Genetic Network Analyzer 7.0 now available

Model and simulate genetic regulatory networks

GNA (Genetic Network Analyzer) is a computer tool for the qualitative modeling and simulation of genetic regulatory networks. GNA assists you in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Moreover, it allows you to simulate the qualitative behavior of the network in response to external perturbations. The mathematical models created with GNA can be tested against observed properties of the network.

New features in release 7.0

New features are associated with model-checking tools now connected to GNA through a webservice architecture:

• Specify biological properties of the qualitative dynamics of a network in temporal logic, using user friendly graphical interfaces
• Test these properties on the state transition graph by means of standard model-checking tools, either locally installed or accessible through a remote web server

Classic features

Classic features of GNA are the following:

• Construct a model using the graphical user interface
• Parametrize the model in a qualitative way, by means of inequality constraints instead of exact numerical values
• Perform a qualitative simulation of the network, resulting in predictions adapted to available gene expression data
  
• Locate all steady states of the model and determine their stability
• Use model examples included in the distribution
• Export and import models in SBML format

Outline of GNA approach

Use cases

GNA has already been used to analyze a variety of regulatory networks:

• carbon starvation response in E. coli
• onset of virulence in E. chrysanthemi
• quorum sensing in P. aeruginosa
• initiation of sporulation in B. subtilis

Publications citing GNA

• D. Ropers, H. de Jong, M. Page, D. Schneider, J. Geiselmann (2006), Qualitative simulation of the carbon starvation response in Escherichia coli, BioSystems, 84(2):124-152.
• J-A. Sepulchre, S. Reverchon, W. Nasser (2007), Modeling the onset of virulence in a pectinolytic bacterium, Journal of Theoretical Biology, 44(2):239-257.
• A. Usseglio Viretta, M. Fussenegger (2004), Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa, Biotechnology Progress, 20(3):670-678.
• H. de Jong, J. Geiselmann, G. Batt, C. Hernandez, M. Page (2004), Qualitative simulation of the initiation of sporulation in Bacillus subtilis, Bulletin of Mathematical Biology, 66(2):261-99

Academic license

A stand-alone version of GNA is available for FREE for non-profit academic research.

Request it here.

Support documents

• Download Installation guide
• Download Tutorial

Acknowledgements

GNA is developed in collaboration with INRIA's Ibis project team and uses the following open-source software: JGraph, SAT4J, and CUP.

The model checker at INRIA is NuSMV.