Dataset Information
A Bayesian approach to targeted experiment design.
Ontology highlight
ABSTRACT: Motivation
Systems biology employs mathematical modelling to further our understanding of biochemical pathways. Since the amount of experimental data on which the models are parameterized is often limited, these models exhibit large uncertainty in both parameters and predictions. Statistical methods can be used to select experiments that will reduce such uncertainty in an optimal manner. However, existing methods for optimal experiment design (OED) rely on assumptions that are inappropriate when data are scarce considering model complexity.Results
We have developed a novel method to perform OED for models that cope with large parameter uncertainty. We employ a Bayesian approach involving importance sampling of the posterior predictive distribution to predict the efficacy of a new measurement at reducing the uncertainty of a selected prediction. We demonstrate the method by applying it to a case where we show that specific combinations of experiments result in more precise predictions.Availability and implementation
Source code is available at: http://bmi.bmt.tue.nl/sysbio/software/pua.html.
SUBMITTER: Vanlier J
PROVIDER: S-EPMC3324513 | biostudies-literature | 2012 Apr
REPOSITORIES: biostudies-literature
Publications
A Bayesian approach to targeted experiment design.
Bioinformatics (Oxford, England) 20120224 8
<h4>Motivation</h4>Systems biology employs mathematical modelling to further our understanding of biochemical pathways. Since the amount of experimental data on which the models are parameterized is often limited, these models exhibit large uncertainty in both parameters and predictions. Statistical methods can be used to select experiments that will reduce such uncertainty in an optimal manner. However, existing methods for optimal experiment design (OED) rely on assumptions that are inappropri ...[more]