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

2015; Oxford University Press; Volume: 32; Issue: 5 Linguagem: Inglês

10.1093/bioinformatics/btv655

1367-4811

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

Single-cell and spatial transcriptomics

Abstract Summary: 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