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 =2;
end
% There are a total of 6 entries in each of the rate and state variable arrays.
% There are a total of 19 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('y1 in component y1 (micromolar)');
LEGEND_CONSTANTS(:,1) = strpad('a1 in component y1 (flux)');
LEGEND_ALGEBRAIC(:,1) = strpad('g1 in component y1 (micromolar)');
LEGEND_CONSTANTS(:,2) = strpad('b1 in component y1 (micromolar)');
LEGEND_CONSTANTS(:,3) = strpad('d1 in component y1 (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('y2 in component y2 (micromolar)');
LEGEND_CONSTANTS(:,4) = strpad('a2 in component y2 (flux)');
LEGEND_ALGEBRAIC(:,2) = strpad('g2 in component y2 (micromolar)');
LEGEND_CONSTANTS(:,5) = strpad('b2 in component y2 (micromolar)');
LEGEND_CONSTANTS(:,6) = strpad('d2 in component y2 (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('y3 in component y3 (micromolar)');
LEGEND_CONSTANTS(:,7) = strpad('f53 in component y3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('f13 in component y3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('h36 in component y3 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('d3 in component y3 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('E in component y3 (micromolar)');
LEGEND_STATES(:,4) = strpad('y5 in component y5 (micromolar)');
LEGEND_STATES(:,5) = strpad('y6 in component y6 (micromolar)');
LEGEND_STATES(:,6) = strpad('y4 in component y4 (micromolar)');
LEGEND_CONSTANTS(:,12) = strpad('f14 in component y4 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,13) = strpad('f24 in component y4 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('d4 in component y4 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('f35 in component y5 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('f45 in component y5 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,17) = strpad('d5 in component y5 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('h36 in component y6 (second_order_rate_constant)');
LEGEND_CONSTANTS(:,19) = strpad('d6 in component y6 (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt y1 in component y1 (micromolar)');
LEGEND_RATES(:,2) = strpad('d/dt y2 in component y2 (micromolar)');
LEGEND_RATES(:,3) = strpad('d/dt y3 in component y3 (micromolar)');
LEGEND_RATES(:,6) = strpad('d/dt y4 in component y4 (micromolar)');
LEGEND_RATES(:,4) = strpad('d/dt y5 in component y5 (micromolar)');
LEGEND_RATES(:,5) = strpad('d/dt y6 in component y6 (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) = 0.0;
CONSTANTS(:,1) = 10.0;
CONSTANTS(:,2) = 10.0;
CONSTANTS(:,3) = 0.2;
STATES(:,2) = 0.0;
CONSTANTS(:,4) = 10.0;
CONSTANTS(:,5) = 10.0;
CONSTANTS(:,6) = 0.1;
STATES(:,3) = 0.0;
CONSTANTS(:,7) = 1.5;
CONSTANTS(:,8) = 0.6;
CONSTANTS(:,9) = 0.1;
CONSTANTS(:,10) = 1.0;
CONSTANTS(:,11) = 10.0;
STATES(:,4) = 0.0;
STATES(:,5) = 0.0;
STATES(:,6) = 0.0;
CONSTANTS(:,12) = 0.1;
CONSTANTS(:,13) = 0.8;
CONSTANTS(:,14) = 1.1;
CONSTANTS(:,15) = 0.3;
CONSTANTS(:,16) = 0.1;
CONSTANTS(:,17) = 1.0;
CONSTANTS(:,18) = 0.1;
CONSTANTS(:,19) = 0.001;
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(:,3) = ( CONSTANTS(:,8).*(CONSTANTS(:,11) - (STATES(:,3)+STATES(:,5))).*STATES(:,1)+ CONSTANTS(:,7).*(CONSTANTS(:,11) - (STATES(:,3)+STATES(:,5))).*STATES(:,4)) - ( CONSTANTS(:,9).*STATES(:,2).*STATES(:,3)+ CONSTANTS(:,10).*STATES(:,3));
RATES(:,6) = ( CONSTANTS(:,12).*STATES(:,1)+ CONSTANTS(:,13).*STATES(:,2)) - CONSTANTS(:,14).*STATES(:,6);
RATES(:,4) = ( CONSTANTS(:,15).*STATES(:,3)+ CONSTANTS(:,16).*STATES(:,6)) - CONSTANTS(:,17).*STATES(:,4);
RATES(:,5) = CONSTANTS(:,18).*STATES(:,2).*STATES(:,3) - CONSTANTS(:,19).*STATES(:,5);
ALGEBRAIC(:,1) = piecewise({VOI>=0.00000&VOI<5.00000, 0.00000 , VOI>=5.00000&VOI<=10.0000, 1.00000 }, 0.00000);
RATES(:,1) = CONSTANTS(:,1).*(ALGEBRAIC(:,1)./(CONSTANTS(:,2)+ALGEBRAIC(:,1))) - CONSTANTS(:,3).*STATES(:,1);
ALGEBRAIC(:,2) = piecewise({VOI>=0.00000&VOI<=5.00000, 1.00000 }, 0.00000);
RATES(:,2) = CONSTANTS(:,4).*(ALGEBRAIC(:,2)./(CONSTANTS(:,5)+ALGEBRAIC(:,2))) - CONSTANTS(:,6).*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) = piecewise({VOI>=0.00000&VOI<5.00000, 0.00000 , VOI>=5.00000&VOI<=10.0000, 1.00000 }, 0.00000);
ALGEBRAIC(:,2) = piecewise({VOI>=0.00000&VOI<=5.00000, 1.00000 }, 0.00000);
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