GINsim

What is GINsim for ?

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 the modeling and simulation of genetic regulatory networks can be found in [2].

GINsim consists of a simulator of qualitative models of genetic regulatory networks based on a discrete, logical formalism (see [1]).

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.

Funding

DIAMONDS, Data Integration And Modelling: On a New Design to enable Systems biology

APO-SYS, An integrated approach of experimental biology, data mining, mathematical modeling, biostatistics, system engineering and molecular medicine

References