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 =5;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 17 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('x1 in component x1 (picomole)');
LEGEND_CONSTANTS(:,15) = strpad('k in component k (flux)');
LEGEND_ALGEBRAIC(:,5) = strpad('lambda_Ca in component lambda_Ca (per_minute)');
LEGEND_CONSTANTS(:,1) = strpad('lambda1 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,16) = strpad('A in component A (per_minute)');
LEGEND_CONSTANTS(:,17) = strpad('B in component B (per_minute)');
LEGEND_ALGEBRAIC(:,1) = strpad('Ca in component Ca (millimolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('S in component S (millimolar)');
LEGEND_ALGEBRAIC(:,3) = strpad('m_Ca in component m_Ca (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('m1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('m2 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('beta in component model_parameters (litre_per_millimole)');
LEGEND_CONSTANTS(:,5) = strpad('R in component model_parameters (millimolar)');
LEGEND_STATES(:,2) = strpad('x2 in component x2 (picomole)');
LEGEND_ALGEBRAIC(:,2) = strpad('PTH in component x2 (picomole)');
LEGEND_CONSTANTS(:,6) = strpad('lambda2 in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,7) = strpad('Ca_0 in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,8) = strpad('Ca_1 in component model_parameters (millimolar)');
LEGEND_CONSTANTS(:,9) = strpad('alpha in component model_parameters (per_minute)');
LEGEND_CONSTANTS(:,10) = strpad('t0 in component model_parameters (minute)');
LEGEND_CONSTANTS(:,11) = strpad('x1_n in component model_parameters (picomole)');
LEGEND_CONSTANTS(:,12) = strpad('x2_n in component model_parameters (picomole)');
LEGEND_CONSTANTS(:,13) = strpad('x2_max in component model_parameters (picomole)');
LEGEND_CONSTANTS(:,14) = strpad('x2_min in component model_parameters (picomole)');
LEGEND_RATES(:,1) = strpad('d/dt x1 in component x1 (picomole)');
LEGEND_RATES(:,2) = strpad('d/dt x2 in component x2 (picomole)');
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) = 0.00;
CONSTANTS(:,1) = 0.0125;
CONSTANTS(:,2) = 112.5200;
CONSTANTS(:,3) = 15.00;
CONSTANTS(:,4) = 1e6;
CONSTANTS(:,5) = 1.2162;
STATES(:,2) = 0.00;
CONSTANTS(:,6) = 0.5595;
CONSTANTS(:,7) = 1.255;
CONSTANTS(:,8) = 0.1817;
CONSTANTS(:,9) = 0.0442;
CONSTANTS(:,10) = 575.0;
CONSTANTS(:,11) = 490.7800;
CONSTANTS(:,12) = 6.6290;
CONSTANTS(:,13) = 14.0430;
CONSTANTS(:,14) = 0.6697;
CONSTANTS(:,15) = CONSTANTS(:,6).*CONSTANTS(:,12)+ CONSTANTS(:,1).*CONSTANTS(:,11);
CONSTANTS(:,16) = ( CONSTANTS(:,1).*CONSTANTS(:,6).*CONSTANTS(:,13))./(CONSTANTS(:,15) - CONSTANTS(:,6).*CONSTANTS(:,13));
CONSTANTS(:,17) = ( CONSTANTS(:,1).*CONSTANTS(:,6).*CONSTANTS(:,14))./(CONSTANTS(:,15) - CONSTANTS(:,6).*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
ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,10), CONSTANTS(:,7) }, CONSTANTS(:,7) - CONSTANTS(:,8).*(1.00000 - exp( - CONSTANTS(:,9).*(VOI - CONSTANTS(:,10)))));
ALGEBRAIC(:,3) = CONSTANTS(:,2)./(1.00000+exp( - CONSTANTS(:,4).*(CONSTANTS(:,5) - ALGEBRAIC(:,1))))+CONSTANTS(:,3);
ALGEBRAIC(:,4) = CONSTANTS(:,7).*power( - (( CONSTANTS(:,11).*CONSTANTS(:,17) - CONSTANTS(:,6).*CONSTANTS(:,12))./( CONSTANTS(:,11).*CONSTANTS(:,16) - CONSTANTS(:,6).*CONSTANTS(:,12))), 1.00000./ALGEBRAIC(:,3));
ALGEBRAIC(:,5) = (CONSTANTS(:,16) - CONSTANTS(:,17))./(1.00000+power(ALGEBRAIC(:,1)./ALGEBRAIC(:,4), ALGEBRAIC(:,3)))+CONSTANTS(:,17);
RATES(:,1) = CONSTANTS(:,15) - ( ALGEBRAIC(:,5).*STATES(:,1)+ CONSTANTS(:,1).*STATES(:,1));
RATES(:,2) = ALGEBRAIC(:,5).*STATES(:,1) - 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<CONSTANTS(:,10), CONSTANTS(:,7) }, CONSTANTS(:,7) - CONSTANTS(:,8).*(1.00000 - exp( - CONSTANTS(:,9).*(VOI - CONSTANTS(:,10)))));
ALGEBRAIC(:,3) = CONSTANTS(:,2)./(1.00000+exp( - CONSTANTS(:,4).*(CONSTANTS(:,5) - ALGEBRAIC(:,1))))+CONSTANTS(:,3);
ALGEBRAIC(:,4) = CONSTANTS(:,7).*power( - (( CONSTANTS(:,11).*CONSTANTS(:,17) - CONSTANTS(:,6).*CONSTANTS(:,12))./( CONSTANTS(:,11).*CONSTANTS(:,16) - CONSTANTS(:,6).*CONSTANTS(:,12))), 1.00000./ALGEBRAIC(:,3));
ALGEBRAIC(:,5) = (CONSTANTS(:,16) - CONSTANTS(:,17))./(1.00000+power(ALGEBRAIC(:,1)./ALGEBRAIC(:,4), ALGEBRAIC(:,3)))+CONSTANTS(:,17);
ALGEBRAIC(:,2) = STATES(:,2)./2.75000;
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