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Bioinformatics Advance Access originally published online on March 25, 2009
Bioinformatics 2009 25(11):1457-1460; doi:10.1093/bioinformatics/btp173
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GetBonNie for building, analyzing and sharing rule-based models

Bin Hu 1,2, G. Matthew Fricke 3, James R. Faeder 4, Richard G. Posner 5 and William S. Hlavacek 1,2,6,*

1Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA

*To whom correspondence should be addressed.


  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{at}cs.unm.edu

Associate Editor: Olga Troyanskaya

Received on November 21, 2008; revised on March 6, 2009; accepted on March 22, 2009

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