Contains functions and helpers to obtain minimal growth media.
184.108.40.206.1.2.1. Module Contents¶
Add a linear version of a minimal medium to the model solver.
Changes the optimization objective to finding the growth medium requiring the smallest total import flux:
minimize sum |r_i| for r_i in import_reactions
Parameters: model (cobra.Model) – The model to modify.
Add a mixed-integer version of a minimal medium to the model.
Changes the optimization objective to finding the medium with the least components:
minimize size(R) where R part of import_reactions
Parameters: model (cobra.model) – The model to modify.
_as_medium(exchanges, tolerance=1e-06, exports=False)¶
Convert a solution to medium.
- exchanges (list of cobra.reaction) – The exchange reactions to consider.
- tolerance (positive double) – The absolute tolerance for fluxes. Fluxes with an absolute value smaller than this number will be ignored.
- exports (bool) – Whether to return export fluxes as well.
The “medium”, meaning all active import fluxes in the solution.
minimal_medium(model, min_objective_value=0.1, exports=False, minimize_components=False, open_exchanges=False)¶
Find the minimal growth medium for the model.
Finds the minimal growth medium for the model which allows for model as well as individual growth. Here, a minimal medium can either be the medium requiring the smallest total import flux or the medium requiring the least components (ergo ingredients), which will be much slower due to being a mixed integer problem (MIP).
- model (cobra.model) – The model to modify.
- min_objective_value (positive float or array-like object) – The minimum growth rate (objective) that has to be achieved.
- exports (boolean) – Whether to include export fluxes in the returned medium. Defaults to False which will only return import fluxes.
- minimize_components (boolean or positive int) – Whether to minimize the number of components instead of the total import flux. Might be more intuitive if set to True but may also be slow to calculate for large communities. If set to a number n will return up to n alternative solutions all with the same number of components.
- open_exchanges (boolean or number) – Whether to ignore currently set bounds and make all exchange reactions in the model possible. If set to a number all exchange reactions will be opened with (-number, number) as bounds.
A series giving the import flux for each required import reaction and (optionally) the associated export fluxes. All exchange fluxes are oriented into the import reaction e.g. positive fluxes denote imports and negative fluxes exports. If minimize_components is a number larger 1 may return a DataFrame where each column is a minimal medium. Returns None if the minimization is infeasible (for instance if min_growth > maximum growth rate).
pandas.Series, pandas.DataFrame or None
Due to numerical issues the minimize_components option will usually only minimize the number of “large” import fluxes. Specifically, the detection limit is given by
integrality_tolerance * max_boundwhere
max_boundis the largest bound on an import reaction. Thus, if you are interested in small import fluxes as well you may have to adjust the integrality tolerance at first with model.solver.configuration.tolerances.integrality = 1e-7 for instance. However, this will be very slow for large models especially with GLPK.