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Bioinformatics Advance Access published online on March 25, 2009
Bioinformatics, 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 and 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, USA 2Theoretical Biology and Biophysics Group, Theoretical Division and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA

*To whom correspondence should be addressed. William S. Hlavacek, E-mail: getbonnie{at}cs.unm.edu


  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 1) an applet for drawing graphs that correspond to BNGL code; 2) a network-generation engine for translating a set of rules into a chemical reaction network; 3) simulation engines that implement generate-first, on-the-fly, and network-free methods for simulating rule-based models; and 4) a database for sharing models, parameter values, annotations, simulation tasks and results.

Availability: GetBonNie is free (http://getbonnie.org).

Contact: getbonnie{at}cs.unm.edu

Associate Editor: Dr. Olga Troyanskaya

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

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