A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation.
As modeling becomes a more widespread practice in the life sciences and biomedical sciences, researchers need reliable tools to calibrate models against ever more complex and detailed data. Here we present an approximate Bayesian computation (ABC) framework and software environment, ABC-SysBio, which is a Python package that runs on Linux and Mac OS X systems and that enables parameter estimation and model selection in the Bayesian formalism by using sequential Monte Carlo (SMC) approaches. We outline the underlying rationale, discuss the computational and practical issues and provide detailed guidance as to how the important tasks of parameter inference and model selection can be performed in practice. Unlike other available packages, ABC-SysBio is highly suited for investigating, in particular, the challenging problem of fitting stochastic models to data. In order to demonstrate the use of ABC-SysBio, in this protocol we postulate the existence of an imaginary reaction network composed of seven interrelated biological reactions (involving a specific mRNA, the protein it encodes and a post-translationally modified version of the protein), a network that is defined by two files containing 'observed' data that we provide as supplementary information. In the first part of the PROCEDURE, ABC-SysBio is used to infer the parameters of this system, whereas in the second part we use ABC-SysBio's relevant functionality to discriminate between two different reaction network models, one of them being the 'true' one. Although computationally expensive, the additional insights gained in the Bayesian formalism more than make up for this cost, especially in complex problems.
Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
Juliane
J
Liepe
Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
Paul
P
Kirk
Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
Sarah
S
Filippi
Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK.
Tina
T
Toni
Department of Cell and Developmental Biology, University College, London, UK.
Chris P
CP
Barnes
1] Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College, London, UK. [2] Institute of Chemical Biology, Imperial College, London, UK.
Michael P H
MP
Stumpf
D001499:Bayes Theorem; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*