Logical modelling of regulatory networks with GINsim 2.3.
Many important problems in cell biology require the consideration of dense nonlinear interactions between functional modules. The requirement of computer simulation for the understanding of cellular processes is now widely accepted, and a variety of modelling frameworks have been designed to meet this need. Here, we present a novel public release of the Gene Interaction Network simulation suite (GINsim), a software designed for the qualitative modelling and analysis of regulatory networks. The main functionalities of GINsim are illustrated through the analysis of a logical model for the core network controlling the fission yeast cell cycle. The last public release of GINsim (version 2.3), as well as development versions, can be downloaded from the dedicated website (http://gin.univ-mrs.fr/GINsim/), which further includes a model library, along with detailed tutorial and user manual.
Naldi
A
A
TAGC-INSERM U928-Université de la Méditerranée, Campus de Luminy, Case 929, F-13288 Marseille Cedex 9, France.
Berenguier
D
D
Fauré
A
A
Lopez
F
F
Thieffry
D
D
Chaouiya
C
C
D000465:Algorithms; D002453:Cell Cycle; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020407:Internet; D008962:Models, Theoretical; D012568:Schizosaccharomyces; D012984:Software; D049490:Systems Biology / Q000379:methods*; D013598:Systems Theory; D014584:User-Computer Interface