BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments
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Updated: Mar 30, 2026
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
Published on: December 1, 2020
Brandon R Thomas1, Lily A Chylek2, Joshua Colvin1
1Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
Unlabelled:
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.
Availability And Implementation:
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 Information:
Supplementary data are available at Bioinformatics online.
Contact:
bionetgen.help@gmail.com.
