Genetic Network Analyzer

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract Genetic Network Analyzer (GNA) is a software tool for the modeling and simulation of genetic regulatory networks.

The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a ‘genetic regulatory network’ using knowledge about regulatory interactions in combination with gene expression data.

Genetic Network Analyzer consists of a simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential equations.

Instead of exact numerical values for the parameters, which are often Not available for networks of biological interest, the user of GNA specifies inequality constraints.

This information is sufficient to generate a state transition graph that describes the qualitative dynamics of the network.

The simulator has been implemented in Java and has been applied to the analysis of various regulatory systems, such as the networks controlling the initiation of sporulation in B. subtilis and the carbon starvation response in E. coli.

Note: The modeling and simulation of ‘genetic regulatory networks’ are currently subject to two (2) major constraints: incomplete knowledge about biochemical reaction mechanisms and a general absence of quantitative information on kinetic parameters and molecular concentrations.

The manufacturers of GNA have developed a qualitative modeling and simulation method that is able to satisfy the above constraints.

Classic features/capabilities of GNA are as follows:

1) Construct a model using the graphical user interface (GUI);

2) Parametrize the model in a qualitative way, by means of inequality constraints instead of exact numerical values;

3) Perform a qualitative simulation of the network, resulting in predictions adapted to available gene expression data;

4) Locate all steady states of the model and determine their stability;

5) Use model examples included in the distribution; and

6) Export and import models in Systems Biology Markup Language (SBML) format.

Features associated with model-checking tools and connected to GNA through the web-service architecture:

1) Specify biological properties of the qualitative dynamics of a network in temporal logic, using user friendly graphical interfaces; and

2) 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.

New features in release 8.0 --

The current version is GNA 8.0. In comparison with the previously distributed versions, GNA 8.0 has the following additional functionalities:

1) The editing and visualization of regulatory networks, in an Systems Biology Graphical Notation (SBGN)-compatible format; and

2) The semi-automatic generation of a prototype model from the network structure.

The GNA process --

1) Construct a model with the Genetic Network Analyzer graphical user interface --

2) Then, use the Genetic Network Analyzer to perform a qualitative simulation of the network --

A ‘simulation’ results -- in a state transition diagram that shows detailed information on the qualitative dynamics of the system.

3) Then, extract and display time trajectories of concentration variables.

4) Compare with experimental gene expression data.

This simulator (GNA) has been used to analyze a variety of regulatory system networks --

1) Carbon starvation response in E. coli.

2) Onset of virulence in E. chrysanthemi.

3) Quorum sensing in P. aeruginosa.

4) Initiation of sporulation in B. subtilis.

Note: A stand-alone version of Genetic Network Analyzer is available for FREE for non-profit academic research.

Acknowledgements --

GNA is developed in collaboration with the INRIA’s Ibis project team and uses the following open-source software:

1) JGraph (Java Graph Visualization and Layout).

2) SAT4J (a Java-based SAT (Boolean or propositional satisfiability) solver.

3) CUP [a LALR (Look-Ahead Left to Right) Parser Generator in Java].

The model checker at INRIA is NuSMV. NuSMV is a symbolic model checker.

Note: See G6G Abstract Number 20151R for additional product info from this manufacturer.

System Requirements

Contact manufacturer.


Manufacturer Web Site Genetic Network Analyzer

Price Free for non-profit academic research..

G6G Abstract Number 20152R

G6G Manufacturer Number 101123