Growth simulation with refineGEMs
Interpreting the results
Outputs a table with the column headers:
essential = metabolites not present in the medium but necessary for growth
missing = all exchanges missing in the model but given in medium
Implementation
Growth rates and thus doubling times can be determined with Flux Balance Analysis (FBA). RefineGEMs uses a COBRApy based implementation that adds metabolites one-by-one to custom media definitions until growth is obtained. The pseudocode is shown below.
There is a flag called basis which can be set to either default_uptake or minimal_uptake. You can decide from which uptake you want to fill your medium of interest when looking for missing metabolites. Either the default_uptake which is the uptake that the model has when no specific medium is set or the minimal_uptake which is the uptake resulting from cobrapys minimal_medium optimization.
Available media
The following media are directly available to be used with the growth module via a config.yaml file.
In the section for the respective medium the description along with the definition is provided. The rules used to get
the media definitions are described in the Section From laboratory to in silico medium.