Usage

Single community

To run SMETANA on a singe community just give it a list of single-species models in SBML format:

$ smetana species1.xml species2.xml ...

$ smetana *.xml

Multiple communities

You can run SMETANA on multiple communities in a single line of code. For that you need to create a table describing the composition of each community. This table is expected to be in long format, tab-separated, with two columns: community id, organism id. The latter should match the SBML filename (without extension). Example:

community1 organism1
community1 organism2
community2 organism1
community2 organism3

After creating this file, invoke SMETANA as follows:

$ smetana *.xml -c communities.tsv

Medium composition

By default, SMETANA will simulate every community using a complete medium composition. To test your communities on different media, give it the list of media and a file containing the media compositions. You can specify multiple media in a single command and SMETANA will run consecutively for each medium.

$ smetana *.xml -m M9,LB --mediadb library.tsv

For an example on how to create your own library file please check this example.

Global vs Detailed mode

SMETANA has two main running modes:

  • Global (-g, --global): runs MIP/MRO and is much faster, recommended when analysing multiple communities.
  • Detailed (-d, --detailed): calculates all inter-species interactions (much slower), check Algorithms for details.

Advanced

SMETANA offers other options, such as:

  • Selecting different SBML flavors (--flavor)
  • Changing the name/directory of your output files (-o, --output)
  • Selecting only a subset of scores to run (-s, --scores)
  • Changing your default solver (--solver)
  • Specifying the identifier of the extracellular compartment in the models (--ext).
  • Calculate minimal media using molecular weights (--molweight).
  • Exclude certain compounds (e.g.: inorganic compounds) from the analysis (--exclude).
  • Do not compute species coupling scores (allow non-growth coupled interactions) (--no-coupling).

For more detailed instructions please type:

$ smetana -h