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 =8;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 22 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 (nanomolar)');
LEGEND_CONSTANTS(:,1) = strpad('delta_R in component R (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,1) = strpad('logR in component R (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('f1 in component f1 (flux)');
LEGEND_STATES(:,2) = strpad('U in component U (nanomolar)');
LEGEND_CONSTANTS(:,2) = strpad('delta_U in component U (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('logU in component U (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('alpha0 in component model_parameters (per_nanomolar_day)');
LEGEND_CONSTANTS(:,4) = strpad('alpha1 in component model_parameters (per_nanomolar_day)');
LEGEND_CONSTANTS(:,5) = strpad('d01 in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('d12 in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,3) = strpad('B1 in component B1 (nanomolar)');
LEGEND_STATES(:,4) = strpad('B2 in component B2 (nanomolar)');
LEGEND_ALGEBRAIC(:,7) = strpad('P in component P (nanomolar)');
LEGEND_ALGEBRAIC(:,8) = strpad('f2 in component f2 (flux)');
LEGEND_CONSTANTS(:,7) = strpad('delta_b1 in component B1 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,5) = strpad('logB1 in component B1 (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('delta_b2 in component B2 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,6) = strpad('logB2 in component B2 (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('PE in component P (nanomolar)');
LEGEND_ALGEBRAIC(:,4) = strpad('q in component P (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('G in component P (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('ti in component P (day)');
LEGEND_CONSTANTS(:,12) = strpad('T in component P (day)');
LEGEND_CONSTANTS(:,13) = strpad('P0 in component model_parameters (nanomolar)');
LEGEND_CONSTANTS(:,14) = strpad('a in component f1 (flux)');
LEGEND_CONSTANTS(:,15) = strpad('a0 in component f1 (flux)');
LEGEND_CONSTANTS(:,16) = strpad('b in component f1 (nanomolar)');
LEGEND_CONSTANTS(:,17) = strpad('b0 in component f1 (nanomolar)');
LEGEND_STATES(:,5) = strpad('x in component x (flux)');
LEGEND_CONSTANTS(:,18) = strpad('P1 in component x (nanomolar)');
LEGEND_CONSTANTS(:,19) = strpad('s in component x (nanomolar_day2)');
LEGEND_CONSTANTS(:,20) = strpad('delta_x in component x (first_order_rate_constant)');
LEGEND_CONSTANTS(:,21) = strpad('kappa in component f2 (flux)');
LEGEND_CONSTANTS(:,22) = strpad('kappa0 in component f2 (nanomolar)');
LEGEND_RATES(:,1) = strpad('d/dt R in component R (nanomolar)');
LEGEND_RATES(:,2) = strpad('d/dt U in component U (nanomolar)');
LEGEND_RATES(:,3) = strpad('d/dt B1 in component B1 (nanomolar)');
LEGEND_RATES(:,4) = strpad('d/dt B2 in component B2 (nanomolar)');
LEGEND_RATES(:,5) = strpad('d/dt x in component x (flux)');
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) = 1.905;
STATES(:,2) = 1.0;
CONSTANTS(:,2) = 7.5;
CONSTANTS(:,3) = 4.15;
CONSTANTS(:,4) = 3.02;
CONSTANTS(:,5) = 13.0;
CONSTANTS(:,6) = 4.72E3;
STATES(:,3) = 1.0;
STATES(:,4) = 1.0;
CONSTANTS(:,7) = 7.5;
CONSTANTS(:,8) = 50.0;
CONSTANTS(:,9) = 20.55;
CONSTANTS(:,10) = 35.6;
CONSTANTS(:,11) = 1.0;
CONSTANTS(:,12) = 9.0;
CONSTANTS(:,13) = 0.25;
CONSTANTS(:,14) = 3.58E5;
CONSTANTS(:,15) = 2.33E4;
CONSTANTS(:,16) = 100.0;
CONSTANTS(:,17) = 263.0;
STATES(:,5) = 0.0;
CONSTANTS(:,18) = 20.0;
CONSTANTS(:,19) = 3.71E5;
CONSTANTS(:,20) = 0.207;
CONSTANTS(:,21) = 2.4E5;
CONSTANTS(:,22) = 6.55E3;
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(:,4) = CONSTANTS(:,4).*STATES(:,3).*STATES(:,2) - ( CONSTANTS(:,6).*STATES(:,4)+ CONSTANTS(:,8).*STATES(:,4));
ALGEBRAIC(:,2) = CONSTANTS(:,15).*(1.00000 - STATES(:,4)./(CONSTANTS(:,16)+STATES(:,4)))+( STATES(:,5).*(1.00000 - exp( - STATES(:,5)./CONSTANTS(:,14))).*STATES(:,4))./(CONSTANTS(:,17)+STATES(:,4));
RATES(:,1) = ALGEBRAIC(:,2) - CONSTANTS(:,1).*STATES(:,1);
ALGEBRAIC(:,4) = piecewise({VOI<CONSTANTS(:,11), 0.00000 , VOI<CONSTANTS(:,12)+CONSTANTS(:,11)&VOI>=CONSTANTS(:,11), 1.00000 - exp( - CONSTANTS(:,10).*(VOI - CONSTANTS(:,11))) }, exp( CONSTANTS(:,10).*CONSTANTS(:,12) - 1.00000).*exp( CONSTANTS(:,10).*(VOI - CONSTANTS(:,11))));
ALGEBRAIC(:,7) = CONSTANTS(:,13)+ CONSTANTS(:,9).*ALGEBRAIC(:,4);
RATES(:,3) = ( CONSTANTS(:,3).*ALGEBRAIC(:,7).*STATES(:,2)+ CONSTANTS(:,6).*STATES(:,4)) - ( CONSTANTS(:,5).*STATES(:,3)+ CONSTANTS(:,7).*STATES(:,3)+ CONSTANTS(:,4).*STATES(:,3).*STATES(:,2));
RATES(:,5) = ( CONSTANTS(:,19).*(ALGEBRAIC(:,7) - CONSTANTS(:,13)))./(ALGEBRAIC(:,7)+CONSTANTS(:,18)) - CONSTANTS(:,20).*STATES(:,5);
ALGEBRAIC(:,8) = ( CONSTANTS(:,21).*STATES(:,1))./(CONSTANTS(:,22)+STATES(:,1));
RATES(:,2) = (ALGEBRAIC(:,8)+ CONSTANTS(:,5).*STATES(:,3)+ CONSTANTS(:,6).*STATES(:,4)) - ( CONSTANTS(:,2).*STATES(:,2)+ CONSTANTS(:,3).*ALGEBRAIC(:,7).*STATES(:,2)+ CONSTANTS(:,4).*STATES(:,3).*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(:,2) = CONSTANTS(:,15).*(1.00000 - STATES(:,4)./(CONSTANTS(:,16)+STATES(:,4)))+( STATES(:,5).*(1.00000 - exp( - STATES(:,5)./CONSTANTS(:,14))).*STATES(:,4))./(CONSTANTS(:,17)+STATES(:,4));
ALGEBRAIC(:,4) = piecewise({VOI<CONSTANTS(:,11), 0.00000 , VOI<CONSTANTS(:,12)+CONSTANTS(:,11)&VOI>=CONSTANTS(:,11), 1.00000 - exp( - CONSTANTS(:,10).*(VOI - CONSTANTS(:,11))) }, exp( CONSTANTS(:,10).*CONSTANTS(:,12) - 1.00000).*exp( CONSTANTS(:,10).*(VOI - CONSTANTS(:,11))));
ALGEBRAIC(:,7) = CONSTANTS(:,13)+ CONSTANTS(:,9).*ALGEBRAIC(:,4);
ALGEBRAIC(:,8) = ( CONSTANTS(:,21).*STATES(:,1))./(CONSTANTS(:,22)+STATES(:,1));
ALGEBRAIC(:,1) = arbitrary_log(STATES(:,1), 10);
ALGEBRAIC(:,3) = arbitrary_log(STATES(:,2), 10);
ALGEBRAIC(:,5) = arbitrary_log(STATES(:,3), 10);
ALGEBRAIC(:,6) = arbitrary_log(STATES(:,4), 10);
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
% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
x = log(a) ./ log(base);
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