Computational protocol: Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization

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Protocol publication

[…] shows the flow of BAFBA. BAFBA is initialized by mimicking a population of bees. In identifying gene knockout strategies, a bee is represented by a binary variable to indicate the absence or the presence of genes in the reaction. In this study, the BAFBA is started with the bees being placed randomly in the search space. The fitness of the sites visited by the bees is evaluated using FBA. Bees with the highest fitness would be denoted as ‘selected bees’ and the sites visited by them would be chosen for neighbourhood search. Small amount of ‘selected bees’ was expected to encourage local exploitation. After performing many tests, it was found that appropriate maximum ‘selected bees’ was (1/4)×n. The amount of selected bees was limited within the range [1,(1/4)×n] to prevent unnecessary selection of sites for neighborhood search. Each bee was required to go through this repetitive local search neighborhood procedure until the best possible answer obtained. Meanwhile, the remaining bees were assigned randomly to search for new potential solutions.Before attempting to propose DBFBA, it is crucial to find the limitations of BAFBA . BA dependence on random search makes it relatively weak in local search activities and it suffers of slow convergence due to the repetitive iteration of the algorithm. Repetition of unnecessary similar process in neighborhood search causes an additional computational time in generating solution. [...] In this paper, DBFBA with OptKnock for identifying optimal gene knockout strategy was proposed to overcome the limitations of BAFBA and previous works –, . DBFBA in this work differs from the BAFBA in the neighborhood search activities. The proposed DBFBA improved the operation by hybridizing DE algorithm into BAFBA. In addition, OptKnock was integrated into DBFBA to improve the reliability of the results. shows the overall framework of DBFBA and is the pseudo code of DBFBA. The important steps are explained in the following subsections. […]

Pipeline specifications

Software tools BAFBA, Optknock
Application Metabolic engineering
Organisms Bacillus subtilis, Escherichia coli, Ruminiclostridium thermocellum, Apis mellifera