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Section: New Software and Platforms

Genetic Network Analyzer (GNA)

Keywords: Bioinformatics - Gene regulatory networks - Qualitative simulation - Model checking

Genetic Network Analyzer (GNA) is a tool for the qualitative modeling and simulation of gene regulatory networks developed in the IBIS project. The input of GNA consists of a model of the regulatory network in the form of a system of piecewise-linear differential equations (PLDEs), supplemented by inequality constraints on the parameters and initial conditions. From this information, GNA generates a state transition graph summarizing the qualitative dynamics of the system. In order to analyze large graphs, GNA allows the user to specify properties of the qualitative dynamics of a network in temporal logic, using high-level query templates, and to verify these properties on the state transition graph by means of standard model-checking tools, either locally installed or accessible through a remote web server. GNA is currently distributed by the company Genostar, but remains freely available for academic research purposes. The current version is GNA 8.7.2 . In comparison with the previously distributed versions, GNA 8.7.2 has the following additional functionalities: (1) it supports the editing and visualization of regulatory networks, in an SBGN-compatible format, (2) it semi-automatically generates a prototype model from the network structure, thus accelerating the modeling process, and (3) it allows models to be exported in the SBML Qual standard.