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 6 entries in each of the rate and state variable arrays.
% There are a total of 16 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_CONSTANTS(:,1) = strpad('n in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('alpha_0 in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('alpha in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('beta in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('K_m in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('efficiency in component parameters (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('mRNA_halflife in component parameters (minute)');
LEGEND_CONSTANTS(:,8) = strpad('t_ave in component parameters (minute)');
LEGEND_CONSTANTS(:,9) = strpad('kd_prot in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('kd_mRNA in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('prot_halflife in component parameters (minute)');
LEGEND_CONSTANTS(:,6) = strpad('tps_repr in component parameters (per_sec)');
LEGEND_CONSTANTS(:,7) = strpad('tps_active in component parameters (per_sec)');
LEGEND_CONSTANTS(:,16) = strpad('k_tl in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('a_tr in component parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('a0_tr in component parameters (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('M_lacl in component M_lacl (dimensionless)');
LEGEND_STATES(:,2) = strpad('P_cl in component P_cl (dimensionless)');
LEGEND_STATES(:,3) = strpad('M_tetR in component M_tetR (dimensionless)');
LEGEND_STATES(:,4) = strpad('P_lacl in component P_lacl (dimensionless)');
LEGEND_STATES(:,5) = strpad('M_cl in component M_cl (dimensionless)');
LEGEND_STATES(:,6) = strpad('P_tetR in component P_tetR (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt M_lacl in component M_lacl (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt M_tetR in component M_tetR (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt M_cl in component M_cl (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt P_lacl in component P_lacl (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt P_tetR in component P_tetR (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt P_cl in component P_cl (dimensionless)');
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 = [];
CONSTANTS(:,1) = 2;
CONSTANTS(:,2) = 40;
CONSTANTS(:,3) = 20;
CONSTANTS(:,4) = 2;
CONSTANTS(:,5) = 10;
CONSTANTS(:,6) = 5e-4;
CONSTANTS(:,7) = 0.5;
STATES(:,1) = 0;
STATES(:,2) = 0;
STATES(:,3) = 20;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
CONSTANTS(:,8) = CONSTANTS(:,4)./log(2.00000);
CONSTANTS(:,9) = log(2.00000)./CONSTANTS(:,5);
CONSTANTS(:,10) = log(2.00000)./CONSTANTS(:,4);
CONSTANTS(:,11) = (CONSTANTS(:,7) - CONSTANTS(:,6)).*60.0000;
CONSTANTS(:,12) = CONSTANTS(:,6).*60.0000;
CONSTANTS(:,13) = ( CONSTANTS(:,12).*CONSTANTS(:,3))./( CONSTANTS(:,9).*CONSTANTS(:,2));
CONSTANTS(:,14) = ( CONSTANTS(:,11).*CONSTANTS(:,3))./( CONSTANTS(:,9).*CONSTANTS(:,2));
CONSTANTS(:,15) = CONSTANTS(:,9)./CONSTANTS(:,10);
CONSTANTS(:,16) = CONSTANTS(:,3).*CONSTANTS(:,10);
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(:,12)+( CONSTANTS(:,11).*power(CONSTANTS(:,2), CONSTANTS(:,1)))./(power(CONSTANTS(:,2), CONSTANTS(:,1))+power(STATES(:,2), CONSTANTS(:,1)))) - CONSTANTS(:,10).*STATES(:,1);
RATES(:,3) = (( CONSTANTS(:,11).*power(CONSTANTS(:,2), CONSTANTS(:,1)))./(power(CONSTANTS(:,2), CONSTANTS(:,1))+power(STATES(:,4), CONSTANTS(:,1)))+CONSTANTS(:,12)) - CONSTANTS(:,10).*STATES(:,3);
RATES(:,5) = (( CONSTANTS(:,11).*power(CONSTANTS(:,2), CONSTANTS(:,1)))./(power(CONSTANTS(:,2), CONSTANTS(:,1))+power(STATES(:,6), CONSTANTS(:,1)))+CONSTANTS(:,12)) - CONSTANTS(:,10).*STATES(:,5);
RATES(:,4) = CONSTANTS(:,16).*STATES(:,1) - CONSTANTS(:,9).*STATES(:,4);
RATES(:,6) = CONSTANTS(:,16).*STATES(:,3) - CONSTANTS(:,9).*STATES(:,6);
RATES(:,2) = CONSTANTS(:,16).*STATES(:,5) - CONSTANTS(:,9).*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
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