Table 2. Example Code and Key Commands.

parpool('local',5);	Open a parallel pool of 5 MATLAB workers (independen
	t MATLAB engines to send each experiment to)
mex main_SSA.cpp	Compile C++ files within MATLAB. Each file is
mex main_ACT.cpp	a separate experiment to be simulated (e.g. SSA–stead
	y state availability, ACT–activation). If possible, the number of workers in ‘parpool’ should equal the number of experiments to be simulated.
Inputs = [	Provide a vector of initial guesses.
0.1027;
…
9.3;
0.250];
LB = [0; 0;…; 0];	Provide bounds on the parameter values (e.g. strictl
UB = [Inf; Inf;…; Inf];	y positive values: LB–lower bound, UB–upper bound)
options = optimset	Provide a list of options to the optimization algorithm
('TolFun', 1e-2, 'MaxIter', 2);	(e.g. Maximum iterations, tolerance on the function etc.)
Inputs_Final = fminsearchbnd (@WT_CHANNEL, Inputs,lb,ub, options);	Main function call to the minimization algorithm. Use the ‘fminsearchbnd’ (Bounded Nelder-Mead) algorithm to compute the minimum of the function ‘WT_CHANNEL’, with initial guesses provided by the ‘Inputs’ vector, bounded by ‘LB’, and ‘UB’, using the ‘options’ provided.
parfor i = 1:n;	Create a parallel ‘for’ loop (‘parfor’) to send each
if i = = 1	experimental protocol to a separate MATLAB worker.
main_SSA(Inputs);	This step simulates each protocol with the vector of
end	‘Inputs’
if i = = 2
main_ACT(Inputs);
end
…
end;