Dataset Information

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

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

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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]

PMID: 26556387

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Dataset Information

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

Unlabelled

Availability and implementation

Supplementary information

Contact

Publications

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

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