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 =0;
end
% There are a total of 3 entries in each of the rate and state variable arrays.
% There are a total of 12 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 (day)');
LEGEND_STATES(:,1) = strpad('Tn in component Tn (cells_per_microlitre)');
LEGEND_CONSTANTS(:,1) = strpad('sn in component Tn (flux)');
LEGEND_CONSTANTS(:,2) = strpad('dn in component Tn (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('kn in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('eta in component model_parameters (cells_per_microlitre)');
LEGEND_STATES(:,2) = strpad('C in component C (cells_per_microlitre)');
LEGEND_STATES(:,3) = strpad('Te in component Te (cells_per_microlitre)');
LEGEND_CONSTANTS(:,5) = strpad('alpha_n in component Te (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('alpha_e in component Te (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('de in component Te (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('gamma_e in component Te (microlitre_per_cells_day)');
LEGEND_CONSTANTS(:,9) = strpad('Cmax in component C (cells_per_microlitre)');
LEGEND_CONSTANTS(:,10) = strpad('rc in component C (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('dc in component C (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('gamma_c in component C (microlitre_per_cells_day)');
LEGEND_RATES(:,1) = strpad('d/dt Tn in component Tn (cells_per_microlitre)');
LEGEND_RATES(:,3) = strpad('d/dt Te in component Te (cells_per_microlitre)');
LEGEND_RATES(:,2) = strpad('d/dt C in component C (cells_per_microlitre)');
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) = 1510.0;
CONSTANTS(:,1) = 0.071;
CONSTANTS(:,2) = 0.050;
CONSTANTS(:,3) = 0.063;
CONSTANTS(:,4) = 43.0;
STATES(:,2) = 9600.0;
STATES(:,3) = 20.0;
CONSTANTS(:,5) = 0.56;
CONSTANTS(:,6) = 0.53;
CONSTANTS(:,7) = 0.12;
CONSTANTS(:,8) = 0.0077;
CONSTANTS(:,9) = 190000;
CONSTANTS(:,10) = 0.23;
CONSTANTS(:,11) = 0.68;
CONSTANTS(:,12) = 0.047;
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(:,1) = CONSTANTS(:,1) - ( CONSTANTS(:,2).*STATES(:,1)+ CONSTANTS(:,3).*STATES(:,1).*(STATES(:,2)./(STATES(:,2)+CONSTANTS(:,4))));
RATES(:,3) = ( CONSTANTS(:,5).*CONSTANTS(:,3).*STATES(:,1).*(STATES(:,2)./(STATES(:,2)+CONSTANTS(:,4)))+ CONSTANTS(:,6).*STATES(:,3).*(STATES(:,2)./(STATES(:,2)+CONSTANTS(:,4)))) - ( CONSTANTS(:,7).*STATES(:,3)+ CONSTANTS(:,8).*STATES(:,2).*STATES(:,3));
RATES(:,2) =  CONSTANTS(:,10).*STATES(:,2).*log(CONSTANTS(:,9)./STATES(:,2)) - ( CONSTANTS(:,11).*STATES(:,2)+ CONSTANTS(:,12).*STATES(:,2).*STATES(:,3));
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
end

% Pad out or shorten strings to a set length
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

```
Source
Derived from workspace Moore, Li, 2004 at changeset adc249fb7f09.
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