BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
Ontology highlight
ABSTRACT: 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.
SUBMITTER: Thomas BR
PROVIDER: S-EPMC4907397 | biostudies-literature | 2016 Mar
REPOSITORIES: biostudies-literature
Publications
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.
Thomas Brandon R BR Chylek Lily A LA Colvin Joshua J Sirimulla Suman S Clayton Andrew H A AH Hlavacek William S WS Posner Richard G RG
Bioinformatics (Oxford, England) 20151109 5
<h4>Unlabelled</h4>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.<h4>Availabili ...[more]
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