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 6 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_ALGEBRAIC(:,1) = strpad('GnRH in component GnRH (nanomolar)');
LEGEND_STATES(:,1) = strpad('F in component F (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('kfb in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('kdf in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('D in component D (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('kbd in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('B in component B (dimensionless)');
LEGEND_STATES(:,4) = strpad('R in component R (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('s in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('a1 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('a2 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,5) = strpad('C in component C (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt F in component F (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt D in component D (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt B in component B (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt R in component R (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt C in component C (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) = 1.0;
CONSTANTS(:,1) = 19.35;
CONSTANTS(:,2) = 2.52;
STATES(:,2) = 0.0;
CONSTANTS(:,3) = 9.91;
STATES(:,3) = 0.0;
STATES(:,4) = 2115.0;
CONSTANTS(:,4) = 6.80;
CONSTANTS(:,5) = 0.0328;
CONSTANTS(:,6) = 0.0830;
STATES(:,5) = 0.0;
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(:,2) = CONSTANTS(:,3).*STATES(:,3) - CONSTANTS(:,2).*STATES(:,2);
RATES(:,4) = CONSTANTS(:,4) - (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,3)).*STATES(:,4);
RATES(:,5) = (CONSTANTS(:,5)+ CONSTANTS(:,6).*STATES(:,3)).*STATES(:,4);
ALGEBRAIC(:,1) = piecewise({VOI>=0.00000&VOI<0.0666667, 0.500000 , VOI>=0.0666667&VOI<0.400000, 0.00000 , VOI>=0.400000&VOI<0.466667, 0.500000 , VOI>=0.466667&VOI<2.46667, 0.00000 , VOI>=2.46667&VOI<2.53333, 0.500000 , VOI>=2.53333&VOI<2.61667, 0.00000 , VOI>=2.61667&VOI<2.68333, 0.500000 , VOI>=2.68333&VOI<4.68333, 0.00000 , VOI>=4.68333&VOI<4.75000, 0.500000 , VOI>=4.75000&VOI<4.91667, 0.00000 , VOI>=4.91667&VOI<4.98333, 0.500000 , VOI>=4.98333&VOI<6.98333, 0.00000 , VOI>=6.98333&VOI<7.06667, 0.500000 , VOI>=7.06667&VOI<7.73333, 0.00000 , VOI>=7.73333&VOI<7.80000, 0.500000 , VOI>=7.80000&VOI<9.80000, 0.00000 }, NaN);
RATES(:,1) = CONSTANTS(:,2).*STATES(:,2) - CONSTANTS(:,1).*STATES(:,1).*ALGEBRAIC(:,1);
RATES(:,3) = CONSTANTS(:,1).*STATES(:,1).*ALGEBRAIC(:,1) - CONSTANTS(:,3).*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
ALGEBRAIC(:,1) = piecewise({VOI>=0.00000&VOI<0.0666667, 0.500000 , VOI>=0.0666667&VOI<0.400000, 0.00000 , VOI>=0.400000&VOI<0.466667, 0.500000 , VOI>=0.466667&VOI<2.46667, 0.00000 , VOI>=2.46667&VOI<2.53333, 0.500000 , VOI>=2.53333&VOI<2.61667, 0.00000 , VOI>=2.61667&VOI<2.68333, 0.500000 , VOI>=2.68333&VOI<4.68333, 0.00000 , VOI>=4.68333&VOI<4.75000, 0.500000 , VOI>=4.75000&VOI<4.91667, 0.00000 , VOI>=4.91667&VOI<4.98333, 0.500000 , VOI>=4.98333&VOI<6.98333, 0.00000 , VOI>=6.98333&VOI<7.06667, 0.500000 , VOI>=7.06667&VOI<7.73333, 0.00000 , VOI>=7.73333&VOI<7.80000, 0.500000 , VOI>=7.80000&VOI<9.80000, 0.00000 }, NaN);
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