BioNetGen 2.2: advances in rule-based modeling.

BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discussing how they facilitate the construction, simulation and analysis of larger and more complex models than previously possible. Availability and Implementation: Stable BioNetGen releases (Linux, Mac OS/X and Windows), with documentation, are available at http://bionetgen.org. Source code is available at http://github.com/RuleWorld/bionetgen. Contact: bionetgen. help@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.