This version brings new functionality to design growth media from a skeleton medium. This also allows for a quicker verification of media against the model databases.
Added workflows:
- `check_db_media` check if models in a model database can grow on a given medium - `complete_db_media`completes a growth medium so all models in the db can grow on it
Together with this we now provide several new revised growth media for the gut on github.com/micom-dev/media. In particular, we finally provide the often requested growth medium for the carveME database.
0.19.0
`minimal_medium` now accepts weighting the fluxes bei molecular weight or any elemental content. For instance, you can now calculate a minimal medium that minimizes carbon import for instance. The used `weigths` argument propagates to any workflow using this function including `complete_medium`, `fix_medium` and `grow`.
0.1.0
`minimal_medium` now has an option to return all fluxes along with the import and export fluxes. Useful if you want to check what every individual taxa consumes.
Addition of `Community.cooperative_tradeoff` which brings a fast method to get nearly unique growth rates for a particular growth tradeoff (for instance 50% maximal growth rate).
Addition of elasticity coefficients which allows you to study which import and export reactions are sensitive to changes in diet or taxa abundances.
Several changes to make `micom` capable of handling numerical instable models. This includes a crossover strategy to obtain an optimal or near-optimal from an incomplete interior point optimization.