Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
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 =13;
end
% There are a total of 14 entries in each of the rate and state variable arrays.
% There are a total of 18 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 (second)');
LEGEND_STATES(:,1) = strpad('O2 in component O2 (molar)');
LEGEND_ALGEBRAIC(:,1) = strpad('v1 in component v1 (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('v5 in component v5 (flux)');
LEGEND_ALGEBRAIC(:,7) = strpad('v7 in component v7 (flux)');
LEGEND_ALGEBRAIC(:,11) = strpad('v11 in component v11 (flux)');
LEGEND_ALGEBRAIC(:,13) = strpad('v13_back in component v13_back (flux)');
LEGEND_CONSTANTS(:,18) = strpad('v13 in component v13 (flux)');
LEGEND_STATES(:,2) = strpad('O2_radical in component O2_radical (molar)');
LEGEND_ALGEBRAIC(:,6) = strpad('v6 in component v6 (flux)');
LEGEND_STATES(:,3) = strpad('NADH in component NADH (molar)');
LEGEND_CONSTANTS(:,17) = strpad('v12 in component v12 (flux)');
LEGEND_ALGEBRAIC(:,12) = strpad('v14 in component v14 (flux)');
LEGEND_STATES(:,4) = strpad('NAD in component NAD (molar)');
LEGEND_ALGEBRAIC(:,8) = strpad('v8 in component v8 (flux)');
LEGEND_ALGEBRAIC(:,10) = strpad('v10 in component v10 (flux)');
LEGEND_STATES(:,5) = strpad('NAD_radical in component NAD_radical (molar)');
LEGEND_ALGEBRAIC(:,9) = strpad('v9 in component v9 (flux)');
LEGEND_STATES(:,6) = strpad('NAD2 in component NAD2 (molar)');
LEGEND_STATES(:,7) = strpad('H2O2 in component H2O2 (molar)');
LEGEND_ALGEBRAIC(:,2) = strpad('v2 in component v2 (flux)');
LEGEND_STATES(:,8) = strpad('Per3 in component Per3 (molar)');
LEGEND_ALGEBRAIC(:,4) = strpad('v4 in component v4 (flux)');
LEGEND_STATES(:,9) = strpad('Per2 in component Per2 (molar)');
LEGEND_STATES(:,10) = strpad('coI in component coI (molar)');
LEGEND_ALGEBRAIC(:,3) = strpad('v3 in component v3 (flux)');
LEGEND_STATES(:,11) = strpad('coII in component coII (molar)');
LEGEND_STATES(:,12) = strpad('coIII in component coIII (molar)');
LEGEND_STATES(:,13) = strpad('Ar_radical in component Ar_radical (molar)');
LEGEND_STATES(:,14) = strpad('ArH in component ArH (molar)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component v1 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k2 in component v2 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k3 in component v3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k4 in component v4 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k5 in component v5 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k6 in component v6 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k7 in component v7 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k8 in component v8 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k9 in component v9 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('k10 in component v10 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k11 in component v11 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('k12 in component v12 (flux)');
LEGEND_CONSTANTS(:,13) = strpad('O2eq in component v13 (molar)');
LEGEND_CONSTANTS(:,14) = strpad('k13 in component v13 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('k13_ in component v13_back (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('k14 in component v14 (second_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt O2 in component O2 (molar)');
LEGEND_RATES(:,2) = strpad('d/dt O2_radical in component O2_radical (molar)');
LEGEND_RATES(:,3) = strpad('d/dt NADH in component NADH (molar)');
LEGEND_RATES(:,4) = strpad('d/dt NAD in component NAD (molar)');
LEGEND_RATES(:,5) = strpad('d/dt NAD_radical in component NAD_radical (molar)');
LEGEND_RATES(:,6) = strpad('d/dt NAD2 in component NAD2 (molar)');
LEGEND_RATES(:,7) = strpad('d/dt H2O2 in component H2O2 (molar)');
LEGEND_RATES(:,8) = strpad('d/dt Per3 in component Per3 (molar)');
LEGEND_RATES(:,9) = strpad('d/dt Per2 in component Per2 (molar)');
LEGEND_RATES(:,10) = strpad('d/dt coI in component coI (molar)');
LEGEND_RATES(:,11) = strpad('d/dt coII in component coII (molar)');
LEGEND_RATES(:,12) = strpad('d/dt coIII in component coIII (molar)');
LEGEND_RATES(:,13) = strpad('d/dt Ar_radical in component Ar_radical (molar)');
LEGEND_RATES(:,14) = strpad('d/dt ArH in component ArH (molar)');
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) = 5.33e-6;
STATES(:,2) = 0.026e-6;
STATES(:,3) = 0.95e-6;
STATES(:,4) = 558e-6;
STATES(:,5) = 5e-10;
STATES(:,6) = 0.12e-6;
STATES(:,7) = 0.013e-6;
STATES(:,8) = 0.059e-6;
STATES(:,9) = 1e-10;
STATES(:,10) = 8.9e-10;
STATES(:,11) = 0.026e-6;
STATES(:,12) = 1.31e-6;
STATES(:,13) = 0.12e-6;
STATES(:,14) = 299.88e-6;
CONSTANTS(:,1) = 3;
CONSTANTS(:,2) = 1.8e7;
CONSTANTS(:,3) = 1.5e5;
CONSTANTS(:,4) = 5.2e3;
CONSTANTS(:,5) = 2e7;
CONSTANTS(:,6) = 1.7e7;
CONSTANTS(:,7) = 2e7;
CONSTANTS(:,8) = 4e7;
CONSTANTS(:,9) = 6e7;
CONSTANTS(:,10) = 1.8e6;
CONSTANTS(:,11) = 1e5;
CONSTANTS(:,12) = 0.08e-6;
CONSTANTS(:,13) = 1.2e-5;
CONSTANTS(:,14) = 6e-3;
CONSTANTS(:,15) = 6e-3;
CONSTANTS(:,16) = 7e5;
CONSTANTS(:,17) = CONSTANTS(:,12);
CONSTANTS(:,18) = CONSTANTS(:,14).*CONSTANTS(:,13);
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(:,4) = CONSTANTS(:,4).*STATES(:,11).*STATES(:,14);
ALGEBRAIC(:,3) = CONSTANTS(:,3).*STATES(:,10).*STATES(:,14);
RATES(:,11) = ALGEBRAIC(:,3) - ALGEBRAIC(:,4);
ALGEBRAIC(:,5) = CONSTANTS(:,5).*STATES(:,5).*STATES(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,7).*power(STATES(:,2), 2.00000);
ALGEBRAIC(:,6) = CONSTANTS(:,6).*STATES(:,2).*STATES(:,8);
RATES(:,2) = (ALGEBRAIC(:,5) - ALGEBRAIC(:,6)) - 2.00000.*ALGEBRAIC(:,7);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*STATES(:,3).*STATES(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,2).*STATES(:,7).*STATES(:,8);
RATES(:,7) = (ALGEBRAIC(:,1) - ALGEBRAIC(:,2)) - ALGEBRAIC(:,7);
ALGEBRAIC(:,8) = CONSTANTS(:,8).*STATES(:,12).*STATES(:,5);
RATES(:,10) = (ALGEBRAIC(:,2) - ALGEBRAIC(:,3))+ALGEBRAIC(:,8);
ALGEBRAIC(:,9) = CONSTANTS(:,9).*power(STATES(:,5), 2.00000);
RATES(:,6) = ALGEBRAIC(:,9);
ALGEBRAIC(:,10) = CONSTANTS(:,10).*STATES(:,8).*STATES(:,5);
RATES(:,4) = ALGEBRAIC(:,1)+ALGEBRAIC(:,5)+ALGEBRAIC(:,8)+ALGEBRAIC(:,10);
RATES(:,8) = (( - ALGEBRAIC(:,2)+ALGEBRAIC(:,4)) - ALGEBRAIC(:,6)) - ALGEBRAIC(:,10);
ALGEBRAIC(:,12) = CONSTANTS(:,16).*STATES(:,13).*STATES(:,3);
RATES(:,3) = ( - ALGEBRAIC(:,1)+CONSTANTS(:,17)) - ALGEBRAIC(:,12);
RATES(:,5) = ((( - 2.00000.*ALGEBRAIC(:,9) - ALGEBRAIC(:,5)) - ALGEBRAIC(:,8)) - ALGEBRAIC(:,10))+ALGEBRAIC(:,12);
ALGEBRAIC(:,11) = CONSTANTS(:,11).*STATES(:,9).*STATES(:,1);
RATES(:,9) = - ALGEBRAIC(:,11)+ALGEBRAIC(:,10);
RATES(:,12) = (ALGEBRAIC(:,6) - ALGEBRAIC(:,8))+ALGEBRAIC(:,11);
RATES(:,13) = (ALGEBRAIC(:,3)+ALGEBRAIC(:,4)) - ALGEBRAIC(:,12);
RATES(:,14) = ( - ALGEBRAIC(:,3) - ALGEBRAIC(:,4))+ALGEBRAIC(:,12);
ALGEBRAIC(:,13) = CONSTANTS(:,15).*STATES(:,1);
RATES(:,1) = (((( - ALGEBRAIC(:,1) - ALGEBRAIC(:,5))+ALGEBRAIC(:,7)) - ALGEBRAIC(:,11))+CONSTANTS(:,18)) - ALGEBRAIC(:,13);
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(:,4) = CONSTANTS(:,4).*STATES(:,11).*STATES(:,14);
ALGEBRAIC(:,3) = CONSTANTS(:,3).*STATES(:,10).*STATES(:,14);
ALGEBRAIC(:,5) = CONSTANTS(:,5).*STATES(:,5).*STATES(:,1);
ALGEBRAIC(:,7) = CONSTANTS(:,7).*power(STATES(:,2), 2.00000);
ALGEBRAIC(:,6) = CONSTANTS(:,6).*STATES(:,2).*STATES(:,8);
ALGEBRAIC(:,1) = CONSTANTS(:,1).*STATES(:,3).*STATES(:,1);
ALGEBRAIC(:,2) = CONSTANTS(:,2).*STATES(:,7).*STATES(:,8);
ALGEBRAIC(:,8) = CONSTANTS(:,8).*STATES(:,12).*STATES(:,5);
ALGEBRAIC(:,9) = CONSTANTS(:,9).*power(STATES(:,5), 2.00000);
ALGEBRAIC(:,10) = CONSTANTS(:,10).*STATES(:,8).*STATES(:,5);
ALGEBRAIC(:,12) = CONSTANTS(:,16).*STATES(:,13).*STATES(:,3);
ALGEBRAIC(:,11) = CONSTANTS(:,11).*STATES(:,9).*STATES(:,1);
ALGEBRAIC(:,13) = CONSTANTS(:,15).*STATES(:,1);
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