GetBonNie for building, analyzing and sharing rule-based models

  • Authors:

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

  • Affiliations:

  • -;-;-;-;-

  • Venue:
  • Bioinformatics
  • Year:
  • 2009

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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. Availability: GetBonNie is free at http://getbonnie.org. Contact: getbonnie@cs.unm.edu