Applications of a formal approach to decipher discrete genetic networks.

BMC Bioinformatics
Fabien CorblinLaurent Trilling

Abstract

A growing demand for tools to assist the building and analysis of biological networks exists in systems biology. We argue that the use of a formal approach is relevant and applicable to address questions raised by biologists about such networks. The behaviour of these systems being complex, it is essential to exploit efficiently every bit of experimental information. In our approach, both the evolution rules and the partial knowledge about the structure and the behaviour of the network are formalized using a common constraint-based language. In this article our formal and declarative approach is applied to three biological applications. The software environment that we developed allows to specifically address each application through a new class of biologically relevant queries. We show that we can describe easily and in a formal manner the partial knowledge about a genetic network. Moreover we show that this environment, based on a constraint algorithmic approach, offers a wide variety of functionalities, going beyond simple simulations, such as proof of consistency, model revision, prediction of properties, search for minimal models relatively to specified criteria. The formal approach proposed here deeply changes the way to ...Continue Reading

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Citations

Feb 6, 2013·Acta Biotheoretica·Hedi Ben AmorNicolas Glade
Dec 24, 2011·BMC Bioinformatics·Gustavo ArellanoElena R Alvarez-Buylla
Nov 20, 2010·Briefings in Bioinformatics·Shuangge Ma, Xiao Song
Dec 29, 2015·Journal of Bioinformatics and Computational Biology·Jonathan BehaegelFranck Delaunay
Apr 25, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Hannes KlarnerAlexander Bockmayr
Jul 22, 2010·BMC Bioinformatics·Fabien CorblinLaurent Trilling
Jun 16, 2016·Frontiers in Genetics·Wassim Abou-JaoudéClaudine Chaouiya
Aug 6, 2014·PloS One·S M Minhaz Ud-Dean, Rudiyanto Gunawan
Sep 27, 2016·NPJ Systems Biology and Applications·Boyan YordanovStephen Emmott
Jul 4, 2017·PloS One·Adnan RashidSofiène Tahar

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Software Mentioned

BIOCHAM
Box
GNBox
GNBox ( Genetic Networks toolBox -
NuSMV
CLP
SAT4J
GINsim
LG
GN

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