC(:,1) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,1));
    ALGEBRAIC(:,7) = CONSTANTS(:,53)+ALGEBRAIC(:,1);
    ALGEBRAIC(:,2) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,13).*STATES(:,2));
    ALGEBRAIC(:,8) = ALGEBRAIC(:,2);
    ALGEBRAIC(:,17) =  CONSTANTS(:,23).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,6) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,21).*STATES(:,6));
    ALGEBRAIC(:,15) = ALGEBRAIC(:,6);
    ALGEBRAIC(:,16) = ALGEBRAIC(:,1)+CONSTANTS(:,51);
    ALGEBRAIC(:,20) =  CONSTANTS(:,28).*(exp(ALGEBRAIC(:,15)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,16)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,22) = ALGEBRAIC(:,20) - ALGEBRAIC(:,17);
    RATES(:,1) = ALGEBRAIC(:,22);
    ALGEBRAIC(:,5) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,19).*STATES(:,5));
    ALGEBRAIC(:,13) = ALGEBRAIC(:,5);
    ALGEBRAIC(:,14) = ALGEBRAIC(:,6)+ CONSTANTS(:,33).*CONSTANTS(:,59);
    ALGEBRAIC(:,19) =  CONSTANTS(:,27).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,23) = ALGEBRAIC(:,19) - ALGEBRAIC(:,20);
    RATES(:,6) = ALGEBRAIC(:,23);
    ALGEBRAIC(:,3) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,15).*STATES(:,3));
    ALGEBRAIC(:,10) = ALGEBRAIC(:,3);
    ALGEBRAIC(:,4) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,17).*STATES(:,4));
    ALGEBRAIC(:,11) = ALGEBRAIC(:,4)+CONSTANTS(:,55);
    ALGEBRAIC(:,18) =  CONSTANTS(:,25).*(exp(ALGEBRAIC(:,10)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,12) = ALGEBRAIC(:,4);
    ALGEBRAIC(:,21) = STATES(:,7);
    ALGEBRAIC(:,24) = ALGEBRAIC(:,21);
    ALGEBRAIC(:,27) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,30) =  CONSTANTS(:,30).*CONSTANTS(:,3).*ALGEBRAIC(:,27);
    ALGEBRAIC(:,31) = ALGEBRAIC(:,5)+ CONSTANTS(:,34).*CONSTANTS(:,49)+ALGEBRAIC(:,30);
    ALGEBRAIC(:,32) =  CONSTANTS(:,26).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,31)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,33) = ALGEBRAIC(:,18) - ALGEBRAIC(:,32);
    RATES(:,4) = ALGEBRAIC(:,33);
    ALGEBRAIC(:,34) = ALGEBRAIC(:,32) - ALGEBRAIC(:,19);
    RATES(:,5) = ALGEBRAIC(:,34);
    ALGEBRAIC(:,9) = ALGEBRAIC(:,2)+ CONSTANTS(:,34).*CONSTANTS(:,47);
    ALGEBRAIC(:,39) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,40) =  CONSTANTS(:,32).*CONSTANTS(:,3).*ALGEBRAIC(:,39);
    ALGEBRAIC(:,41) = ALGEBRAIC(:,3)+ CONSTANTS(:,33).*CONSTANTS(:,57)+ALGEBRAIC(:,40);
    ALGEBRAIC(:,42) =  CONSTANTS(:,24).*(exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,41)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,43) = ALGEBRAIC(:,17) - ALGEBRAIC(:,42);
    RATES(:,2) = ALGEBRAIC(:,43);
    ALGEBRAIC(:,44) = ALGEBRAIC(:,42) - ALGEBRAIC(:,18);
    RATES(:,3) = ALGEBRAIC(:,44);
   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(:,1) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,11).*STATES(:,1));
    ALGEBRAIC(:,7) = CONSTANTS(:,53)+ALGEBRAIC(:,1);
    ALGEBRAIC(:,2) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,13).*STATES(:,2));
    ALGEBRAIC(:,8) = ALGEBRAIC(:,2);
    ALGEBRAIC(:,17) =  CONSTANTS(:,23).*(exp(ALGEBRAIC(:,7)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,8)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,6) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,21).*STATES(:,6));
    ALGEBRAIC(:,15) = ALGEBRAIC(:,6);
    ALGEBRAIC(:,16) = ALGEBRAIC(:,1)+CONSTANTS(:,51);
    ALGEBRAIC(:,20) =  CONSTANTS(:,28).*(exp(ALGEBRAIC(:,15)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,16)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,22) = ALGEBRAIC(:,20) - ALGEBRAIC(:,17);
    ALGEBRAIC(:,5) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,19).*STATES(:,5));
    ALGEBRAIC(:,13) = ALGEBRAIC(:,5);
    ALGEBRAIC(:,14) = ALGEBRAIC(:,6)+ CONSTANTS(:,33).*CONSTANTS(:,59);
    ALGEBRAIC(:,19) =  CONSTANTS(:,27).*(exp(ALGEBRAIC(:,13)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,14)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,23) = ALGEBRAIC(:,19) - ALGEBRAIC(:,20);
    ALGEBRAIC(:,3) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,15).*STATES(:,3));
    ALGEBRAIC(:,10) = ALGEBRAIC(:,3);
    ALGEBRAIC(:,4) =  CONSTANTS(:,1).*CONSTANTS(:,2).*log( CONSTANTS(:,17).*STATES(:,4));
    ALGEBRAIC(:,11) = ALGEBRAIC(:,4)+CONSTANTS(:,55);
    ALGEBRAIC(:,18) =  CONSTANTS(:,25).*(exp(ALGEBRAIC(:,10)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,11)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,12) = ALGEBRAIC(:,4);
    ALGEBRAIC(:,21) = STATES(:,7);
    ALGEBRAIC(:,24) = ALGEBRAIC(:,21);
    ALGEBRAIC(:,27) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,30) =  CONSTANTS(:,30).*CONSTANTS(:,3).*ALGEBRAIC(:,27);
    ALGEBRAIC(:,31) = ALGEBRAIC(:,5)+ CONSTANTS(:,34).*CONSTANTS(:,49)+ALGEBRAIC(:,30);
    ALGEBRAIC(:,32) =  CONSTANTS(:,26).*(exp(ALGEBRAIC(:,12)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,31)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,33) = ALGEBRAIC(:,18) - ALGEBRAIC(:,32);
    ALGEBRAIC(:,34) = ALGEBRAIC(:,32) - ALGEBRAIC(:,19);
    ALGEBRAIC(:,9) = ALGEBRAIC(:,2)+ CONSTANTS(:,34).*CONSTANTS(:,47);
    ALGEBRAIC(:,39) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,40) =  CONSTANTS(:,32).*CONSTANTS(:,3).*ALGEBRAIC(:,39);
    ALGEBRAIC(:,41) = ALGEBRAIC(:,3)+ CONSTANTS(:,33).*CONSTANTS(:,57)+ALGEBRAIC(:,40);
    ALGEBRAIC(:,42) =  CONSTANTS(:,24).*(exp(ALGEBRAIC(:,9)./( CONSTANTS(:,1).*CONSTANTS(:,2))) - exp(ALGEBRAIC(:,41)./( CONSTANTS(:,1).*CONSTANTS(:,2))));
    ALGEBRAIC(:,43) = ALGEBRAIC(:,17) - ALGEBRAIC(:,42);
    ALGEBRAIC(:,44) = ALGEBRAIC(:,42) - ALGEBRAIC(:,18);
    ALGEBRAIC(:,25) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,26) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,28) =  CONSTANTS(:,29).*CONSTANTS(:,3).*ALGEBRAIC(:,25);
    ALGEBRAIC(:,29) =  CONSTANTS(:,31).*CONSTANTS(:,3).*ALGEBRAIC(:,26);
    ALGEBRAIC(:,35) = ALGEBRAIC(:,32);
    ALGEBRAIC(:,36) =  CONSTANTS(:,29).*CONSTANTS(:,3).*ALGEBRAIC(:,35);
    ALGEBRAIC(:,37) = ALGEBRAIC(:,32);
    ALGEBRAIC(:,38) =  CONSTANTS(:,30).*CONSTANTS(:,3).*ALGEBRAIC(:,37);
    ALGEBRAIC(:,45) = ALGEBRAIC(:,42);
    ALGEBRAIC(:,46) =  CONSTANTS(:,31).*CONSTANTS(:,3).*ALGEBRAIC(:,45);
    ALGEBRAIC(:,47) = ALGEBRAIC(:,42);
    ALGEBRAIC(:,48) =  CONSTANTS(:,32).*CONSTANTS(:,3).*ALGEBRAIC(:,47);
    ALGEBRAIC(:,49) = ALGEBRAIC(:,36)+ALGEBRAIC(:,38)+ALGEBRAIC(:,46)+ALGEBRAIC(:,48);
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