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 =0;
end
% There are a total of 8 entries in each of the rate and state variable arrays.
% There are a total of 12 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('Rs in component Rs (number_per_cell)');
LEGEND_STATES(:,2) = strpad('L in component L (picomolar)');
LEGEND_STATES(:,3) = strpad('Cs in component Cs (number_per_cell)');
LEGEND_CONSTANTS(:,1) = strpad('Vs in component model_parameters (number_per_cell_minute)');
LEGEND_CONSTANTS(:,2) = strpad('kf in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('kr in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('kt in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('ksyn in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('ke in component model_parameters (first_order_rate_constant)');
LEGEND_STATES(:,4) = strpad('Ri in component Ri (number_per_cell)');
LEGEND_STATES(:,5) = strpad('Li in component Li (picomolar)');
LEGEND_STATES(:,6) = strpad('Ci in component Ci (number_per_cell)');
LEGEND_CONSTANTS(:,7) = strpad('kfe in component model_parameters (second_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('kre in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('kh in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('kx in component model_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('Ve in component model_parameters (L_per_cell)');
LEGEND_CONSTANTS(:,12) = strpad('NA in component model_parameters (number_per_mole)');
LEGEND_STATES(:,7) = strpad('Ld in component Ld (number_per_cell)');
LEGEND_STATES(:,8) = strpad('Y in component Y (cell_per_L)');
LEGEND_RATES(:,1) = strpad('d/dt Rs in component Rs (number_per_cell)');
LEGEND_RATES(:,3) = strpad('d/dt Cs in component Cs (number_per_cell)');
LEGEND_RATES(:,4) = strpad('d/dt Ri in component Ri (number_per_cell)');
LEGEND_RATES(:,6) = strpad('d/dt Ci in component Ci (number_per_cell)');
LEGEND_RATES(:,5) = strpad('d/dt Li in component Li (picomolar)');
LEGEND_RATES(:,7) = strpad('d/dt Ld in component Ld (number_per_cell)');
LEGEND_RATES(:,2) = strpad('d/dt L in component L (picomolar)');
LEGEND_RATES(:,8) = strpad('d/dt Y in component Y (cell_per_L)');
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) = 1500.0;
STATES(:,2) = 10.0;
STATES(:,3) = 1.0;
CONSTANTS(:,1) = 11;
CONSTANTS(:,2) = 0.0012432;
CONSTANTS(:,3) = 0.0138;
CONSTANTS(:,4) = 0.007;
CONSTANTS(:,5) = 0.0011;
CONSTANTS(:,6) = 0.04;
STATES(:,4) = 300.0;
STATES(:,5) = 0.01;
STATES(:,6) = 1.0;
CONSTANTS(:,7) = 0.0001104;
CONSTANTS(:,8) = 0.1104;
CONSTANTS(:,9) = 0.035;
CONSTANTS(:,10) = 0.15;
CONSTANTS(:,11) = 1E-14;
CONSTANTS(:,12) = 6.02E23;
STATES(:,7) = 1.0;
STATES(:,8) = 2.5E8;
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(:,3)+CONSTANTS(:,5)).*STATES(:,3)+CONSTANTS(:,1)) - ( CONSTANTS(:,2).*STATES(:,2).*STATES(:,1)+ CONSTANTS(:,4).*STATES(:,1));
RATES(:,3) = CONSTANTS(:,2).*STATES(:,2).*STATES(:,1) - (CONSTANTS(:,3)+CONSTANTS(:,6)).*STATES(:,3);
RATES(:,4) = ( CONSTANTS(:,8).*STATES(:,6)+ CONSTANTS(:,4).*STATES(:,1)) - ( CONSTANTS(:,7).*STATES(:,5).*STATES(:,4)+ CONSTANTS(:,9).*STATES(:,4));
RATES(:,6) = ( CONSTANTS(:,7).*STATES(:,5).*STATES(:,4)+ CONSTANTS(:,6).*STATES(:,3)) - (CONSTANTS(:,8)+CONSTANTS(:,9)).*STATES(:,6);
RATES(:,5) = ( CONSTANTS(:,8).*STATES(:,6) - CONSTANTS(:,7).*STATES(:,5).*STATES(:,4))./( CONSTANTS(:,11).*CONSTANTS(:,12)) - CONSTANTS(:,10).*STATES(:,5);
RATES(:,7) = CONSTANTS(:,9).*STATES(:,6);
RATES(:,2) = ( (( CONSTANTS(:,3).*STATES(:,3)+ CONSTANTS(:,10).*STATES(:,5).*CONSTANTS(:,11).*CONSTANTS(:,12)) - CONSTANTS(:,2).*STATES(:,2).*STATES(:,1)).*STATES(:,8))./CONSTANTS(:,12);
RATES(:,8) = max([utilOnes.*(( 600.000.*STATES(:,3))./(250.000+STATES(:,3)) - 200.000)],[],2).*1000.00;
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
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