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 =1;
end
% There are a total of 5 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 (hour)');
LEGEND_STATES(:,1) = strpad('M in component M (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('Km in component M (micromolar)');
LEGEND_CONSTANTS(:,2) = strpad('vs in component M (flux)');
LEGEND_CONSTANTS(:,3) = strpad('vm in component M (flux)');
LEGEND_CONSTANTS(:,4) = strpad('n in component M (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('KI in component M (micromolar)');
LEGEND_STATES(:,2) = strpad('PN in component PN (micromolar)');
LEGEND_STATES(:,3) = strpad('P0 in component P0 (micromolar)');
LEGEND_CONSTANTS(:,6) = strpad('ks in component P0 (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('P1 in component P1 (micromolar)');
LEGEND_CONSTANTS(:,7) = strpad('K1 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,8) = strpad('V1 in component parameters (flux)');
LEGEND_CONSTANTS(:,9) = strpad('K2 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,10) = strpad('V2 in component parameters (flux)');
LEGEND_STATES(:,5) = strpad('P2 in component P2 (micromolar)');
LEGEND_CONSTANTS(:,11) = strpad('K3 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,12) = strpad('V3 in component parameters (flux)');
LEGEND_CONSTANTS(:,13) = strpad('K4 in component parameters (micromolar)');
LEGEND_CONSTANTS(:,14) = strpad('V4 in component parameters (flux)');
LEGEND_CONSTANTS(:,15) = strpad('Kd in component P2 (micromolar)');
LEGEND_CONSTANTS(:,16) = strpad('vd in component P2 (flux)');
LEGEND_CONSTANTS(:,17) = strpad('k1 in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('k2 in component parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('Pt in component Pt (micromolar)');
LEGEND_RATES(:,1) = strpad('d/dt M in component M (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt P0 in component P0 (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt P1 in component P1 (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt P2 in component P2 (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt PN in component PN (micromolar)');
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) = 0.6;
CONSTANTS(:,1) = 0.5;
CONSTANTS(:,2) = 0.76;
CONSTANTS(:,3) = 0.65;
CONSTANTS(:,4) = 4.0;
CONSTANTS(:,5) = 1.0;
STATES(:,2) = 1.1;
STATES(:,3) = 0.5;
CONSTANTS(:,6) = 0.38;
STATES(:,4) = 0.6;
CONSTANTS(:,7) = 2.0;
CONSTANTS(:,8) = 3.2;
CONSTANTS(:,9) = 2.0;
CONSTANTS(:,10) = 1.58;
STATES(:,5) = 0.6;
CONSTANTS(:,11) = 2.0;
CONSTANTS(:,12) = 5.0;
CONSTANTS(:,13) = 2.0;
CONSTANTS(:,14) = 2.5;
CONSTANTS(:,15) = 0.2;
CONSTANTS(:,16) = 0.95;
CONSTANTS(:,17) = 1.9;
CONSTANTS(:,18) = 1.3;
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(:,2).*(power(CONSTANTS(:,5), CONSTANTS(:,4))./(power(CONSTANTS(:,5), CONSTANTS(:,4))+power(STATES(:,2), CONSTANTS(:,4)))) - CONSTANTS(:,3).*(STATES(:,1)./(CONSTANTS(:,1)+STATES(:,1)));
RATES(:,3) = ( CONSTANTS(:,6).*STATES(:,1) - CONSTANTS(:,8).*(STATES(:,3)./(CONSTANTS(:,7)+STATES(:,3))))+ CONSTANTS(:,10).*(STATES(:,4)./(CONSTANTS(:,9)+STATES(:,4)));
RATES(:,4) = ( CONSTANTS(:,8).*(STATES(:,3)./(CONSTANTS(:,7)+STATES(:,3))) - ( CONSTANTS(:,10).*(STATES(:,4)./(CONSTANTS(:,9)+STATES(:,4)))+ CONSTANTS(:,12).*(STATES(:,4)./(CONSTANTS(:,11)+STATES(:,4)))))+ CONSTANTS(:,14).*(STATES(:,5)./(CONSTANTS(:,13)+STATES(:,5)));
RATES(:,5) = (( CONSTANTS(:,12).*(STATES(:,4)./(CONSTANTS(:,11)+STATES(:,4))) - ( CONSTANTS(:,14).*(STATES(:,5)./(CONSTANTS(:,13)+STATES(:,5)))+ CONSTANTS(:,17).*STATES(:,5)))+ CONSTANTS(:,18).*STATES(:,2)) - CONSTANTS(:,16).*(STATES(:,5)./(CONSTANTS(:,15)+STATES(:,5)));
RATES(:,2) = CONSTANTS(:,17).*STATES(:,5) - CONSTANTS(:,18).*STATES(:,2);
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) = STATES(:,3)+STATES(:,4)+STATES(:,5)+STATES(:,2);
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