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.Comment: 3 pages, 1 figure, 1 supplementary text file. Supplementary text
includes a brief discussion of the RK-PLA along with a performance analysis,
two tables listing all new actions/arguments added in BioNetGen 2.2, and the
"BioNetGen Quick Reference Guide". Accepted for publication in Bioinformatic
