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Updated: May 26, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
Logical modelling of gene regulatory networks with GINsim
Claudine Chaouiya1, Aurélien Naldi, Denis Thieffry
1Instituto Gulbenkian de Ciência, Oeiras, Portugal. chaouira@igc.gulbenkian.pt
Abstract:
Discrete mathematical formalisms are well adapted to model large biological networks, for which detailed kinetic data are scarce. This chapter introduces the reader to a well-established qualitative (logical) framework for the modelling of regulatory networks. Relying on GINsim, a software implementing this logical formalism, we guide the reader step by step towards the definition and the analysis of a simple model of the lysis-lysogeny decision in the bacteriophage λ.
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