Reference : optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/17563
optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks
English
Trairatphisan, Panuwat mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
Mizera, Andrzej mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
Pang, Jun mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Computer Science and Communications Research Unit (CSC) >]
Tantar, Alexandru-Adrian mailto [University of Luxembourg > Interdisciplinary Centre for Security, Reliability and Trust (SNT) > >]
Sauter, Thomas mailto [University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >]
1-Jul-2014
PLoS ONE
Public Library of Science
9
7
e98001 (1-15)
Yes (verified by ORBilu)
International
1932-6203
San Franscisco
CA
[en] probabilistic Boolean networks ; optimisation ; software ; network analysis ; Matlab ; network inference
[en] Background

There exist several computational tools which allow for the optimisation and inference of biological networks using a Boolean formalism. Nevertheless, the results from such tools yield only limited quantitative insights into the complexity of biological systems because of the inherited qualitative nature of Boolean networks.

Results

We introduce optPBN, a Matlab-based toolbox for the optimisation of probabilistic Boolean networks (PBN) which operates under the framework of the BN/PBN toolbox. optPBN offers an easy generation of probabilistic Boolean networks from rule-based Boolean model specification and it allows for flexible measurement data integration from multiple experiments. Subsequently, optPBN generates integrated optimisation problems which can be solved by various optimisers.

In term of functionalities, optPBN allows for the construction of a probabilistic Boolean network from a given set of potential constitutive Boolean networks by optimising the selection probabilities for these networks so that the resulting PBN fits experimental data. Furthermore, the optPBN pipeline can also be operated on large-scale computational platforms to solve complex optimisation problems. Apart from exemplary case studies which we correctly inferred the original network, we also successfully applied optPBN to study a large-scale Boolean model of apoptosis where it allows identifying the inverse correlation between UVB irradiation, NFκB and Caspase 3 activations, and apoptosis in primary hepatocytes quantitatively. Also, the results from optPBN help elucidating the relevancy of crosstalk interactions in the apoptotic network.

Summary

The optPBN toolbox provides a simple yet comprehensive pipeline for integrated optimisation problem generation in the PBN formalism that can readily be solved by various optimisers on local or grid-based computational platforms. optPBN can be further applied to various biological studies such as the inference of gene regulatory networks or the identification of the interaction's relevancy in signal transduction networks.
Fonds National de la Recherche - FnR
Researchers ; Professionals ; Students ; General public
http://hdl.handle.net/10993/17563
10.1371/journal.pone.0098001
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098001

File(s) associated to this reference

Fulltext file(s):

FileCommentaryVersionSizeAccess
Open access
optPBN_an_optimisation_toolbox_for_probabilistic_Boolean_networks.pdfPublisher postprint1.38 MBView/Open

Bookmark and Share SFX Query

All documents in ORBilu are protected by a user license.