Section: New Software and Platforms
Genetic Network Analyzer (GNA)
Keywords: Bioinformatics - Gene regulatory networks - Qualitative simulation - Model checking
Genetic Network Analyzer (GNA) is the implementation of methods 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 8.7.1 . In comparison with the previously distributed versions, GNA 8.7.1 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.