BioBayes: Bayesian Inference for Systems Biology

BioBayes is updated to version 1.3 This version includes major bug fixes and we strongly recommend all users to update as soon as possible. The major updates are:

1. BioBayes is now compatible with Mac OS X 10.6 "Snow Leopard"
2. The core of BioBayes is updated to work with Java SE 6
3. XML parsers are updated to JAXB 2
4. The user interface core is updated to Eclipse RCP 3.5
5. Updates system is updated to Equinox p2 provisioning
6. Experimental algorithms are removed from the default package and are now avalable as an optional installation
7. Many optimisations and interface improvements.

We strongly recommend reinstalling BioBayes from a freshly downloaded archive.

The source code is available to the community on request. Please contact the authors at vvv@dcs.gla.ac.uk if you are interested in contributing to the project.

Brief video tutorial on installing and using BioBayes is also available from this page.

BioBayes is updated to version 1.2 The major updates are:

1. Three major chrashes have been fixed, the stability of the programme is significantly improved.
2. The core of BioBayes has been updated to the latest version of Eclipse platform (3.4.1) providing significant improvement in user interface compatibility.
3. Problems with importing existing projects from nonstandard locations have been resolved.
4. MAJOR UPDATE: Annealed importance sampling algorithm has been corrected, please, re-run all your experiments that you have performed using this algorithm as the previous version was introducing a bias in the estimate.
5. The software updates system has been significantly improved, BioBayes will now fetch new updates automatically.
6. Several optimisations and interface improvements.

BioBayes is updated to version 1.1 The major updates are:

1. Gaussian priors are replaced with truncated Gaussians to [0, +inf).
2. Uniform priors are limited to nonnegative numbers.
3. Annealed Importance Sampling algorithm has been added.
4. A number of bugs have been fixed and overall optimisation of the code has been performed

This is a major version release. BioBayes is updated to version 1.0 Most of the defects found in version 0.1 are corrected.

Published papers

• V. Vyshemirsky and M. Girolami (2008a), "Bayesian Ranking of Biochemical System Models", Bioinformatics 24(6):833-839.  [Erratum]
• V. Vyshemirsky and M. Girolami (2008b), "BioBayes: A software package for Bayesian inference in Systems Biology", Bioinformatics, in print.

Talks

• M. Girolami: "On stratified path sampling of the Thermodynamic Integral: computing Bayes factors for nonlinear dynamical systems models" , PASCAL Workshop AISPDS, May 2008.
• M. Girolami: "On stratified path sampling of the thermodynamic integral: computing Bayes factors for nonlinear ODE models of biochemical pathways" , Newton Institute in Cambridge, May 2008.
• V. Vyshemirsky: "BioBayes: Bayesian inference for Systems Biology", LICSB'08.
• V. Vyshemirsky: "A software tool for Bayesian inference of ODE Biochemical Models", PIM'07

Recent publications referencing our papers

• P. Gao, A. Honkela, M. Rattray, N. D. Lawrence (2008), "Gaussian process modelling of latent chemical species: applications to inferring transcription factor activities" , Bioinformatics 24(16):i70-i75.
• B. Jayawardhana, D. B. Kell, M. Rattray (2008), "Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo" , Bioinformatics 24(9):1191-1197