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Genetic Network Analyzer 8.4 now available

 Download GNA

 

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 8.4

 

The current version is GNA 8.4. In comparison with the previously distributed versions, GNA 8.3 has the following additional functionalities :

  • The editing and visualization of regulatory networks, in an SBGN-compatible format ;
  • The semi-automatic generation of a prototype model from the network structure.

 

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

 

Features associated with model-checking tools and 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

 

 

genome  network

Qualitative simulation performed on a genetic regulatory network

 

 

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

 

 

Academic license

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

Request it here.

 

Support documents

 

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.

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