metage2metabo | annotated genomes to metabolic

metage2metabo is a Jupyter Notebook library. metage2metabo has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

M2M has two main dependencies for modelling metabolic networks: MeneTools and Miscoto. Accordingly metabolic models in M2M follow the producibility in metabolic networks as defined by the network expansion algorithm. Mainly, two rules are followed:. A metabolite that is producible from a set of nutrients is described as being "in the scope of the seeds". The computation is made using logic solvers (Answer Set Programming). The present modelling ignores the stoichiometry of reactions (2A + B --> C is considered equivalent to A + B --> C), and is therefore suited to non-curated or draft metabolic networks, as the ones built using M2M with the PathoLogic software of Pathway Tools handled by Mpwt. Many works have relied on network expansion to study organisms (here, here or there) and communities (here, here, or here). It has been compared, combined to steady-state modelling (Flux Balance Analysis).