Sampling on the flux space of multiple metabolic networks

[hariszaf]

Two main modules are included on this PR:

• about 6,000 bacterial metabolic models have been converted to .mat format using the embl_model_convert.m script. The The script has been used to convert EMBL models that are publicly available here as well as models that were built using publicly available genomes and the carveme software tool for automatic metabolic modelling reconstruction
• 2 classes called CommunityMetabolicNetwork and CommunityPolytopeSampler that enable sampling on the flux space of multiple metabolic networks.

To enable testing this new module of dingo an input example has been added under the ext_data directory.

The new module has been integrated in the __init__.py and can be used both from terminal and as a function of the dingo package.

[vissarion]

This is quite old and should be re-implemented from scratch

[hariszaf]

Way to go:

• implement approach from cobra toolbox to build merged model
• sample by asking biomass of species A to be 0 and biomass of species B to be max
• sample with the vice versa conditions
• sample asking for both biomass functions to be max

[vissarion]

Thanks @hariszaf I added issue https://github.com/GeomScale/dingo/issues/67 to keep track on it!