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 =28;
end
% There are a total of 14 entries in each of the rate and state variable arrays.
% There are a total of 98 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('actCycA in component actCycA (dimensionless)');
    LEGEND_CONSTANTS(:,1) = strpad('k_asa in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,2) = strpad('k_sap in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,3) = strpad('k_sapp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,4) = strpad('k_dia in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,16) = strpad('V_di in component V_di (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,10) = strpad('V_da in component V_da (first_order_rate_constant)');
    LEGEND_STATES(:,2) = strpad('mass in component mass (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('Tri_A in component Tri_A (dimensionless)');
    LEGEND_ALGEBRAIC(:,8) = strpad('TF_E in component TF_E (dimensionless)');
    LEGEND_ALGEBRAIC(:,4) = strpad('freeCKI in component freeCKI (dimensionless)');
    LEGEND_STATES(:,3) = strpad('actCycB in component actCycB (dimensionless)');
    LEGEND_CONSTANTS(:,5) = strpad('k_asb in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,6) = strpad('k_dib in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,19) = strpad('V_sb in component V_sb (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,20) = strpad('V_db in component V_db (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,28) = strpad('V_25 in component V_25 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,24) = strpad('V_wee in component V_wee (first_order_rate_constant)');
    LEGEND_STATES(:,4) = strpad('CycB in component CycB (dimensionless)');
    LEGEND_STATES(:,5) = strpad('Tri_B in component Tri_B (dimensionless)');
    LEGEND_STATES(:,6) = strpad('preMPF in component preMPF (dimensionless)');
    LEGEND_STATES(:,7) = strpad('actCycE in component actCycE (dimensionless)');
    LEGEND_CONSTANTS(:,7) = strpad('k_die in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,8) = strpad('k_ase in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,9) = strpad('k_sep in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,10) = strpad('k_sepp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,9) = strpad('V_de in component V_de (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,3) = strpad('Tri_E in component Tri_E (dimensionless)');
    LEGEND_STATES(:,8) = strpad('CycA in component CycA (dimensionless)');
    LEGEND_STATES(:,9) = strpad('CycE in component CycE (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('CycD in component CycD (dimensionless)');
    LEGEND_CONSTANTS(:,11) = strpad('CycD_0 in component CycD (dimensionless)');
    LEGEND_STATES(:,10) = strpad('Cdc20_A in component Cdc20_A (dimensionless)');
    LEGEND_CONSTANTS(:,12) = strpad('k_a20 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,13) = strpad('k_i20 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,14) = strpad('k_d20 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_STATES(:,11) = strpad('APCP in component APCP (dimensionless)');
    LEGEND_STATES(:,12) = strpad('Cdc20_T in component Cdc20_T (dimensionless)');
    LEGEND_CONSTANTS(:,15) = strpad('J_a20 in component Cdc20_A (dimensionless)');
    LEGEND_CONSTANTS(:,16) = strpad('J_i20 in component Cdc20_A (dimensionless)');
    LEGEND_CONSTANTS(:,17) = strpad('k_s20p in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,18) = strpad('k_s20pp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,19) = strpad('n in component Cdc20_T (dimensionless)');
    LEGEND_CONSTANTS(:,20) = strpad('J_20 in component Cdc20_T (dimensionless)');
    LEGEND_CONSTANTS(:,21) = strpad('k_aAPC in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,22) = strpad('k_iAPC in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,23) = strpad('J_aAPC in component APCP (dimensionless)');
    LEGEND_CONSTANTS(:,24) = strpad('J_iAPC in component APCP (dimensionless)');
    LEGEND_STATES(:,13) = strpad('CKI in component CKI (dimensionless)');
    LEGEND_STATES(:,14) = strpad('Cdh1 in component Cdh1 (dimensionless)');
    LEGEND_CONSTANTS(:,25) = strpad('k_ah1p in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,26) = strpad('k_ah1pp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,27) = strpad('k_ih1p in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,28) = strpad('k_ih1pp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,29) = strpad('k_ih1ppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,30) = strpad('k_ih1pppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,31) = strpad('k_ih1ppppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,12) = strpad('Cdc14 in component TF_I (dimensionless)');
    LEGEND_CONSTANTS(:,32) = strpad('J_ah1 in component Cdh1 (dimensionless)');
    LEGEND_CONSTANTS(:,33) = strpad('J_ih1 in component Cdh1 (dimensionless)');
    LEGEND_CONSTANTS(:,34) = strpad('mu in component mass (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,35) = strpad('maxmass in component mass (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('V_atf in component V_atf (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,36) = strpad('k_atfp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,37) = strpad('k_atfpp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,38) = strpad('k_atfppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,39) = strpad('k_atfpppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,40) = strpad('k_itfp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,41) = strpad('k_itfpp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,42) = strpad('k_itfppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,43) = strpad('J_itf in component TF_E (dimensionless)');
    LEGEND_CONSTANTS(:,44) = strpad('J_atf in component TF_E (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('A1 in component TF_E (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,7) = strpad('A2 in component TF_E (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,89) = strpad('A3 in component TF_E (dimensionless)');
    LEGEND_CONSTANTS(:,92) = strpad('A4 in component TF_E (dimensionless)');
    LEGEND_CONSTANTS(:,45) = strpad('k_dep in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,46) = strpad('k_depp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,47) = strpad('k_deppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,48) = strpad('k_depppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,49) = strpad('k_dap in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,50) = strpad('k_dapp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,51) = strpad('k_dappp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,14) = strpad('TF_I in component TF_I (dimensionless)');
    LEGEND_CONSTANTS(:,52) = strpad('k_afi in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,53) = strpad('k_ifip in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,54) = strpad('k_ifipp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,55) = strpad('J_ifi in component TF_I (dimensionless)');
    LEGEND_CONSTANTS(:,56) = strpad('J_afi in component TF_I (dimensionless)');
    LEGEND_ALGEBRAIC(:,13) = strpad('A1 in component TF_I (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,11) = strpad('A2 in component TF_I (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,88) = strpad('A3 in component TF_I (dimensionless)');
    LEGEND_CONSTANTS(:,91) = strpad('A4 in component TF_I (dimensionless)');
    LEGEND_ALGEBRAIC(:,15) = strpad('V_si in component V_si (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,57) = strpad('k_sip in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,58) = strpad('k_sipp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,59) = strpad('k_dip in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,60) = strpad('k_dipp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,61) = strpad('k_dippp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,62) = strpad('k_dipppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,63) = strpad('k_dippppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,64) = strpad('J_14di in component kinetic_parameters (dimensionless)');
    LEGEND_ALGEBRAIC(:,18) = strpad('TF_B in component TF_B (dimensionless)');
    LEGEND_CONSTANTS(:,65) = strpad('k_afb in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,66) = strpad('k_ifb in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,67) = strpad('J_ifb in component TF_B (dimensionless)');
    LEGEND_CONSTANTS(:,68) = strpad('J_afb in component TF_B (dimensionless)');
    LEGEND_ALGEBRAIC(:,17) = strpad('A1 in component TF_B (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,90) = strpad('A2 in component TF_B (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,93) = strpad('A3 in component TF_B (dimensionless)');
    LEGEND_CONSTANTS(:,95) = strpad('A4 in component TF_B (dimensionless)');
    LEGEND_CONSTANTS(:,69) = strpad('k_sbp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,70) = strpad('k_sbpp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,71) = strpad('k_dbp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,72) = strpad('k_dbpp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,73) = strpad('k_dbppp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,23) = strpad('Wee1 in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,74) = strpad('k_aweep in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,75) = strpad('k_aweepp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,76) = strpad('k_iwee in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,77) = strpad('J_iwee in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,78) = strpad('J_awee in component Wee1 (dimensionless)');
    LEGEND_ALGEBRAIC(:,21) = strpad('A1 in component Wee1 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,22) = strpad('A2 in component Wee1 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,94) = strpad('A3 in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,96) = strpad('A4 in component Wee1 (dimensionless)');
    LEGEND_CONSTANTS(:,79) = strpad('k_weep in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,80) = strpad('k_weepp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,27) = strpad('Cdc25 in component Cdc25 (dimensionless)');
    LEGEND_CONSTANTS(:,81) = strpad('k_a25 in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,82) = strpad('k_i25p in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,83) = strpad('k_i25pp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,84) = strpad('J_i25 in component Cdc25 (dimensionless)');
    LEGEND_CONSTANTS(:,85) = strpad('J_a25 in component Cdc25 (dimensionless)');
    LEGEND_ALGEBRAIC(:,25) = strpad('A1 in component Cdc25 (first_order_rate_constant)');
    LEGEND_ALGEBRAIC(:,26) = strpad('A2 in component Cdc25 (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,97) = strpad('A3 in component Cdc25 (dimensionless)');
    LEGEND_CONSTANTS(:,98) = strpad('A4 in component Cdc25 (dimensionless)');
    LEGEND_CONSTANTS(:,86) = strpad('k_25p in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_CONSTANTS(:,87) = strpad('k_25pp in component kinetic_parameters (first_order_rate_constant)');
    LEGEND_RATES(:,1) = strpad('d/dt actCycA in component actCycA (dimensionless)');
    LEGEND_RATES(:,3) = strpad('d/dt actCycB in component actCycB (dimensionless)');
    LEGEND_RATES(:,7) = strpad('d/dt actCycE in component actCycE (dimensionless)');
    LEGEND_RATES(:,8) = strpad('d/dt CycA in component CycA (dimensionless)');
    LEGEND_RATES(:,4) = strpad('d/dt CycB in component CycB (dimensionless)');
    LEGEND_RATES(:,9) = strpad('d/dt CycE in component CycE (dimensionless)');
    LEGEND_RATES(:,10) = strpad('d/dt Cdc20_A in component Cdc20_A (dimensionless)');
    LEGEND_RATES(:,12) = strpad('d/dt Cdc20_T in component Cdc20_T (dimensionless)');
    LEGEND_RATES(:,11) = strpad('d/dt APCP in component APCP (dimensionless)');
    LEGEND_RATES(:,14) = strpad('d/dt Cdh1 in component Cdh1 (dimensionless)');
    LEGEND_RATES(:,2) = strpad('d/dt mass in component mass (dimensionless)');
    LEGEND_RATES(:,6) = strpad('d/dt preMPF in component preMPF (dimensionless)');
    LEGEND_RATES(:,5) = strpad('d/dt Tri_B in component Tri_B (dimensionless)');
    LEGEND_RATES(:,13) = strpad('d/dt CKI in component CKI (dimensionless)');
    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) = 0.09450308233499527;
    CONSTANTS(:,1) = 50;
    CONSTANTS(:,2) = 0.0015;
    CONSTANTS(:,3) = 0.01;
    CONSTANTS(:,4) = 0.06;
    STATES(:,2) = 1.338267803192139;
    STATES(:,3) = 0.1903585940599442;
    CONSTANTS(:,5) = 60;
    CONSTANTS(:,6) = 0.05;
    STATES(:,4) = 0.09450308233499527;
    STATES(:,5) = 0.01;
    STATES(:,6) = 0.01;
    STATES(:,7) = 0.2092024385929108;
    CONSTANTS(:,7) = 0;
    CONSTANTS(:,8) = 0;
    CONSTANTS(:,9) = 0;
    CONSTANTS(:,10) = 0.15;
    STATES(:,8) = 0.09450308233499527;
    STATES(:,9) = 0.09450308233499527;
    CONSTANTS(:,11) = 0.108;
    STATES(:,10) = 0.3572723865509033;
    CONSTANTS(:,12) = 1;
    CONSTANTS(:,13) = 0.16;
    CONSTANTS(:,14) = 0.05;
    STATES(:,11) = 0.07591402530670166;
    STATES(:,12) = 0.7702387571334839;
    CONSTANTS(:,15) = 1;
    CONSTANTS(:,16) = 1;
    CONSTANTS(:,17) = 0.001;
    CONSTANTS(:,18) = 1;
    CONSTANTS(:,19) = 1;
    CONSTANTS(:,20) = 10;
    CONSTANTS(:,21) = 0.1;
    CONSTANTS(:,22) = 0.15;
    CONSTANTS(:,23) = 0.1;
    CONSTANTS(:,24) = 0.1;
    STATES(:,13) = 0.01;
    STATES(:,14) = 0.7189393639564514;
    CONSTANTS(:,25) = 0.02;
    CONSTANTS(:,26) = 0.8;
    CONSTANTS(:,27) = 0.001;
    CONSTANTS(:,28) = 0.35;
    CONSTANTS(:,29) = 0.1;
    CONSTANTS(:,30) = 0.06;
    CONSTANTS(:,31) = 0.005;
    CONSTANTS(:,32) = 0.03;
    CONSTANTS(:,33) = 0.03;
    CONSTANTS(:,34) = 0.005776;
    CONSTANTS(:,35) = 10000;
    CONSTANTS(:,36) = 0;
    CONSTANTS(:,37) = 1.5;
    CONSTANTS(:,38) = 0.38;
    CONSTANTS(:,39) = 3;
    CONSTANTS(:,40) = 0.75;
    CONSTANTS(:,41) = 8;
    CONSTANTS(:,42) = 0;
    CONSTANTS(:,43) = 0.01;
    CONSTANTS(:,44) = 0.01;
    CONSTANTS(:,45) = 0.12;
    CONSTANTS(:,46) = 0;
    CONSTANTS(:,47) = 0;
    CONSTANTS(:,48) = 0;
    CONSTANTS(:,49) = 0.01;
    CONSTANTS(:,50) = 0.16;
    CONSTANTS(:,51) = 0;
    CONSTANTS(:,52) = 6;
    CONSTANTS(:,53) = 0.008;
    CONSTANTS(:,54) = 0.05;
    CONSTANTS(:,55) = 2;
    CONSTANTS(:,56) = 1;
    CONSTANTS(:,57) = 0.018;
    CONSTANTS(:,58) = 0.18;
    CONSTANTS(:,59) = 0.02;
    CONSTANTS(:,60) = 0.1;
    CONSTANTS(:,61) = 0.8;
    CONSTANTS(:,62) = 0.12;
    CONSTANTS(:,63) = 0.1;
    CONSTANTS(:,64) = 12;
    CONSTANTS(:,65) = 1;
    CONSTANTS(:,66) = 0.15;
    CONSTANTS(:,67) = 0.1;
    CONSTANTS(:,68) = 0.1;
    CONSTANTS(:,69) = 0.004;
    CONSTANTS(:,70) = 0.04;
    CONSTANTS(:,71) = 0.003;
    CONSTANTS(:,72) = 0.4;
    CONSTANTS(:,73) = 0.15;
    CONSTANTS(:,74) = 0.3;
    CONSTANTS(:,75) = 0;
    CONSTANTS(:,76) = 1;
    CONSTANTS(:,77) = 0.05;
    CONSTANTS(:,78) = 0.05;
    CONSTANTS(:,79) = 0.02;
    CONSTANTS(:,80) = 0.2;
    CONSTANTS(:,81) = 0;
    CONSTANTS(:,82) = 0.3;
    CONSTANTS(:,83) = 0;
    CONSTANTS(:,84) = 0.1;
    CONSTANTS(:,85) = 0.1;
    CONSTANTS(:,86) = 0.01;
    CONSTANTS(:,87) = 5;
    CONSTANTS(:,88) = CONSTANTS(:,56);
    CONSTANTS(:,89) = CONSTANTS(:,44);
    CONSTANTS(:,90) = CONSTANTS(:,66);
    CONSTANTS(:,91) = CONSTANTS(:,55);
    CONSTANTS(:,92) = CONSTANTS(:,43);
    CONSTANTS(:,93) = CONSTANTS(:,68);
    CONSTANTS(:,94) = CONSTANTS(:,78);
    CONSTANTS(:,95) = CONSTANTS(:,67);
    CONSTANTS(:,96) = CONSTANTS(:,77);
    CONSTANTS(:,97) = CONSTANTS(:,85);
    CONSTANTS(:,98) = CONSTANTS(:,84);
    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(:,10) = ( CONSTANTS(:,12).*STATES(:,11).*(STATES(:,12) - STATES(:,10)))./((CONSTANTS(:,15)+STATES(:,12)) - STATES(:,10)) -  (CONSTANTS(:,13)./(CONSTANTS(:,16)+STATES(:,10))+CONSTANTS(:,14)).*STATES(:,10);
    RATES(:,12) = (CONSTANTS(:,17)+ CONSTANTS(:,18).*power(STATES(:,3), CONSTANTS(:,19)))./(power(CONSTANTS(:,20), CONSTANTS(:,19))+power(STATES(:,3), CONSTANTS(:,19))) -  CONSTANTS(:,14).*STATES(:,12);
    RATES(:,11) = ( CONSTANTS(:,21).*STATES(:,3).*(1.00000 - STATES(:,11)))./((CONSTANTS(:,23)+1.00000) - STATES(:,11)) - ( CONSTANTS(:,22).*STATES(:,11))./(CONSTANTS(:,24)+STATES(:,11));
    RATES(:,2) =  CONSTANTS(:,34).*STATES(:,2).*(1.00000 - STATES(:,2)./CONSTANTS(:,35));
    ALGEBRAIC(:,1) =  CONSTANTS(:,11).*STATES(:,2);
    ALGEBRAIC(:,5) = CONSTANTS(:,36)+ CONSTANTS(:,37).*STATES(:,1)+ CONSTANTS(:,38).*STATES(:,7)+ CONSTANTS(:,39).*ALGEBRAIC(:,1);
    ALGEBRAIC(:,6) = ALGEBRAIC(:,5);
    ALGEBRAIC(:,7) = CONSTANTS(:,40)+ CONSTANTS(:,41).*STATES(:,3)+ CONSTANTS(:,42).*STATES(:,1);
    ALGEBRAIC(:,8) = ( 2.00000.*CONSTANTS(:,92).*ALGEBRAIC(:,6))./((ALGEBRAIC(:,7)+ - ALGEBRAIC(:,6)+ CONSTANTS(:,89).*ALGEBRAIC(:,7)+ CONSTANTS(:,92).*ALGEBRAIC(:,6))+power((power(ALGEBRAIC(:,7)+ - ALGEBRAIC(:,6)+ CONSTANTS(:,89).*ALGEBRAIC(:,7)+ CONSTANTS(:,92).*ALGEBRAIC(:,6), 2.00000) -  4.00000.*(ALGEBRAIC(:,7) - ALGEBRAIC(:,6)).*CONSTANTS(:,92).*ALGEBRAIC(:,6)), 1.0 ./ 2));
    ALGEBRAIC(:,9) = CONSTANTS(:,45)+ CONSTANTS(:,46).*STATES(:,7)+ CONSTANTS(:,47).*STATES(:,1)+ CONSTANTS(:,48).*STATES(:,3);
    RATES(:,9) =  (CONSTANTS(:,9)+ CONSTANTS(:,10).*ALGEBRAIC(:,8)).*STATES(:,2) -  ALGEBRAIC(:,9).*STATES(:,9);
    ALGEBRAIC(:,10) = CONSTANTS(:,49)+ CONSTANTS(:,50).*STATES(:,10)+ CONSTANTS(:,51).*STATES(:,12);
    RATES(:,8) =  (CONSTANTS(:,2)+ CONSTANTS(:,3).*ALGEBRAIC(:,8)).*STATES(:,2) -  ALGEBRAIC(:,10).*STATES(:,8);
    ALGEBRAIC(:,12) = STATES(:,10);
    RATES(:,14) = ( (CONSTANTS(:,25)+ CONSTANTS(:,26).*ALGEBRAIC(:,12)).*(1.00000 - STATES(:,14)))./((CONSTANTS(:,32)+1.00000) - STATES(:,14)) - ( (CONSTANTS(:,27)+ CONSTANTS(:,28).*STATES(:,1)+ CONSTANTS(:,29).*STATES(:,3)+ CONSTANTS(:,30).*STATES(:,7)+ CONSTANTS(:,31).*ALGEBRAIC(:,1)).*STATES(:,14))./(CONSTANTS(:,33)+STATES(:,14));
    ALGEBRAIC(:,16) = (CONSTANTS(:,59)+ CONSTANTS(:,60).*STATES(:,1)+ CONSTANTS(:,61).*STATES(:,3)+ CONSTANTS(:,62).*STATES(:,7)+ CONSTANTS(:,63).*ALGEBRAIC(:,1))./(1.00000+ALGEBRAIC(:,12)./CONSTANTS(:,64));
    ALGEBRAIC(:,2) = STATES(:,8) - STATES(:,1);
    ALGEBRAIC(:,3) = STATES(:,9) - STATES(:,7);
    ALGEBRAIC(:,4) = STATES(:,13) - (STATES(:,5)+ALGEBRAIC(:,2)+ALGEBRAIC(:,3));
    RATES(:,1) = ( (CONSTANTS(:,2)+ CONSTANTS(:,3).*ALGEBRAIC(:,8)).*STATES(:,2)+ (ALGEBRAIC(:,16)+CONSTANTS(:,4)).*ALGEBRAIC(:,2)) -  (ALGEBRAIC(:,10)+ CONSTANTS(:,1).*ALGEBRAIC(:,4)).*STATES(:,1);
    RATES(:,7) = ( (CONSTANTS(:,9)+ CONSTANTS(:,10).*ALGEBRAIC(:,8)).*STATES(:,2)+ (ALGEBRAIC(:,16)+CONSTANTS(:,7)).*ALGEBRAIC(:,3)) -  (ALGEBRAIC(:,9)+ CONSTANTS(:,8).*ALGEBRAIC(:,4)).*STATES(:,7);
    ALGEBRAIC(:,13) =  CONSTANTS(:,52).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,11) = CONSTANTS(:,53)+ CONSTANTS(:,54).*STATES(:,3);
    ALGEBRAIC(:,14) = ( 2.00000.*CONSTANTS(:,91).*ALGEBRAIC(:,13))./((ALGEBRAIC(:,11)+ - ALGEBRAIC(:,13)+ CONSTANTS(:,88).*ALGEBRAIC(:,11)+ CONSTANTS(:,91).*ALGEBRAIC(:,13))+power((power(ALGEBRAIC(:,11)+ - ALGEBRAIC(:,13)+ CONSTANTS(:,88).*ALGEBRAIC(:,11)+ CONSTANTS(:,91).*ALGEBRAIC(:,13), 2.00000) -  4.00000.*(ALGEBRAIC(:,11) - ALGEBRAIC(:,13)).*CONSTANTS(:,91).*ALGEBRAIC(:,13)), 1.0 ./ 2));
    ALGEBRAIC(:,15) = CONSTANTS(:,57)+ CONSTANTS(:,58).*ALGEBRAIC(:,14);
    RATES(:,13) = ALGEBRAIC(:,15) -  ALGEBRAIC(:,16).*STATES(:,13);
    ALGEBRAIC(:,17) =  CONSTANTS(:,65).*STATES(:,3);
    ALGEBRAIC(:,18) = ( 2.00000.*CONSTANTS(:,95).*ALGEBRAIC(:,17))./((CONSTANTS(:,90)+ - ALGEBRAIC(:,17)+ CONSTANTS(:,93).*CONSTANTS(:,90)+ CONSTANTS(:,95).*ALGEBRAIC(:,17))+power((power(CONSTANTS(:,90)+ - ALGEBRAIC(:,17)+ CONSTANTS(:,93).*CONSTANTS(:,90)+ CONSTANTS(:,95).*ALGEBRAIC(:,17), 2.00000) -  4.00000.*(CONSTANTS(:,90) - ALGEBRAIC(:,17)).*CONSTANTS(:,95).*ALGEBRAIC(:,17)), 1.0 ./ 2));
    ALGEBRAIC(:,19) = CONSTANTS(:,69)+ CONSTANTS(:,70).*ALGEBRAIC(:,18);
    ALGEBRAIC(:,20) = CONSTANTS(:,71)+ CONSTANTS(:,72).*STATES(:,14)+ CONSTANTS(:,73).*STATES(:,10);
    RATES(:,4) =  ALGEBRAIC(:,19).*STATES(:,2) -  ALGEBRAIC(:,20).*STATES(:,4);
    RATES(:,5) =  CONSTANTS(:,5).*(STATES(:,4) - STATES(:,5)).*ALGEBRAIC(:,4) -  (CONSTANTS(:,6)+ALGEBRAIC(:,20)+ALGEBRAIC(:,16)).*STATES(:,5);
    ALGEBRAIC(:,25) =  CONSTANTS(:,81).*STATES(:,3);
    ALGEBRAIC(:,26) = CONSTANTS(:,82)+ CONSTANTS(:,83).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,27) = ( 2.00000.*CONSTANTS(:,98).*ALGEBRAIC(:,25))./((ALGEBRAIC(:,26)+ - ALGEBRAIC(:,25)+ CONSTANTS(:,97).*ALGEBRAIC(:,26)+ CONSTANTS(:,98).*ALGEBRAIC(:,25))+power((power(ALGEBRAIC(:,26)+ - ALGEBRAIC(:,25)+ CONSTANTS(:,97).*ALGEBRAIC(:,26)+ CONSTANTS(:,98).*ALGEBRAIC(:,25), 2.00000) -  4.00000.*(ALGEBRAIC(:,26) - ALGEBRAIC(:,25)).*CONSTANTS(:,98).*ALGEBRAIC(:,25)), 1.0 ./ 2));
    ALGEBRAIC(:,28) = CONSTANTS(:,86)+ CONSTANTS(:,87).*ALGEBRAIC(:,27);
    ALGEBRAIC(:,21) = CONSTANTS(:,74)+ CONSTANTS(:,75).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,22) =  CONSTANTS(:,76).*STATES(:,3);
    ALGEBRAIC(:,23) = ( 2.00000.*CONSTANTS(:,96).*ALGEBRAIC(:,21))./((ALGEBRAIC(:,22)+ - ALGEBRAIC(:,21)+ CONSTANTS(:,94).*ALGEBRAIC(:,22)+ CONSTANTS(:,96).*ALGEBRAIC(:,21))+power((power(ALGEBRAIC(:,22)+ - ALGEBRAIC(:,21)+ CONSTANTS(:,94).*ALGEBRAIC(:,22)+ CONSTANTS(:,96).*ALGEBRAIC(:,21), 2.00000) -  4.00000.*(ALGEBRAIC(:,22) - ALGEBRAIC(:,21)).*CONSTANTS(:,96).*ALGEBRAIC(:,21)), 1.0 ./ 2));
    ALGEBRAIC(:,24) = CONSTANTS(:,79)+ CONSTANTS(:,80).*ALGEBRAIC(:,23);
    RATES(:,3) = ( ALGEBRAIC(:,19).*STATES(:,2)+ ALGEBRAIC(:,28).*(STATES(:,4) - (STATES(:,5)+STATES(:,3)))+ (CONSTANTS(:,6)+ALGEBRAIC(:,16)).*(STATES(:,4) - (STATES(:,6)+STATES(:,3)))) -  (ALGEBRAIC(:,20)+ALGEBRAIC(:,24)+ CONSTANTS(:,5).*ALGEBRAIC(:,4)).*STATES(:,3);
    RATES(:,6) =  ALGEBRAIC(:,24).*(STATES(:,4) - STATES(:,6)) -  (ALGEBRAIC(:,28)+ALGEBRAIC(:,20)).*STATES(:,6);
   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(:,11).*STATES(:,2);
    ALGEBRAIC(:,5) = CONSTANTS(:,36)+ CONSTANTS(:,37).*STATES(:,1)+ CONSTANTS(:,38).*STATES(:,7)+ CONSTANTS(:,39).*ALGEBRAIC(:,1);
    ALGEBRAIC(:,6) = ALGEBRAIC(:,5);
    ALGEBRAIC(:,7) = CONSTANTS(:,40)+ CONSTANTS(:,41).*STATES(:,3)+ CONSTANTS(:,42).*STATES(:,1);
    ALGEBRAIC(:,8) = ( 2.00000.*CONSTANTS(:,92).*ALGEBRAIC(:,6))./((ALGEBRAIC(:,7)+ - ALGEBRAIC(:,6)+ CONSTANTS(:,89).*ALGEBRAIC(:,7)+ CONSTANTS(:,92).*ALGEBRAIC(:,6))+power((power(ALGEBRAIC(:,7)+ - ALGEBRAIC(:,6)+ CONSTANTS(:,89).*ALGEBRAIC(:,7)+ CONSTANTS(:,92).*ALGEBRAIC(:,6), 2.00000) -  4.00000.*(ALGEBRAIC(:,7) - ALGEBRAIC(:,6)).*CONSTANTS(:,92).*ALGEBRAIC(:,6)), 1.0 ./ 2));
    ALGEBRAIC(:,9) = CONSTANTS(:,45)+ CONSTANTS(:,46).*STATES(:,7)+ CONSTANTS(:,47).*STATES(:,1)+ CONSTANTS(:,48).*STATES(:,3);
    ALGEBRAIC(:,10) = CONSTANTS(:,49)+ CONSTANTS(:,50).*STATES(:,10)+ CONSTANTS(:,51).*STATES(:,12);
    ALGEBRAIC(:,12) = STATES(:,10);
    ALGEBRAIC(:,16) = (CONSTANTS(:,59)+ CONSTANTS(:,60).*STATES(:,1)+ CONSTANTS(:,61).*STATES(:,3)+ CONSTANTS(:,62).*STATES(:,7)+ CONSTANTS(:,63).*ALGEBRAIC(:,1))./(1.00000+ALGEBRAIC(:,12)./CONSTANTS(:,64));
    ALGEBRAIC(:,2) = STATES(:,8) - STATES(:,1);
    ALGEBRAIC(:,3) = STATES(:,9) - STATES(:,7);
    ALGEBRAIC(:,4) = STATES(:,13) - (STATES(:,5)+ALGEBRAIC(:,2)+ALGEBRAIC(:,3));
    ALGEBRAIC(:,13) =  CONSTANTS(:,52).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,11) = CONSTANTS(:,53)+ CONSTANTS(:,54).*STATES(:,3);
    ALGEBRAIC(:,14) = ( 2.00000.*CONSTANTS(:,91).*ALGEBRAIC(:,13))./((ALGEBRAIC(:,11)+ - ALGEBRAIC(:,13)+ CONSTANTS(:,88).*ALGEBRAIC(:,11)+ CONSTANTS(:,91).*ALGEBRAIC(:,13))+power((power(ALGEBRAIC(:,11)+ - ALGEBRAIC(:,13)+ CONSTANTS(:,88).*ALGEBRAIC(:,11)+ CONSTANTS(:,91).*ALGEBRAIC(:,13), 2.00000) -  4.00000.*(ALGEBRAIC(:,11) - ALGEBRAIC(:,13)).*CONSTANTS(:,91).*ALGEBRAIC(:,13)), 1.0 ./ 2));
    ALGEBRAIC(:,15) = CONSTANTS(:,57)+ CONSTANTS(:,58).*ALGEBRAIC(:,14);
    ALGEBRAIC(:,17) =  CONSTANTS(:,65).*STATES(:,3);
    ALGEBRAIC(:,18) = ( 2.00000.*CONSTANTS(:,95).*ALGEBRAIC(:,17))./((CONSTANTS(:,90)+ - ALGEBRAIC(:,17)+ CONSTANTS(:,93).*CONSTANTS(:,90)+ CONSTANTS(:,95).*ALGEBRAIC(:,17))+power((power(CONSTANTS(:,90)+ - ALGEBRAIC(:,17)+ CONSTANTS(:,93).*CONSTANTS(:,90)+ CONSTANTS(:,95).*ALGEBRAIC(:,17), 2.00000) -  4.00000.*(CONSTANTS(:,90) - ALGEBRAIC(:,17)).*CONSTANTS(:,95).*ALGEBRAIC(:,17)), 1.0 ./ 2));
    ALGEBRAIC(:,19) = CONSTANTS(:,69)+ CONSTANTS(:,70).*ALGEBRAIC(:,18);
    ALGEBRAIC(:,20) = CONSTANTS(:,71)+ CONSTANTS(:,72).*STATES(:,14)+ CONSTANTS(:,73).*STATES(:,10);
    ALGEBRAIC(:,25) =  CONSTANTS(:,81).*STATES(:,3);
    ALGEBRAIC(:,26) = CONSTANTS(:,82)+ CONSTANTS(:,83).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,27) = ( 2.00000.*CONSTANTS(:,98).*ALGEBRAIC(:,25))./((ALGEBRAIC(:,26)+ - ALGEBRAIC(:,25)+ CONSTANTS(:,97).*ALGEBRAIC(:,26)+ CONSTANTS(:,98).*ALGEBRAIC(:,25))+power((power(ALGEBRAIC(:,26)+ - ALGEBRAIC(:,25)+ CONSTANTS(:,97).*ALGEBRAIC(:,26)+ CONSTANTS(:,98).*ALGEBRAIC(:,25), 2.00000) -  4.00000.*(ALGEBRAIC(:,26) - ALGEBRAIC(:,25)).*CONSTANTS(:,98).*ALGEBRAIC(:,25)), 1.0 ./ 2));
    ALGEBRAIC(:,28) = CONSTANTS(:,86)+ CONSTANTS(:,87).*ALGEBRAIC(:,27);
    ALGEBRAIC(:,21) = CONSTANTS(:,74)+ CONSTANTS(:,75).*ALGEBRAIC(:,12);
    ALGEBRAIC(:,22) =  CONSTANTS(:,76).*STATES(:,3);
    ALGEBRAIC(:,23) = ( 2.00000.*CONSTANTS(:,96).*ALGEBRAIC(:,21))./((ALGEBRAIC(:,22)+ - ALGEBRAIC(:,21)+ CONSTANTS(:,94).*ALGEBRAIC(:,22)+ CONSTANTS(:,96).*ALGEBRAIC(:,21))+power((power(ALGEBRAIC(:,22)+ - ALGEBRAIC(:,21)+ CONSTANTS(:,94).*ALGEBRAIC(:,22)+ CONSTANTS(:,96).*ALGEBRAIC(:,21), 2.00000) -  4.00000.*(ALGEBRAIC(:,22) - ALGEBRAIC(:,21)).*CONSTANTS(:,96).*ALGEBRAIC(:,21)), 1.0 ./ 2));
    ALGEBRAIC(:,24) = CONSTANTS(:,79)+ CONSTANTS(:,80).*ALGEBRAIC(:,23);
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