Growth Yield Difference (GYD)

gyd()

The relative difference in the maximal growth yields between two members in a given environment is calculated:

CommScores.gyd(member_models:Iterable=None, model_utils:Iterable=None, environment=None, coculture_growth=False,
               community=None, anme_comm=False)

  • member_models list|set: The models from which pairwise combinations will be created and then evaluated.

  • model_utils list|set: The MSModeulUtils objects of the member models that can be provided as an alternative to member_models and offers quicker execution time.

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

  • coculture_growth bool: specifies whether the evaluated growth yields are for their growths in the community or as isolates.

  • community cobrakbase.core.kbasefba.fbamodel.FBAModel: The community that is used when coculture_growth is True and the member growths within the community must be determined. A fresh Community model can be constructed from the member_models and model_utils when community remains None.

  • anme_comm bool: specifies whether an environment is parameterized to the models, which may be undesirable for some communities that fail to growth in isolation, such as syntrophic ANME members.

Returns dict: A tuple of the GYD score followed by each of the two member growths, with keys of the model IDs delimited by ” ++ “.