Paper Info
Title
Composition and abstraction of logical regulatory modules: application to multicellular systems.
Abstract
Motivation: Logical (Boolean or multi-valued) modelling is widely used to study regulatory or signalling networks. Even though these discrete models constitute a coarse, yet useful, abstraction of reality, the analysis of large networks faces a classical combinatorial problem. Here, we propose to take advantage of the intrinsic modularity of inter-cellular networks to set up a compositional procedure that enables a significant reduction of the dynamics, yet preserving the reachability of stable states. To that end, we rely on process algebras, a well-established computational technique for the specification and verification of interacting systems. Results: We develop a novel compositional approach to support the logical modelling of interconnected cellular networks. First, we formalize the concept of logical regulatory modules and their composition. Then, we make this framework operational by transposing the composition of logical modules into a process algebra framework. Importantly, the combination of incremental composition, abstraction and minimization using an appropriate equivalence relation (here the safety equivalence) yields huge reductions of the dynamics. We illustrate the potential of this approach with two case-studies: the Segment-Polarity and the Delta-Notch modules. Availability and implementation: GINsim (http://ginsim.org) and CADP (http://cadp.inria.fr) are freely available for academic users. Files needed to reproduce our results are provided at http://comp bio.igc.gulbenkian.pt/nmd/node/45. Contact: chaouiya@igc.gulbenkian.pt Supplementary information: Supplementary data are available at Bioinformatics online
Year
DOI
Venue
2013
10.1093/bioinformatics/btt033
BIOINFORMATICS
Field
DocType
Volume
Equivalence relation,Abstraction,Computer science,Theoretical computer science,Reachability,Minification,Equivalence (measure theory),Cellular network,Bioinformatics,Process calculus,Modularity
Journal
29
Issue
ISSN
Citations 
6
1367-4803
3
PageRank 
References 
Authors
0.38
20
6
Name
Order
Citations
PageRank
Nuno D. Mendes1443.61
Frédéric Lang235417.87
Yves-Stan Le Cornec330.38
Radu Mateescu4128777.10
Grégory Batt536425.79
Claudine Chaouiya668951.82