Antibiotic and carbon source data

[jcasadogp]

Improve the antibiotic and carbon source's input on the YAML file. Currently, it is only a true/false field, but we should capture much more information about it. For the moment, set it as text file that admits a small description of which antibiotic or carbon source has been used. In case of null/empty, we assume none was used.

These two papers mention both antibiotics and carbon sources:

• The role of pH in determining the species composition of the human colonic microbiota
• Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis

[jcasadogp]

Other related changes to be made:

• Reactor: a single float is not sufficient to describe the atmosphere, which is often a mixture of gasses
• There are different stirring modes (linear motion, orbital, etc.)
• Bacteria (better named Taxon): Why not storing the entire lineage, so people can query for family, e.g. plot all Prevotellaceae across all experiments with inulin as carbon source? One day, we may want to add bacteriophages, so that's why 'Bacteria' is a bit restrictive as a name

[jcasadogp]

This changes has to be yet included in the Python code, for writing and reading YAML files.