Nicotine

Nicotine Is a COnstraint-based T and p-INvariant Extractor.

Besides being a famous alkaloid found in tobacco, Nicotine (Nicotine Is a COnstraint-based T and p-INvariant Extractor) is a (GNU Prolog) program that computes a Petri-net’s invariants by using Constraint Programming and has grown to encompass many other utilities.

It allows and provides a command line (only) interface (details are given in the included README file).

Features include:

• import and export of several formats
  • APNN (a subset),
  • PNML,
  • SBML,
  • BIOCHAM,
  • etc.
• P/T-invariant computation (cf. MATHMOD 2009 and AlMoB 2012 proceedings for technical explanations)
• Extraction of structure from XPP ODE files as detailed in this PLoS One article
• Subgraph EPImorphism detection as explained in that Bioinformatics article.

Download

Nicotine download has been suspended as it is currently being integrated into Biocham v4. You can try the find_pinvar and tropicalize commands from the online notebook version.

The recommended means for feedback and support is email.