GINsim Provides support for modeling and simulation of genetic regulatory networks.
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design simulate model simulate network genetic regulatory network genetic network modelling

GINsim Description

Provides support for modeling and simulation of genetic regulatory networks. 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. Taking this into account, formal simulation and modelling 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. 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.NOTE: GINsim is freely available for academics. Contact the developers for other uses. Requirements: · Java 1.4 What's New in This Release: New Features: · logical functions: logical parameters can now be generated by writing logical functions. These functions support parenthesis and logical operators ("!", "&" and "|" as "NOT", "AND" and "OR", respectvely). · These logical functions automatically generate the corresponding parameters, which are then listed (and grayed out as they cannot be edited) in the "parameter" panel. The interface for function definition is still expected to change. · input nodes: the values of these components are determined by their initial values (implicit self-regulation). Any defined parameters will be ignored. · the basal value is now defined as a regular logical parameter (deselecting all incoming interactions). · model reduction: this new feature enables the definition of a "reduced" version of a model by "hidding" a user-selected list of components. See http://gin.univ-mrs.fr/GINsim/publications/naldi2009.html · documentation export: export the list of components along with their annotation and logic...

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