BioBayes: a software package for Bayesian inference in systems biology

Vyshemirsky, V. and Girolami, M. (2008) BioBayes: a software package for Bayesian inference in systems biology. Bioinformatics, 24(17), pp. 1933-1934. (doi: 10.1093/bioinformatics/btn338) (PMID:18632751)

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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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Vyshemirsky, Dr Vladislav and Girolami, Prof Mark
Authors: Vyshemirsky, V., and Girolami, M.
College/School:College of Science and Engineering > School of Computing Science
College of Science and Engineering > School of Mathematics and Statistics > Statistics
Journal Name:Bioinformatics
Publisher:Oxford University Press
ISSN:1367-4803
ISSN (Online):1460-2059
Published Online:16 July 2008

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
450691The integration of probabilistic prediction and mechanistic modelling within a computational and systems biology contextMark GirolamiEngineering & Physical Sciences Research Council (EPSRC)EP/E052029/1COM - COMPUTING SCIENCE