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Bioinformatics 2006 22(14):e124-e131; doi:10.1093/bioinformatics/btl210
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle

Adrien Fauré , Aurélien Naldi , Claudine Chaouiya and Denis Thieffry *

Institut de Biologie du Développement de Marseille-Luminy, Campus scientifique de Luminy CNRS case 907, 13288 Marseille, France

*To whom correspondence should be addressed.

Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks.

Results: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge.

Availability: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim (http://gin.univ-mrs.fr/GINsim). Higher resolution state transitions graphs are also found on this web site (Model Repository page).

Contact: thieffry{at}ibdm.univ-mrs.fr


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