README

This directory contains Genome Scale Metabolic Models of Methanotrophyc organisms.
Each model is available in SBML format, together with two tab separated files containing lists of reactions and metabolites.
The list of reactions (with the ending _reactions) includes their ids, names, stoichiometry and gene associations, the list of metabolites (with the ending _metabolites) contains ids and names.
Gene annotations from RAST are contained in excel files.

A python script that generates tab separated lists of reactions and metabolites from SBML models is included (makelists.py)
Running it requires the previous instalation of COBRApy.

https://github.com/opencobra/cobrapy

For each model, there are also available tab separated files with:

Lists of essential reactions, with the ending Ess.
Connectivity of each metabolite (number of reactions in which it takes part), with the ending Mets.
Connectivity of each metabolite to reactions carrying non zero metabolic fluxes during growth, with the ending MetsFlux.


The models currently available are for the methanotrophs:

Methylocystis hirsuta
Methylocystis sp. SC2
Methylocystis sp. SB2
Methylocystis parvus