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 3 entries in each of the rate and state variable arrays.
% There are a total of 28 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('R in component R (picomolar)');
LEGEND_CONSTANTS(:,1) = strpad('DR in component model_parameters (flux)');
LEGEND_ALGEBRAIC(:,3) = strpad('pi_C in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,24) = strpad('DB in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('B in component B (picomolar)');
LEGEND_ALGEBRAIC(:,1) = strpad('f in component B (flux)');
LEGEND_CONSTANTS(:,2) = strpad('kB in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('C in component C (picomolar)');
LEGEND_CONSTANTS(:,3) = strpad('DC in component model_parameters (flux)');
LEGEND_ALGEBRAIC(:,2) = strpad('pi_L in component pi_L (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('DA in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('k1 in component pi_L (second_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('k2 in component pi_L (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k3 in component pi_L (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('k4 in component pi_L (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('K in component pi_L (picomolar)');
LEGEND_CONSTANTS(:,10) = strpad('ko in component pi_L (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('Io in component pi_L (flux)');
LEGEND_CONSTANTS(:,12) = strpad('IL in component pi_L (flux)');
LEGEND_CONSTANTS(:,13) = strpad('rL in component pi_L (flux)');
LEGEND_CONSTANTS(:,14) = strpad('KOP in component pi_L (picomole_day_picomole_cells)');
LEGEND_CONSTANTS(:,15) = strpad('KLP in component pi_L (picomole_picomole_cells)');
LEGEND_CONSTANTS(:,28) = strpad('pi_P in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('f0 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('dB in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,18) = strpad('IP in component model_parameters (flux)');
LEGEND_CONSTANTS(:,19) = strpad('kP in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,25) = strpad('P in component model_parameters (picomolar)');
LEGEND_CONSTANTS(:,26) = strpad('P_0 in component model_parameters (picomolar)');
LEGEND_CONSTANTS(:,27) = strpad('P_s in component model_parameters (picomolar)');
LEGEND_CONSTANTS(:,20) = strpad('C_s in component model_parameters (picomolar)');
LEGEND_CONSTANTS(:,21) = strpad('SP in component model_parameters (flux)');
LEGEND_CONSTANTS(:,22) = strpad('k5 in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,23) = strpad('k6 in component model_parameters (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt R in component R (picomolar)');
LEGEND_RATES(:,2) = strpad('d/dt B in component B (picomolar)');
LEGEND_RATES(:,3) = strpad('d/dt C in component C (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) = 0.00077;
CONSTANTS(:,1) = 7e-4;
STATES(:,2) = 0.00073;
CONSTANTS(:,2) = 0.189;
STATES(:,3) = 0.00091;
CONSTANTS(:,3) = 2.1e-3;
CONSTANTS(:,4) = 0.7;
CONSTANTS(:,5) = 1e-2;
CONSTANTS(:,6) = 10;
CONSTANTS(:,7) = 5.8e-4;
CONSTANTS(:,8) = 1.7e-2;
CONSTANTS(:,9) = 10;
CONSTANTS(:,10) = 0.35;
CONSTANTS(:,11) = 0;
CONSTANTS(:,12) = 0;
CONSTANTS(:,13) = 1e3;
CONSTANTS(:,14) = 2e5;
CONSTANTS(:,15) = 3e6;
CONSTANTS(:,16) = 0.05;
CONSTANTS(:,17) = 0.7;
CONSTANTS(:,18) = 0;
CONSTANTS(:,19) = 86;
CONSTANTS(:,20) = 5e-3;
CONSTANTS(:,21) = 250;
CONSTANTS(:,22) = 0.02;
CONSTANTS(:,23) = 3;
CONSTANTS(:,24) = CONSTANTS(:,16).*CONSTANTS(:,17);
CONSTANTS(:,25) = CONSTANTS(:,18)./CONSTANTS(:,19);
CONSTANTS(:,26) = CONSTANTS(:,21)./CONSTANTS(:,19);
CONSTANTS(:,27) = CONSTANTS(:,23)./CONSTANTS(:,22);
CONSTANTS(:,28) = (CONSTANTS(:,25)+CONSTANTS(:,26))./(CONSTANTS(:,25)+CONSTANTS(:,27));
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(:,3) = (STATES(:,3)+ CONSTANTS(:,16).*CONSTANTS(:,20))./(STATES(:,3)+CONSTANTS(:,20));
RATES(:,1) = CONSTANTS(:,1).*ALGEBRAIC(:,3) - (CONSTANTS(:,24)./ALGEBRAIC(:,3)).*STATES(:,1);
ALGEBRAIC(:,1) = piecewise({VOI>20.0000&VOI<=80.0000, 0.000100000 }, 0.00000);
RATES(:,2) = ( (CONSTANTS(:,24)./ALGEBRAIC(:,3)).*STATES(:,1) - CONSTANTS(:,2).*STATES(:,2))+ALGEBRAIC(:,1);
ALGEBRAIC(:,2) = (( (( (CONSTANTS(:,7)./CONSTANTS(:,8)).*CONSTANTS(:,15))./1.00000).*CONSTANTS(:,28).*STATES(:,2))./(1.00000+( CONSTANTS(:,7).*CONSTANTS(:,9))./CONSTANTS(:,8)+ (CONSTANTS(:,5)./( CONSTANTS(:,6).*CONSTANTS(:,10))).*( ((CONSTANTS(:,14)./1.00000)./CONSTANTS(:,28)).*STATES(:,1)+CONSTANTS(:,11)))).*(1.00000+CONSTANTS(:,12)./CONSTANTS(:,13));
RATES(:,3) = CONSTANTS(:,3).*ALGEBRAIC(:,2) - CONSTANTS(:,4).*ALGEBRAIC(:,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(:,3) = (STATES(:,3)+ CONSTANTS(:,16).*CONSTANTS(:,20))./(STATES(:,3)+CONSTANTS(:,20));
ALGEBRAIC(:,1) = piecewise({VOI>20.0000&VOI<=80.0000, 0.000100000 }, 0.00000);
ALGEBRAIC(:,2) = (( (( (CONSTANTS(:,7)./CONSTANTS(:,8)).*CONSTANTS(:,15))./1.00000).*CONSTANTS(:,28).*STATES(:,2))./(1.00000+( CONSTANTS(:,7).*CONSTANTS(:,9))./CONSTANTS(:,8)+ (CONSTANTS(:,5)./( CONSTANTS(:,6).*CONSTANTS(:,10))).*( ((CONSTANTS(:,14)./1.00000)./CONSTANTS(:,28)).*STATES(:,1)+CONSTANTS(:,11)))).*(1.00000+CONSTANTS(:,12)./CONSTANTS(:,13));
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