title: GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.
abstract: This paper presents GINsim, a Java software suite devoted to the qualitative modelling, analysis and simulation of genetic regulatory networks. Formally, our approach leans on discrete mathematical and graph-theoretical concepts. GINsim encompasses an intuitive graph editor, enabling the definition and the parameterisation of a regulatory graph, as well as a simulation engine to compute the corresponding qualitative dynamical behaviour. Our computational approach is illustrated by a preliminary model analysis of the inter-cellular regulatory network activating Notch at the dorsal-ventral boundary in the wing imaginal disc of Drosophila. We focus on the cross-regulations between five genes (within and between two cells), which implements the dorsal-ventral border in the developing imaginal disc. Our simulations qualitatively reproduce the wild-type developmental pathway, as well as the outcome of various types of experimental perturbations, such as loss-of-function mutations or ectopically induced gene expression.
authors.affiliation: Institut de Biologie du Développement de Marseille (IBDM), CNRS/INSERM/Université de la Méditerranée, Campus de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
authors.forename: A Gonzalez
authors.initials: AG
authors.lastname: Gonzalez
authors.forename: A
authors.initials: A
authors.lastname: Naldi
authors.forename: L
authors.initials: L
authors.lastname: Sánchez
authors.forename: D
authors.initials: D
authors.lastname: Thieffry
authors.forename: C
authors.initials: C
authors.lastname: Chaouiya
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004330:Drosophila; D012984:Software; D014921:Wings, Animal / Q000254:growth & development