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