title: BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
abstract: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.
  
  
  
  BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu).
  
  
  
  Supplementary data are available at Bioinformatics online.
  
  
  
  bionetgen.help@gmail.com.
authors.affiliation: Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
authors.forename: Brandon R
authors.initials: BR
authors.lastname: Thomas
authors.affiliation: Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
authors.forename: Lily A
authors.initials: LA
authors.lastname: Chylek
authors.affiliation: Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Colvin
authors.affiliation: Department of Basic Sciences, Saint Louis College of Pharmacy, Saint Louis, MO, USA.
authors.forename: Suman
authors.initials: S
authors.lastname: Sirimulla
authors.affiliation: Center for Microphotonics, Faculty of Science, Engineering and Technology, Cell Biophysics Laboratory, Swinburne University of Technology, Hawthorn, VIC, Australia and.
authors.forename: Andrew H A
authors.initials: AH
authors.lastname: Clayton
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
authors.forename: William S
authors.initials: WS
authors.lastname: Hlavacek
authors.affiliation: Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
authors.forename: Richard G
authors.initials: RG
authors.lastname: Posner
mesh_terms: D012984:Software