@article {14,
	title = {GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.},
	journal = {Bio Systems},
	volume = {84},
	year = {2006},
	month = {2006 May},
	pages = {91-100},
	abstract = {<p>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.</p>},
	keywords = {Animals, Computer Simulation, Drosophila, Software, Wing},
	issn = {0303-2647},
	author = {Gonzalez, A Gonzalez and Naldi, A and S{\'a}nchez, L and Thieffry, D and Chaouiya, C}
}
