Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
Fig 3
Examples of customizable GSM reconstruction pipelines.
PADMet allows a user to easily implement flexible and personalized pipelines adapted to the wideness of the considered species and resource data. PADMet traces multiple complex reconstruction paradigms. 4 customizations of the reconstruction are presented here: the orthology- and gap-filling-based reconstruction of a) Enterococcus faecalis and b) Sulfobacillus thermosulfidooxidans str. Cutipay models, and the reconstructions of c) Ectocarpus siliculosus and d) Tisochrysis lutea models, using orthology, annotation and gap-filling. All models include manual curations and several analysis steps.