BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Brandon R Thomas; Lily A Chylek; Joshua Colvin; Suman Sirimulla; Andrew H A Clayton; William S Hlavacek; Richard G Posner

doi:10.1093/bioinformatics/btv655

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

Bioinformatics. 2016 Mar 1;32(5):798-800. doi: 10.1093/bioinformatics/btv655. Epub 2015 Nov 9.

Authors

Brandon R Thomas¹, Lily A Chylek², Joshua Colvin¹, Suman Sirimulla³, Andrew H A Clayton⁴, William S Hlavacek⁵, Richard G Posner¹

Affiliations

¹ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
² Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA, Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
³ Department of Basic Sciences, Saint Louis College of Pharmacy, Saint Louis, MO, USA.
⁴ Center for Microphotonics, Faculty of Science, Engineering and Technology, Cell Biophysics Laboratory, Swinburne University of Technology, Hawthorn, VIC, Australia and.
⁵ Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.

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.

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.

MeSH terms

Software*

Abstract

MeSH terms

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