BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
basic_science · Level V
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- Record sourced from PubMed, PMID 26556387.
- Also identified by DOI 10.1093/bioinformatics/btv655 and PMC identifier 4907397.
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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.
Medical subject headings
- Software