BioBayes: a software package for Bayesian inference in systems biology

Vladislav Vyshemirsky, Mark Girolami

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

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.
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.
LanguageEnglish
Pages1933-1934
Number of pages2
JournalBioinformatics
Volume24
Issue number17
DOIs
Publication statusPublished - 1 Sep 2008

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Systems Biology
Bayesian inference
Software Package
Software packages
Uncertainty
Software
Bayes Theorem
Bayesian Estimation
Kinetic parameters
Ordinary differential equations
Mathematical Modeling
Parameter estimation
Parameter Estimation
Ranking
Ordinary differential equation
Kinetics
Model
Module
Methodology
Modeling

Keywords

  • biobayes
  • software package
  • Bayesian inference
  • systems biology

Cite this

Vyshemirsky, Vladislav ; Girolami, Mark. / BioBayes : a software package for Bayesian inference in systems biology. In: Bioinformatics. 2008 ; Vol. 24, No. 17. pp. 1933-1934.
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BioBayes : a software package for Bayesian inference in systems biology. / Vyshemirsky, Vladislav; Girolami, Mark.

In: Bioinformatics, Vol. 24, No. 17, 01.09.2008, p. 1933-1934.

Research output: Contribution to journalArticle

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