GetBonNie for building, analyzing and sharing rule-based models

Bin Hu, G. Matthew Fricke, James R. Faeder, Richard G Posner, William S. Hlavacek

Research output: Contribution to journalArticle

13 Scopus citations

Abstract

Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.

Original languageEnglish (US)
Pages (from-to)1457-1460
Number of pages4
JournalBioinformatics
Volume25
Issue number11
DOIs
StatePublished - Jun 2009
Externally publishedYes

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ASJC Scopus subject areas

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

Cite this

Hu, B., Matthew Fricke, G., Faeder, J. R., Posner, R. G., & Hlavacek, W. S. (2009). GetBonNie for building, analyzing and sharing rule-based models. Bioinformatics, 25(11), 1457-1460. https://doi.org/10.1093/bioinformatics/btp173