Metabolic Interaction Potential (MIP)

mip()

The metabolic capacity for a member to support the other member is quantified:

CommScores.mip(member_models: Iterable, com_model=None, min_growth=0.1, interacting_media_dict=None,
               noninteracting_media_dict=None, environment=None, printing=False, compatibilized=False,
               costless=False, multi_output=False, skip_bad_media=False)

  • member_models list|set: The models from which the MSModelUtil objects and the community model can be constructed.

  • com_model cobrakbase.core.kbasefba.fbamodel.FBAModel: The community model that will be simulated, which can alternatively be constructed from the member_models or model_utils arguments when comm_model remains None.

  • min_growth float: The model minimum growth in the specified media, which is used as the lower boundary when computing the minimal media for each model.

  • interacting_media_dict & noninteracting_media_dict dict: The media dictionaries of exchange IDs and fluxes when the members are allowed and disallowed to interact through cross-feeding, respectively.

  • environment dict|cobrakbase.core.kbasebiochem.media.Media: The media environment in which the member models will be simulated.

  • printing bool: specifies whether progress and errors during computation are printed.

  • compatibilized bool: specifies whether the member models have been aligned with ModelSEED conventions.

  • costless bool: specifies whether the costless MIP subscore is computed and reported, which is the number of cross-fed compounds that are also costlessly excreted.

  • multi_output bool: specifies whether the costless MIP is reported in addition to, or in lieu of, the standard MIP score.

  • skip_bad_media bool: specifies whether media in which the members do not grow are skipped without error or throw an error.

Returns list|dict: A list is returned unless multi_output is False, in which case a dictionary of the costlessly cross-fed compounds donated from each model is returned. The first element of the returned list is a dictionary of cross-fed compounds donated from each model. A second list element is added when costless is True, which is the set of costlessly cross-fed compounds donated from each model.