Dataset Information

Mammalian Cell Cycle 2006

ABSTRACT: 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).

SUBMITTER: Tomas Helikar

PROVIDER: 2396 | Cell Collective |

REPOSITORIES: Cell Collective

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Publications

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

Fauré Adrien A Naldi Aurélien A Chaouiya Claudine C Thieffry Denis D

Bioinformatics (Oxford, England) 20060701 14

<h4>Motivation</h4>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.<h4>Results</h4>Transposing a generic model of the core network controlling the mammalian cell cycle into the logical ...[more]

PMID: 16873462

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Project description:Traynard2016 - Mammalian cell cycle regulation - Logical Model This model is described in the article: Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Traynard P, Fauré A, Fages F, Thieffry D. Bioinformatics 2016 Sep; 32(17): i772-i780 Abstract: Understanding the temporal behaviour of biological regulatory networks requires the integration of molecular information into a formal model. However, the analysis of model dynamics faces a combinatorial explosion as the number of regulatory components and interactions increases.We use model-checking techniques to verify sophisticated dynamical properties resulting from the model regulatory structure in the absence of kinetic assumption. We demonstrate the power of this approach by analysing a logical model of the molecular network controlling mammalian cell cycle. This approach enables a systematic analysis of model properties, the delineation of model limitations, and the assessment of various refinements and extensions based on recent experimental observations. The resulting logical model accounts for the main irreversible transitions between cell cycle phases, the sequential activation of cyclins, and the inhibitory role of Skp2, and further emphasizes the multifunctional role for the cell cycle inhibitor Rb.The original and revised mammalian cell cycle models are available in the model repository associated with the public modelling software GINsim (http://ginsim.org/node/189).thieffry@ens.frSupplementary data are available at Bioinformatics online. This model is hosted on BioModels Database and identified by: MODEL1611230001. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Mammalian Cell Cycle 2006

Publications

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.

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