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Section: New Software and Platforms
GNA
Genetic Network Analyzer
Keywords: Model Checking - Bioinformatics - Gene regulatory networks - Qualitative simulation
Scientific Description: Genetic Network Analyzer (GNA) is the implementation of methods for the qualitative modeling and simulation of gene regulatory networks developed in the IBIS project-team.
Functional Description: 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.
Release Functional Description: (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.
News Of The Year: New mode of distribution from the IBIS web site. Tutorial on the use of the model formalism for analyzing synthetic genetic circuits.
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Participants: Hidde de Jong, Michel Page and Delphine Ropers
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Publications: Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks - Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens