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 =4;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 16 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('P in component P (picomolar)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('k1_ in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k2 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('k2_ in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('kcl in component model_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('D in component model_parameters (flux)');
LEGEND_STATES(:,2) = strpad('Ca in component Ca (picomolar)');
LEGEND_STATES(:,3) = strpad('Ci in component Ci (picomolar)');
LEGEND_STATES(:,4) = strpad('Ra in component Ra (picomolar)');
LEGEND_STATES(:,5) = strpad('Ri in component Ri (picomolar)');
LEGEND_CONSTANTS(:,6) = strpad('k3 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k3_ in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k4 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('k4_ in component model_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,2) = strpad('rho in component rho (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('De in component model_parameters (flux)');
LEGEND_ALGEBRAIC(:,3) = strpad('Dd in component model_parameters (flux)');
LEGEND_CONSTANTS(:,11) = strpad('dmax in component model_parameters (flux)');
LEGEND_CONSTANTS(:,12) = strpad('dmin in component model_parameters (flux)');
LEGEND_CONSTANTS(:,13) = strpad('tau_on in component model_parameters (hour)');
LEGEND_CONSTANTS(:,14) = strpad('tau_off in component model_parameters (hour)');
LEGEND_CONSTANTS(:,16) = strpad('cycle_length in component model_parameters (hour)');
LEGEND_CONSTANTS(:,15) = strpad('j in component model_parameters (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('time_hour in component model_parameters (hour)');
LEGEND_RATES(:,1) = strpad('d/dt P in component P (picomolar)');
LEGEND_RATES(:,4) = strpad('d/dt Ra in component Ra (picomolar)');
LEGEND_RATES(:,5) = strpad('d/dt Ri in component Ri (picomolar)');
LEGEND_RATES(:,2) = strpad('d/dt Ca in component Ca (picomolar)');
LEGEND_RATES(:,3) = strpad('d/dt Ci in component Ci (picomolar)');
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) = 3;
CONSTANTS(:,1) = 1e-6;
CONSTANTS(:,2) = 1e-3;
CONSTANTS(:,3) = 1e-7;
CONSTANTS(:,4) = 1e-3;
CONSTANTS(:,5) = 5e-3;
STATES(:,2) = 4e-4;
STATES(:,3) = 0.05;
STATES(:,4) = 16.9;
STATES(:,5) = 1.7;
CONSTANTS(:,6) = 1e-3;
CONSTANTS(:,7) = 1e-4;
CONSTANTS(:,8) = 2e-3;
CONSTANTS(:,9) = 0.4;
CONSTANTS(:,10) = 0;
CONSTANTS(:,11) = 7.5;
CONSTANTS(:,12) = 0;
CONSTANTS(:,13) = 0.5;
CONSTANTS(:,14) = 0.5;
CONSTANTS(:,15) = 9;
CONSTANTS(:,16) = CONSTANTS(:,13)+CONSTANTS(:,14);
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(:,4) = ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,6).*STATES(:,5)) - ( CONSTANTS(:,1).*STATES(:,4).*STATES(:,1)+ CONSTANTS(:,7).*STATES(:,4));
RATES(:,5) = ( CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,7).*STATES(:,4)) - ( CONSTANTS(:,3).*STATES(:,5).*STATES(:,1)+ CONSTANTS(:,6).*STATES(:,5));
RATES(:,2) = ( CONSTANTS(:,1).*STATES(:,4).*STATES(:,1)+ CONSTANTS(:,8).*STATES(:,3)) - ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,9).*STATES(:,2));
RATES(:,3) = ( CONSTANTS(:,3).*STATES(:,5).*STATES(:,1)+ CONSTANTS(:,9).*STATES(:,2)) - ( CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,8).*STATES(:,3));
ALGEBRAIC(:,1) = ( VOI.*1.00000)./3600.00;
ALGEBRAIC(:,3) = piecewise({ALGEBRAIC(:,1)./CONSTANTS(:,16)>=CONSTANTS(:,15), CONSTANTS(:,12) , ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)>=0.00000&ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)<CONSTANTS(:,13), CONSTANTS(:,11) , ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)>=CONSTANTS(:,13)&ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)<CONSTANTS(:,16), CONSTANTS(:,12) }, NaN);
ALGEBRAIC(:,4) = CONSTANTS(:,10)+ALGEBRAIC(:,3);
RATES(:,1) = ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,3)+ALGEBRAIC(:,4)) - ( CONSTANTS(:,1).*STATES(:,4).*STATES(:,1)+ CONSTANTS(:,3).*STATES(:,5).*STATES(:,1)+ CONSTANTS(:,5).*STATES(:,1));
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) = ( VOI.*1.00000)./3600.00;
ALGEBRAIC(:,3) = piecewise({ALGEBRAIC(:,1)./CONSTANTS(:,16)>=CONSTANTS(:,15), CONSTANTS(:,12) , ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)>=0.00000&ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)<CONSTANTS(:,13), CONSTANTS(:,11) , ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)>=CONSTANTS(:,13)&ALGEBRAIC(:,1) - floor(ALGEBRAIC(:,1)./CONSTANTS(:,16)).*CONSTANTS(:,16)<CONSTANTS(:,16), CONSTANTS(:,12) }, NaN);
ALGEBRAIC(:,4) = CONSTANTS(:,10)+ALGEBRAIC(:,3);
ALGEBRAIC(:,2) = (STATES(:,4)+STATES(:,2))./(STATES(:,4)+STATES(:,2)+STATES(:,5)+STATES(:,3));
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
end
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