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 18 entries in each of the rate and state variable arrays.
% There are a total of 37 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_CONSTANTS(:,1) = strpad('kappa_R_12 in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,2) = strpad('kappa_R_34 in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,3) = strpad('kappa_R_56 in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,4) = strpad('kappa_R_78 in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,5) = strpad('kappa_R_1a_cGMP in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,6) = strpad('kappa_R_1b_cGMP in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,7) = strpad('kappa_R_2a_cGMP in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,8) = strpad('kappa_R_2b_cGMP in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,9) = strpad('kappa_R_1_sGC in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,10) = strpad('kappa_R_2_sGC in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,11) = strpad('kappa_R_3_sGC in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,12) = strpad('kappa_R_4_sGC in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,13) = strpad('kappa_R_DNO_sGC in component BG_parameters (fmol_per_sec)');
    LEGEND_CONSTANTS(:,14) = strpad('K_A in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,15) = strpad('K_M in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,16) = strpad('K_Mp in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,17) = strpad('K_AM in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,18) = strpad('K_AMp in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,19) = strpad('K_Pi in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,20) = strpad('K_Ca_i in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,21) = strpad('K_cGMP in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,22) = strpad('K_GTP in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,23) = strpad('K_E5c in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,24) = strpad('K_PDE in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,25) = strpad('K_GTP_E5c in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,26) = strpad('K_cGMP_PDE in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,27) = strpad('K_GMP in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,28) = strpad('K_Eb in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,29) = strpad('K_NO in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,30) = strpad('K_E6c in component BG_parameters (per_fmol)');
    LEGEND_CONSTANTS(:,31) = strpad('K_NO_product in component BG_parameters (per_fmol)');
    LEGEND_VOI = strpad('t in component environment (second)');
    LEGEND_CONSTANTS(:,32) = strpad('vol_myo in component environment (pL)');
    LEGEND_STATES(:,1) = strpad('q_A in component environment (fmol)');
    LEGEND_STATES(:,2) = strpad('q_M in component environment (fmol)');
    LEGEND_STATES(:,3) = strpad('q_Mp in component environment (fmol)');
    LEGEND_STATES(:,4) = strpad('q_AM in component environment (fmol)');
    LEGEND_STATES(:,5) = strpad('q_AMp in component environment (fmol)');
    LEGEND_STATES(:,6) = strpad('q_Pi in component environment (fmol)');
    LEGEND_STATES(:,7) = strpad('q_Ca_i in component environment (fmol)');
    LEGEND_STATES(:,8) = strpad('q_cGMP in component environment (fmol)');
    LEGEND_STATES(:,9) = strpad('q_GTP in component environment (fmol)');
    LEGEND_STATES(:,10) = strpad('q_E5c in component environment (fmol)');
    LEGEND_STATES(:,11) = strpad('q_PDE in component environment (fmol)');
    LEGEND_STATES(:,12) = strpad('q_GTP_E5c in component environment (fmol)');
    LEGEND_STATES(:,13) = strpad('q_cGMP_PDE in component environment (fmol)');
    LEGEND_STATES(:,14) = strpad('q_GMP in component environment (fmol)');
    LEGEND_STATES(:,15) = strpad('q_Eb in component environment (fmol)');
    LEGEND_STATES(:,16) = strpad('q_NO in component environment (fmol)');
    LEGEND_STATES(:,17) = strpad('q_E6c in component environment (fmol)');
    LEGEND_STATES(:,18) = strpad('q_NO_product in component environment (fmol)');
    LEGEND_ALGEBRAIC(:,10) = strpad('v_R_12 in component HaiMurphy (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,11) = strpad('v_R_34 in component HaiMurphy (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,12) = strpad('v_R_56 in component HaiMurphy (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,13) = strpad('v_R_78 in component HaiMurphy (fmol_per_sec)');
    LEGEND_CONSTANTS(:,33) = strpad('n_Cai_SM in component environment (dimensionless)');
    LEGEND_ALGEBRAIC(:,21) = strpad('v_R_1a_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,22) = strpad('v_R_1b_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,23) = strpad('v_R_2a_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,24) = strpad('v_R_2b_cGMP in component cGMP (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,31) = strpad('v_R_1_sGC in component sGC (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,32) = strpad('v_R_2_sGC in component sGC (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,33) = strpad('v_R_3_sGC in component sGC (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,34) = strpad('v_R_4_sGC in component sGC (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,35) = strpad('v_R_DNO_sGC in component sGC (fmol_per_sec)');
    LEGEND_CONSTANTS(:,34) = strpad('v_NO_generation in component environment (fmol_per_sec)');
    LEGEND_ALGEBRAIC(:,2) = strpad('stress in component environment (dimensionless)');
    LEGEND_CONSTANTS(:,35) = strpad('R in component constants (J_per_K_per_mol)');
    LEGEND_CONSTANTS(:,36) = strpad('T in component constants (kelvin)');
    LEGEND_CONSTANTS(:,37) = strpad('F in component constants (C_per_mol)');
    LEGEND_ALGEBRAIC(:,1) = strpad('mu_A in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,3) = strpad('mu_M in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,4) = strpad('mu_Mp in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,5) = strpad('mu_AM in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,6) = strpad('mu_AMp in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,7) = strpad('mu_Pi in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,8) = strpad('mu_Ca_i in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,9) = strpad('mu_cGMP in component HaiMurphy (J_per_mol)');
    LEGEND_ALGEBRAIC(:,14) = strpad('mu_GTP in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,15) = strpad('mu_E5c in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,16) = strpad('mu_cGMP in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,17) = strpad('mu_PDE in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,18) = strpad('mu_GTP_E5c in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,19) = strpad('mu_cGMP_PDE in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,20) = strpad('mu_GMP in component cGMP (J_per_mol)');
    LEGEND_ALGEBRAIC(:,25) = strpad('mu_Eb in component sGC (J_per_mol)');
    LEGEND_ALGEBRAIC(:,26) = strpad('mu_NO in component sGC (J_per_mol)');
    LEGEND_ALGEBRAIC(:,27) = strpad('mu_E6c in component sGC (J_per_mol)');
    LEGEND_ALGEBRAIC(:,28) = strpad('mu_E5c in component sGC (J_per_mol)');
    LEGEND_ALGEBRAIC(:,29) = strpad('mu_cGMP in component sGC (J_per_mol)');
    LEGEND_ALGEBRAIC(:,30) = strpad('mu_NO_product in component sGC (J_per_mol)');
    LEGEND_RATES(:,1) = strpad('d/dt q_A in component environment (fmol)');
    LEGEND_RATES(:,2) = strpad('d/dt q_M in component environment (fmol)');
    LEGEND_RATES(:,3) = strpad('d/dt q_Mp in component environment (fmol)');
    LEGEND_RATES(:,4) = strpad('d/dt q_AM in component environment (fmol)');
    LEGEND_RATES(:,5) = strpad('d/dt q_AMp in component environment (fmol)');
    LEGEND_RATES(:,6) = strpad('d/dt q_Pi in component environment (fmol)');
    LEGEND_RATES(:,7) = strpad('d/dt q_Ca_i in component environment (fmol)');
    LEGEND_RATES(:,8) = strpad('d/dt q_cGMP in component environment (fmol)');
    LEGEND_RATES(:,9) = strpad('d/dt q_GTP in component environment (fmol)');
    LEGEND_RATES(:,10) = strpad('d/dt q_E5c in component environment (fmol)');
    LEGEND_RATES(:,11) = strpad('d/dt q_PDE in component environment (fmol)');
    LEGEND_RATES(:,12) = strpad('d/dt q_GTP_E5c in component environment (fmol)');
    LEGEND_RATES(:,13) = strpad('d/dt q_cGMP_PDE in component environment (fmol)');
    LEGEND_RATES(:,14) = strpad('d/dt q_GMP in component environment (fmol)');
    LEGEND_RATES(:,15) = strpad('d/dt q_Eb in component environment (fmol)');
    LEGEND_RATES(:,16) = strpad('d/dt q_NO in component environment (fmol)');
    LEGEND_RATES(:,17) = strpad('d/dt q_E6c in component environment (fmol)');
    LEGEND_RATES(:,18) = strpad('d/dt q_NO_product in component environment (fmol)');
    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) = 0.0628586;
    CONSTANTS(:,2) = 10.3507;
    CONSTANTS(:,3) = 1.13145;
    CONSTANTS(:,4) = 0.031236;
    CONSTANTS(:,5) = 192.663;
    CONSTANTS(:,6) = 0.00328297;
    CONSTANTS(:,7) = 56591.2;
    CONSTANTS(:,8) = 0.0110353;
    CONSTANTS(:,9) = 3.61127e+06;
    CONSTANTS(:,10) = 0.00328297;
    CONSTANTS(:,11) = 4.92446;
    CONSTANTS(:,12) = 0.0361127;
    CONSTANTS(:,13) = 0.01;
    CONSTANTS(:,14) = 1.65213;
    CONSTANTS(:,15) = 15.6959;
    CONSTANTS(:,16) = 0.105259;
    CONSTANTS(:,17) = 1.44065;
    CONSTANTS(:,18) = 0.00966114;
    CONSTANTS(:,19) = 723.915;
    CONSTANTS(:,20) = 1;
    CONSTANTS(:,21) = 1;
    CONSTANTS(:,22) = 17040;
    CONSTANTS(:,23) = 0.304602;
    CONSTANTS(:,24) = 17.6706;
    CONSTANTS(:,25) = 5190.42;
    CONSTANTS(:,26) = 35.3412;
    CONSTANTS(:,27) = 0.0051282;
    CONSTANTS(:,28) = 0.0276911;
    CONSTANTS(:,29) = 1;
    CONSTANTS(:,30) = 30.4602;
    CONSTANTS(:,31) = 0.1;
    CONSTANTS(:,32) = 1;
    STATES(:,1) = 1e-6;
    STATES(:,2) = 1e-6;
    STATES(:,3) = 0;
    STATES(:,4) = 0;
    STATES(:,5) = 0;
    STATES(:,6) = 15;
    STATES(:,7) = 1e-3;
    STATES(:,8) = 1e-6;
    STATES(:,9) = 0.0005;
    STATES(:,10) = 1e-16;
    STATES(:,11) = 1e-10;
    STATES(:,12) = 1e-16;
    STATES(:,13) = 1e-16;
    STATES(:,14) = 1e-16;
    STATES(:,15) = 1e-6;
    STATES(:,16) = 0.00836;
    STATES(:,17) = 1e-16;
    STATES(:,18) = 1e-16;
    CONSTANTS(:,33) = 1.66;
    CONSTANTS(:,34) = 0.000114;
    CONSTANTS(:,35) = 8.31;
    CONSTANTS(:,36) = 310;
    CONSTANTS(:,37) = 96485;
    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(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,15).*STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,16).*STATES(:,3));
    ALGEBRAIC(:,7) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,19).*STATES(:,6));
    ALGEBRAIC(:,8) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,20).*STATES(:,7));
    ALGEBRAIC(:,9) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,10) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,7)+ CONSTANTS(:,33).*ALGEBRAIC(:,8))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,9))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,1) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,14).*STATES(:,1));
    ALGEBRAIC(:,6) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,18).*STATES(:,5));
    ALGEBRAIC(:,11) =  CONSTANTS(:,2).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,4))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,3) = ALGEBRAIC(:,10) - ALGEBRAIC(:,11);
    ALGEBRAIC(:,5) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,17).*STATES(:,4));
    ALGEBRAIC(:,12) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,6)+ CONSTANTS(:,33).*ALGEBRAIC(:,8))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,7)+ALGEBRAIC(:,9))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,5) = ALGEBRAIC(:,11) - ALGEBRAIC(:,12);
    RATES(:,6) =  - ALGEBRAIC(:,10)+ALGEBRAIC(:,12);
    RATES(:,7) =  CONSTANTS(:,33).*( - ALGEBRAIC(:,10) - ALGEBRAIC(:,12));
    ALGEBRAIC(:,13) =  CONSTANTS(:,4).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,3))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,1) =  - ALGEBRAIC(:,11)+ALGEBRAIC(:,13);
    RATES(:,2) =  - ALGEBRAIC(:,10)+ALGEBRAIC(:,13);
    RATES(:,4) = ALGEBRAIC(:,12) - ALGEBRAIC(:,13);
    ALGEBRAIC(:,14) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,22).*STATES(:,9));
    ALGEBRAIC(:,15) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,23).*STATES(:,10));
    ALGEBRAIC(:,18) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,25).*STATES(:,12));
    ALGEBRAIC(:,21) =  CONSTANTS(:,5).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,18)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,9) =  - ALGEBRAIC(:,21);
    ALGEBRAIC(:,16) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,22) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,18)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,15))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,12) = ALGEBRAIC(:,21) - ALGEBRAIC(:,22);
    ALGEBRAIC(:,17) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,24).*STATES(:,11));
    ALGEBRAIC(:,19) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,26).*STATES(:,13));
    ALGEBRAIC(:,23) =  CONSTANTS(:,7).*(exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,17))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,19)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,20) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,27).*STATES(:,14));
    ALGEBRAIC(:,24) =  CONSTANTS(:,8).*(exp((ALGEBRAIC(:,19)+ALGEBRAIC(:,16))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,20)+ALGEBRAIC(:,17))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,11) =  - ALGEBRAIC(:,23)+ALGEBRAIC(:,24);
    RATES(:,13) = ALGEBRAIC(:,23) - ALGEBRAIC(:,24);
    RATES(:,14) = ALGEBRAIC(:,24);
    ALGEBRAIC(:,25) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,28).*STATES(:,15));
    ALGEBRAIC(:,26) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,29).*STATES(:,16));
    ALGEBRAIC(:,27) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,30).*STATES(:,17));
    ALGEBRAIC(:,31) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,25)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,27)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,28) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,23).*STATES(:,10));
    ALGEBRAIC(:,32) =  CONSTANTS(:,10).*(exp(ALGEBRAIC(:,27)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,28)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,33) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,28)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,17) = (ALGEBRAIC(:,31) - ALGEBRAIC(:,32)) - ALGEBRAIC(:,33);
    ALGEBRAIC(:,29) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,34) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,28)+ ALGEBRAIC(:,29).*2.00000)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,25)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,8) = (((ALGEBRAIC(:,10)+ALGEBRAIC(:,12)+ALGEBRAIC(:,22)) - ALGEBRAIC(:,23)) - ALGEBRAIC(:,24)) -  2.00000.*ALGEBRAIC(:,34);
    RATES(:,10) = ( - ALGEBRAIC(:,21)+ALGEBRAIC(:,22)+ALGEBRAIC(:,32)+ALGEBRAIC(:,33)) - ALGEBRAIC(:,34);
    RATES(:,15) =  - ALGEBRAIC(:,31)+ALGEBRAIC(:,34);
    ALGEBRAIC(:,30) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,31).*STATES(:,18));
    ALGEBRAIC(:,35) =  CONSTANTS(:,13).*(exp(ALGEBRAIC(:,26)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    RATES(:,16) = (( - ALGEBRAIC(:,31)+ALGEBRAIC(:,34)) - ALGEBRAIC(:,35))+CONSTANTS(:,34);
    RATES(:,18) = ALGEBRAIC(:,35);
   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(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,15).*STATES(:,2));
    ALGEBRAIC(:,4) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,16).*STATES(:,3));
    ALGEBRAIC(:,7) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,19).*STATES(:,6));
    ALGEBRAIC(:,8) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,20).*STATES(:,7));
    ALGEBRAIC(:,9) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,10) =  CONSTANTS(:,1).*(exp((ALGEBRAIC(:,3)+ALGEBRAIC(:,7)+ CONSTANTS(:,33).*ALGEBRAIC(:,8))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,4)+ALGEBRAIC(:,9))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,1) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,14).*STATES(:,1));
    ALGEBRAIC(:,6) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,18).*STATES(:,5));
    ALGEBRAIC(:,11) =  CONSTANTS(:,2).*(exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,4))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,6)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,5) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,17).*STATES(:,4));
    ALGEBRAIC(:,12) =  CONSTANTS(:,3).*(exp((ALGEBRAIC(:,6)+ CONSTANTS(:,33).*ALGEBRAIC(:,8))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,5)+ALGEBRAIC(:,7)+ALGEBRAIC(:,9))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,13) =  CONSTANTS(:,4).*(exp(ALGEBRAIC(:,5)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,1)+ALGEBRAIC(:,3))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,14) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,22).*STATES(:,9));
    ALGEBRAIC(:,15) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,23).*STATES(:,10));
    ALGEBRAIC(:,18) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,25).*STATES(:,12));
    ALGEBRAIC(:,21) =  CONSTANTS(:,5).*(exp((ALGEBRAIC(:,14)+ALGEBRAIC(:,15))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,18)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,16) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,22) =  CONSTANTS(:,6).*(exp(ALGEBRAIC(:,18)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,15))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,17) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,24).*STATES(:,11));
    ALGEBRAIC(:,19) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,26).*STATES(:,13));
    ALGEBRAIC(:,23) =  CONSTANTS(:,7).*(exp((ALGEBRAIC(:,16)+ALGEBRAIC(:,17))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,19)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,20) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,27).*STATES(:,14));
    ALGEBRAIC(:,24) =  CONSTANTS(:,8).*(exp((ALGEBRAIC(:,19)+ALGEBRAIC(:,16))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,20)+ALGEBRAIC(:,17))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,25) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,28).*STATES(:,15));
    ALGEBRAIC(:,26) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,29).*STATES(:,16));
    ALGEBRAIC(:,27) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,30).*STATES(:,17));
    ALGEBRAIC(:,31) =  CONSTANTS(:,9).*(exp((ALGEBRAIC(:,25)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,27)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,28) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,23).*STATES(:,10));
    ALGEBRAIC(:,32) =  CONSTANTS(:,10).*(exp(ALGEBRAIC(:,27)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,28)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,33) =  CONSTANTS(:,11).*(exp((ALGEBRAIC(:,27)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,28)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,29) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,21).*STATES(:,8));
    ALGEBRAIC(:,34) =  CONSTANTS(:,12).*(exp((ALGEBRAIC(:,28)+ ALGEBRAIC(:,29).*2.00000)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp((ALGEBRAIC(:,25)+ALGEBRAIC(:,26))./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,30) =  CONSTANTS(:,35).*CONSTANTS(:,36).*log( CONSTANTS(:,31).*STATES(:,18));
    ALGEBRAIC(:,35) =  CONSTANTS(:,13).*(exp(ALGEBRAIC(:,26)./( CONSTANTS(:,35).*CONSTANTS(:,36))) - exp(ALGEBRAIC(:,30)./( CONSTANTS(:,35).*CONSTANTS(:,36))));
    ALGEBRAIC(:,2) = (STATES(:,4)+STATES(:,5))./1.00000;
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