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Welcome to GINsim

GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of genetic regulatory networks.

Recent developments in functional genomics have generated large amounts of data on gene expression and on the underlying regulatory mechanisms. This has resulted in the progressive mapping of complex regulatory networks. As these networks usually include numerous intertwined feedback circuits, gaining an understanding of their spatio-temporal behaviour defies the intuition of the biologists. In this respect, formal modelling and simulation tools become a necessary complement to experimental tools. As precise information on molecular mechanisms and the value of kinetic parameters are currently difficult to establish, qualitative methods offer a highly attractive approach to model and analyse essential properties of genetic regulatory networks.
General information on modelling and analysis of genetic regulatory networks can be found in [1].

GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism.

GINsim allows the user to specify a model of a genetic regulatory network in term of asynchronous, multivalued logical functions, and to simulate and/or analyse its qualitative dynamical behaviour [2].


GINsim is OS independent (Linux, Mac OS 10.3+, Windows).

Feel free to grab it at the downloads section and please contact us with your comments or suggestions.


References

  1. de Jong H.  2002.  Modeling and simulation of genetic regulatory systems: a literature review.. J Comput Biol. 9(1):67-103.
  2. Chaouiya C, Naldi A, Thieffry D.  2012.  Logical Modelling of Gene Regulatory Networks with GINsim.. Methods in molecular biology (Clifton, N.J.). 804:463-79.


by Dr. Radut