GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks. 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.

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  1. Matache, Mihaela T.; Matache, Valentin: Logical reduction of biological networks to their most determinative components (2016)
  2. Chaves, Madalena; Carta, Alfonso: Attractor computation using interconnected Boolean networks: testing growth rate models in \itE. coli (2015)
  3. Zinovyev, A.: Overcoming complexity of biological systems: from data analysis to mathematical modeling (2015)
  4. Acary, Vincent; de Jong, Hidde; Brogliato, Bernard: Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems (2014)
  5. Bérenguier, D.; Chaouiya, C.; Monteiro, P.T.; Naldi, A.; Remy, E.; Thieffry, D.; Tichit, L.: Dynamical modeling and analysis of large cellular regulatory networks (2013)
  6. Thomas, R.: Remarks on the respective roles of logical parameters and time delays in asynchronous logic: an homage to El Houssine Snoussi (2013)
  7. Veliz-Cuba, Alan; Buschur, Kristina; Hamershock, Rose; Kniss, Ariel; Wolff, Esther; Laubenbacher, Reinhard: AND-NOT logic framework for steady state analysis of Boolean network models (2013)
  8. Chaouiya, C.; Naldi, A.; Remy, E.; Thieffry, D.: Petri net representation of multi-valued logical regulatory graphs (2011)
  9. Didier, Gilles; Remy, Elisabeth; Chaouiya, Claudine: Mapping multivalued onto Boolean dynamics (2011)
  10. Naldi, Aurélien; Remy, Elisabeth; Thieffry, Denis; Chaouiya, Claudine: Dynamically consistent reduction of logical regulatory graphs (2011)
  11. Siebert, Heike: Analysis of discrete bioregulatory networks using symbolic steady states (2011)
  12. Richard, Adrien: Positive circuits and maximal number of fixed points in discrete dynamical systems (2009)
  13. Chaouiya, Claudine; Remy, Elisabeth; Thieffry, Denis: Petri net modelling of biological regulatory networks (2008)