title: BioNetGen 2.2: advances in rule-based modeling.
abstract: : 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.
  
  
  
  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.comSupplementary information: Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Leonard A
authors.initials: LA
authors.lastname: Harris
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Justin S
authors.initials: JS
authors.lastname: Hogg
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: José-Juan
authors.initials: JJ
authors.lastname: Tapia
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: John A P
authors.initials: JA
authors.lastname: Sekar
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Sanjana
authors.initials: S
authors.lastname: Gupta
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Ilya
authors.initials: I
authors.lastname: Korsunsky
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Arshi
authors.initials: A
authors.lastname: Arora
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Dipak
authors.initials: D
authors.lastname: Barua
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Sheehan
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Faeder
mesh_terms: D001671:Biochemistry; D006801:Humans; D008962:Models, Theoretical; D011381:Programming Languages; D012984:Software