Tutorial

Upon installation TRuML can be used from the command line by invoking the truml command with various options. All options can be seen with the command:

truml -h

Converting from Kappa to BNGL

In order to convert a model written in Kappa syntax to BNGL syntax, run the following command:

truml -k model.ka

where model.ka is the Kappa model of interest.

Converting from BNGL to Kappa

Converting from BNGL to Kappa is similarly straightforward:

truml -b model.bngl

Verbose conversion

The default settings are to output warnings to the terminal. To enable a slightly more verbose output, describing the various steps in translation, the -v flag is available. Output useful for debugging is available by using the -d flag. This output can be redirected to a file by specifying a file name after the -l flag.