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 =3;
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 (day)');
LEGEND_STATES(:,1) = strpad('T in component T (per_ml)');
LEGEND_CONSTANTS(:,1) = strpad('lamda in component T (second_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('d in component T (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('k in component kinetic_parameters (flux)');
LEGEND_STATES(:,2) = strpad('VI in component VI (per_ml)');
LEGEND_STATES(:,3) = strpad('T_ in component T_ (per_ml)');
LEGEND_CONSTANTS(:,4) = strpad('tau in component T_ (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('m in component T_ (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('delta in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('N in component kinetic_parameters (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('c in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('epsilon_PI in component epsilon_PI (dimensionless)');
LEGEND_STATES(:,4) = strpad('VNI in component VNI (per_ml)');
LEGEND_CONSTANTS(:,9) = strpad('IC50 in component epsilon_PI (mg_per_ml)');
LEGEND_STATES(:,5) = strpad('Cc in component Cc (mg_per_ml)');
LEGEND_ALGEBRAIC(:,2) = strpad('Cb in component Cb (mg_per_ml)');
LEGEND_CONSTANTS(:,10) = strpad('Vd in component Cb (ml)');
LEGEND_CONSTANTS(:,11) = strpad('F in component Cb (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('D in component Cb (mg)');
LEGEND_CONSTANTS(:,13) = strpad('ka in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,14) = strpad('ke in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,15) = strpad('kacell in component Cc (first_order_rate_constant)');
LEGEND_CONSTANTS(:,16) = strpad('kecell in component Cc (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('Cx in component Cx (mg_per_ml)');
LEGEND_CONSTANTS(:,17) = strpad('H in component Cx (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('fb in component Cx (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt T in component T (per_ml)');
LEGEND_RATES(:,3) = strpad('d/dt T_ in component T_ (per_ml)');
LEGEND_RATES(:,2) = strpad('d/dt VI in component VI (per_ml)');
LEGEND_RATES(:,4) = strpad('d/dt VNI in component VNI (per_ml)');
LEGEND_RATES(:,5) = strpad('d/dt Cc in component Cc (mg_per_ml)');
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) = 1e6;
CONSTANTS(:,1) = 1e4;
CONSTANTS(:,2) = 0.01;
CONSTANTS(:,3) = 2.4e-8;
STATES(:,2) = 1;
STATES(:,3) = 1;
CONSTANTS(:,4) = 1.5;
CONSTANTS(:,5) = 0.01;
CONSTANTS(:,6) = 0.01;
CONSTANTS(:,7) = 2500;
CONSTANTS(:,8) = 23;
STATES(:,4) = 2;
CONSTANTS(:,9) = 9e-7;
STATES(:,5) = 0;
CONSTANTS(:,10) = 28000;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 600;
CONSTANTS(:,13) = 14.64;
CONSTANTS(:,14) = 6.86;
CONSTANTS(:,15) = 24000;
CONSTANTS(:,16) = 1.1;
CONSTANTS(:,17) = 0.052;
CONSTANTS(:,18) = 0.99;
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(:,1) - ( CONSTANTS(:,2).*STATES(:,1)+ CONSTANTS(:,3).*STATES(:,1).*STATES(:,2));
RATES(:,3) = CONSTANTS(:,3).*STATES(:,1).*(VOI - CONSTANTS(:,4)).*STATES(:,2).*(VOI - CONSTANTS(:,4)).*exp( - CONSTANTS(:,5).*CONSTANTS(:,4)) - CONSTANTS(:,6).*STATES(:,3);
ALGEBRAIC(:,1) = STATES(:,5)./(CONSTANTS(:,9)+STATES(:,5));
RATES(:,2) = CONSTANTS(:,7).*CONSTANTS(:,6).*STATES(:,3).*(1.00000 - ALGEBRAIC(:,1)) - CONSTANTS(:,8).*STATES(:,2);
RATES(:,4) = CONSTANTS(:,7).*CONSTANTS(:,6).*STATES(:,3).*ALGEBRAIC(:,1) - CONSTANTS(:,8).*STATES(:,4);
ALGEBRAIC(:,2) = (( CONSTANTS(:,11).*CONSTANTS(:,12))./CONSTANTS(:,10)).*(CONSTANTS(:,13)./(CONSTANTS(:,14) - CONSTANTS(:,13))).*(exp( - CONSTANTS(:,13).*VOI) - exp( - CONSTANTS(:,14).*VOI));
ALGEBRAIC(:,3) = piecewise({ (1.00000 - CONSTANTS(:,18)).*CONSTANTS(:,17).*ALGEBRAIC(:,2) - STATES(:,5)>0.00000, (1.00000 - CONSTANTS(:,18)).*CONSTANTS(:,17).*ALGEBRAIC(:,2) - STATES(:,5) }, 0.00000);
RATES(:,5) = CONSTANTS(:,15).*ALGEBRAIC(:,3) - CONSTANTS(:,16).*STATES(:,5);
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(:,5)./(CONSTANTS(:,9)+STATES(:,5));
ALGEBRAIC(:,2) = (( CONSTANTS(:,11).*CONSTANTS(:,12))./CONSTANTS(:,10)).*(CONSTANTS(:,13)./(CONSTANTS(:,14) - CONSTANTS(:,13))).*(exp( - CONSTANTS(:,13).*VOI) - exp( - CONSTANTS(:,14).*VOI));
ALGEBRAIC(:,3) = piecewise({ (1.00000 - CONSTANTS(:,18)).*CONSTANTS(:,17).*ALGEBRAIC(:,2) - STATES(:,5)>0.00000, (1.00000 - CONSTANTS(:,18)).*CONSTANTS(:,17).*ALGEBRAIC(:,2) - STATES(:,5) }, 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