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Title of article :
GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks
Author/Authors :
A. Gonzalez Gonzalez، نويسنده , , A. Naldi، نويسنده , , L. S?nchez، نويسنده , , D. Thieffry، نويسنده , , C. Chaouiya، نويسنده ,
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روزنامه با شماره پیاپی سال 2006
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Abstract :
This paper presents GINsim,1 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.
Keywords :
Logical modelling , Wing imaginal disc , Dynamical simulation , Regulatory networks , Boundary formation
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