The process for genome-scale metabolic reconstruction of B. cenocepacia J2315. The left side indicates resources used for reconstruction, and the right side indicates the reconstruction process. Initial reconstruction started from genome annotation and other biological databases. Gap-filling was a continuous step throughout the reconstruction by probing missing reactions in a pathway which causes in silico growth infeasible, and subsequently closing these gaps by referring to the biological databases, extensive literature mining, and comparison with BIOLOG substrate utilization assays [89, 90]. This improved model was then extended by adding key metabolic virulence factors for B. cenocepacia from the literature. The process of model development and validation against experimental data was iteratively repeated until the genome-scale metabolic model was robust.