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

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)798-800
Number of pages3
JournalBioinformatics
Volume32
Issue number5
DOIs
StatePublished - May 8 2015

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Open Source Software
Distributed computer systems
Distributed Computing
Software Package
Software packages
Simulator
Software
Simulators
Resources
Optimization
Simulation
Model
Open source software

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability

Cite this

Thomas, B. R., Chylek, L. A., Colvin, J., Sirimulla, S., Clayton, A. H. A., Hlavacek, W. S., & Posner, R. G. (2015). BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments. Bioinformatics, 32(5), 798-800. https://doi.org/10.1093/bioinformatics/btv655

BioNetFit : A fitting tool compatible with BioNetGen, NFsim and distributed computing environments. / Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; Sirimulla, Suman; Clayton, Andrew H A; Hlavacek, William S.; Posner, Richard G.

In: Bioinformatics, Vol. 32, No. 5, 08.05.2015, p. 798-800.

Research output: Contribution to journalArticle

Thomas, BR, Chylek, LA, Colvin, J, Sirimulla, S, Clayton, AHA, Hlavacek, WS & Posner, RG 2015, 'BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments', Bioinformatics, vol. 32, no. 5, pp. 798-800. https://doi.org/10.1093/bioinformatics/btv655
Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AHA, Hlavacek WS et al. BioNetFit: A fitting tool compatible with BioNetGen, NFsim and distributed computing environments. Bioinformatics. 2015 May 8;32(5):798-800. https://doi.org/10.1093/bioinformatics/btv655
Thomas, Brandon R. ; Chylek, Lily A. ; Colvin, Joshua ; Sirimulla, Suman ; Clayton, Andrew H A ; Hlavacek, William S. ; Posner, Richard G. / BioNetFit : A fitting tool compatible with BioNetGen, NFsim and distributed computing environments. In: Bioinformatics. 2015 ; Vol. 32, No. 5. pp. 798-800.
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