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Bioinformatics Advance Access originally published online on July 16, 2008
Bioinformatics 2008 24(17):1933-1934; doi:10.1093/bioinformatics/btn338
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

BioBayes: A software package for Bayesian inference in systems biology

Vladislav Vyshemirsky * and Mark Girolami

Department of Computing Science, University of Glasgow, G12 8QQ, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: There are several levels of uncertainty involved in the mathematical modelling of biochemical systems. There often may be a degree of uncertainty about the values of kinetic parameters, about the general structure of the model and about the behaviour of biochemical species which cannot be observed directly. The methods of Bayesian inference provide a consistent framework for modelling and predicting in these uncertain conditions. We present a software package for applying the Bayesian inferential methodology to problems in systems biology.

Results: Described herein is a software package, BioBayes, which provides a framework for Bayesian parameter estimation and evidential model ranking over models of biochemical systems defined using ordinary differential equations. The package is extensible allowing additional modules to be included by developers. There are no other such packages available which provide this functionality.

Availability: http://www.dcs.gla.ac.uk/BioBayes/

Contact: vvv@dcs.gla.ac.uk

Associate Editor: Olga Troyanskaya

Received on March 6, 2008; revised on June 3, 2008; accepted on July 1, 2008

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