BioNetFit

BioNetFit is a general-purpose fitting tool compatible with BioNetGen and NFsim. It is designed to optimize parameter values for consistency with data, especially in rule-based models that are analyzed with specialized simulators. BioNetFit takes advantage of distributed computing resources, making it useful when simulations are computationally expensive. The software is freely available in Perl and can be used on standalone Mac, Windows/Cygwin, and Linux platforms, as well as on Linux-based clusters running SLURM, Torque/PBS, or SGE.

Topic

Systems biology;Molecular interactions, pathways and networks;Bioinformatics

Detail

  • Operation: Modelling and simulation

  • Software interface: Command-line user interface

  • Language: Shell;Perl

  • License: BSD-3

  • Cost: Free

  • Version name: v1.1.9

  • Credit: NIH-NIGMS, Arizona Technology and Research Initiative Fund.

  • Input: -

  • Output: -

  • Contact: Brandon R Thomas brandonthomas@nau.edu

  • Collection: -

  • Maturity: -

Publications

  • BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
  • Thomas BR, et al. BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. 2016; 32:798-800. doi: 10.1093/bioinformatics/btv655
  • https://doi.org/10.1093/bioinformatics/btv655
  • PMID: 26556387
  • PMC: PMC4907397

Download and documentation

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