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 =6;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 20 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('C in component C (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ctot in component C (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('vi in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,2) = strpad('k1 in component model_parameters (per_minute)');
LEGEND_STATES(:,2) = strpad('X in component X (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('K5 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('kd in component model_parameters (per_minute)');
LEGEND_STATES(:,3) = strpad('Z in component Z (dimensionless)');
LEGEND_STATES(:,4) = strpad('M in component M (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('M_ in component M (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('V1 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,5) = strpad('K1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('V2 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,7) = strpad('K2 in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('X_ in component X (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('V3 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,8) = strpad('K3 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('V4 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,10) = strpad('K4 in component model_parameters (dimensionless)');
LEGEND_STATES(:,5) = strpad('Y in component Y (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('Ytot in component Y (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('vs in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,12) = strpad('d1 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,13) = strpad('a1 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,14) = strpad('a2 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,15) = strpad('alpha in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('BP in component BP (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('Kd in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('K6 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('V1_dash in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,19) = strpad('V3_dash in component model_parameters (per_minute)');
LEGEND_RATES(:,1) = strpad('d/dt C in component C (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt M in component M (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt X in component X (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt Y in component Y (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt Z in component Z (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) = 0.01;
CONSTANTS(:,1) = 0.1;
CONSTANTS(:,2) = 0.5;
STATES(:,2) = 0.01;
CONSTANTS(:,3) = 0.02;
CONSTANTS(:,4) = 0.02;
STATES(:,3) = 0.28;
STATES(:,4) = 0.01;
CONSTANTS(:,5) = 0.02;
CONSTANTS(:,6) = 0.25;
CONSTANTS(:,7) = 0.02;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 0.1;
CONSTANTS(:,10) = 0.1;
STATES(:,5) = 0.01;
CONSTANTS(:,11) = 0.1;
CONSTANTS(:,12) = 0.05;
CONSTANTS(:,13) = 1.5;
CONSTANTS(:,14) = 1.5;
CONSTANTS(:,15) = 0.1;
CONSTANTS(:,16) = 1;
CONSTANTS(:,17) = 0.3;
CONSTANTS(:,18) = 0.75;
CONSTANTS(:,19) = 0.3;
CONSTANTS(:,20) = - 1.00000;
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(:,2).*STATES(:,1))./(STATES(:,1)+CONSTANTS(:,3))) - CONSTANTS(:,4).*STATES(:,1);
RATES(:,5) = ((CONSTANTS(:,11) - CONSTANTS(:,12).*STATES(:,5)) - CONSTANTS(:,13).*STATES(:,1).*STATES(:,5))+ (CONSTANTS(:,14)+ CONSTANTS(:,15).*CONSTANTS(:,4)).*STATES(:,3);
RATES(:,3) = CONSTANTS(:,13).*STATES(:,1).*STATES(:,5) - (CONSTANTS(:,14)+ CONSTANTS(:,15).*CONSTANTS(:,4)+ CONSTANTS(:,15).*CONSTANTS(:,12)).*STATES(:,3);
ALGEBRAIC(:,2) = ( STATES(:,1).*CONSTANTS(:,18))./(STATES(:,1)+CONSTANTS(:,17));
RATES(:,4) = ( ALGEBRAIC(:,2).*CONSTANTS(:,20))./(CONSTANTS(:,20)+CONSTANTS(:,5)) - ( CONSTANTS(:,6).*STATES(:,4))./(STATES(:,4)+CONSTANTS(:,7));
ALGEBRAIC(:,3) = 1.00000 - STATES(:,2);
ALGEBRAIC(:,5) = STATES(:,4).*CONSTANTS(:,19);
RATES(:,2) = ( ALGEBRAIC(:,5).*ALGEBRAIC(:,3))./(ALGEBRAIC(:,3)+CONSTANTS(:,8)) - ( CONSTANTS(:,9).*STATES(:,2))./(STATES(:,2)+CONSTANTS(:,10));
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(:,2) = ( STATES(:,1).*CONSTANTS(:,18))./(STATES(:,1)+CONSTANTS(:,17));
ALGEBRAIC(:,3) = 1.00000 - STATES(:,2);
ALGEBRAIC(:,5) = STATES(:,4).*CONSTANTS(:,19);
ALGEBRAIC(:,1) = STATES(:,1)+STATES(:,3);
ALGEBRAIC(:,4) = STATES(:,5)+STATES(:,3);
ALGEBRAIC(:,6) = 1.00000+( CONSTANTS(:,16).*ALGEBRAIC(:,4))./power(STATES(:,1)+CONSTANTS(:,16), 2.00000);
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