After installation, detailed usage instructions can be found with:

misosoup -h

To use misosoup with its default settings, you can use the following command:

misosoup MODEL_PATH/*.xml --output OUTPUT_FILE --media MEDIA_FILE --strain STRAIN

Arguments

  • MODEL_PATH: indicates the path to the directory where the metabolic models are described. Strains with metabolic models included in this directory will be considered as potential members in the minimal communities. The models should be in sbml format and follow the same naming conventions (e.g. if glucose’s id in one model is ‘glc__D’, the same id should be used in the other models).
  • --output
    • Use OUTPUT_FILE for output in yaml format. If it is not given, the results will be printed to stdout.
  • --media
    • Load media from MEDIA_FILE. An example file with a correct format to introduce a media composition can be found in examples/.
  • --strain
    • Indicates the focal STRAIN model id. If no strain is provided, misosoup computes minimal communities.

Additional arguments

misosoup can be used with additional arguments.

misosoup MODEL_PATH/*.xml --output OUTPUT_FILE --media MEDIA_FILE --strain STRAIN --parsimony --community-size COMMUNITY_SIZE --minimal-growth MINIMAL_GROWTH
  • --parsimony
    • If this flag is used the algorithm will return the solution that minimizes the total flux. This does not affect the community members but can alter what each member consumes and secretes.
  • --community-size
    • Instead of looking for all communities, find all communities up to size COMMUNITY_SIZE
  • --minimal-growth
    • Set the MINIMAL_GROWTH rate of strains. Every strain that makes up a community needs to satisfy this minimal growth constraint. The default growth rate is 0.01 (1/h).

Output file

As output misosoup will generate a yaml file with the following general structure:

medium:
  strain|min:
    - <Solution1>
    - <Solution2>

The solutions indicated above contain two entries, the first is a dictionary with the community composition, and the second is a dictionary with the growth rates and fluxes through exchange reactions of the respective optimized solution. An example of an output file can be found in examples/.

Workflows

snakemake is a useful tool to execute many experiments and gather results. See misosoup Workflow Template on how to use it.