If (ti, yi) is the experimental normalized YFP:CFP data for a given strain and (ti, yi) represents simulated normalized YFP:CFP, then the squared residual error for time course is calculated as

Similar residual errors for all strains are then added together to give a total time course residual error Et.

Steady state simulated YFP:CFP at each signal level is normalized to the simulated value at 30mM (x^js) and compared against the experimental value (xjs) leading to the residual error

In addition, steady state YFP:CFP is simulated at very high signal (equivalent of 10−4mM). If this value is not > 6 × [YFP:CFP(0.03mM)], then an error penalty of 25 (comparable to the maximum squared residual at 0.03 mM) is added to Es.

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