Main steps for the development of the iNJ 661v network. In Step I, we compared the gene essentiality of iNJ 661m with experimental in vivo data and identified the set of false positive (FP) and false negative (FN) predictions. In Step II, for each incorrect prediction, we attempted to obtain a set of possible modifications. In Step III, we combined all the suggested modifications for each different incorrect prediction and screened the network realizations to obtain adequate and consistent metabolic modifications. In Step IV, we analyzed the availability and blockage of nutrient uptakes. In Step V, we reviewed the relevant literature to verify the biochemical and biological veracity of the introduced modifications. TN, true negative; TP, true positive.