In algorithms.py,function binary_search()

[weif000]

Hi, I use cobrame to calculate a prouduct , but I dont' know how to set the parameter mu_accuracy in function binary_search() and what it means.
Thank you.

[coltonlloyd]

Hello,

The binary search algorithm optimizes for the maximum feasible mu by systematically trying different mu values until (max_feasible_mu - min_infeasible_mu) < mu_accuracy. We recommend using mu_accuracy= ~1e-14 to ensure that all computed fluxes in the model converge. If you are prototyping different model formulations and want the model to solve faster, you can use a higher mu_accuracy value, though the computed fluxes might differ from those obtained from a smaller mu_accuracy

[weif000]

Thanks for your response. I have some questions to set a higher mu_accuracy value. When I set serine production as objective function in iJL1678b-ME and respectively set the values of this mu_accuracy to 1e-2 and 1e-3, the flux of the reaction EX_ser__L_e is 1.0520735667708063 and 0.020030971080013924. The flux is a big difference. I dont' know how to set feasible mu_accuracy value to get the reaction flux.