Journal Article

GetBonNie for building, analyzing and sharing rule-based models

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

in Bioinformatics

Volume 25, issue 11, pages 1457-1460
Published in print June 2009 | ISSN: 1367-4803
Published online March 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp173
GetBonNie for building, analyzing and sharing rule-based models

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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

Journal Article.  1924 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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