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    IOGMA Genetic Network Analyzer

    Category  Cross-Omics>Pathway Analysis/Tools

    Abstract  IOGMA 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 1.5 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.

    The current version is GNA 6.0 running on the IOGMA® platform version
    3.4. In comparison with the previously distributed version, GNA 6.0 has
    the following additional features:

    1) A finer-grained representation of the qualitative dynamics, better
    adapted to available gene expression data.

    2) A module for locating all steady states of a qualitative model and
    determining their stability.

    3) The export of the state transition graph to standard model-checking
    tools in order to automate the analysis of important model properties.

    4) The export and import of models in Systems Biology Markup
    Language (SBML) format.

    The GNA process --

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

    a) Model examples are included.

    b) The GNA Tutorial helps guide you through the model-building
    process, to define appropriate variables, parameters, and constraints.

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

    a) Instead of exact numerical values for the parameters, often Not
    available for networks of biological interest, specify qualitative
    constraints.

    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 Helix Group at INRIA
    Grenoble - Rhône-Alpes 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].

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

    System Requirements  

    To install and comfortably work with GNA, the following hardware and
    software resources are necessary:

    Linux Fedora Core 4 or MacOS or Windows XP

    Environment Java version 1.5 or later. The virtual machine proposed by
    SUN MicroSystems is available at http://java.sun.com.

    512 Mb of RAM. GNA can run with less than 512 Mb of memory, but the
    size of the models that can be treated are reduced accordingly.

    100 Mb of disk space to install the environment. Some additional disk
    space is needed for temporary files.

    GNA has been tested with the configurations described above. This
    does not mean that it will not function in a different environment (e.g.
    with a different version of Linux, or with another Java virtual machine),
    but no guarantees can be given for these alternative configurations.

    Manufacturer   Home office; see web site for international locations.

    Genostar
    Head Office: 78 bis, avenue Henri Martin, 75116 Paris France
    Sales / Service / Research & Development Group:
    60 rue Lavoisier, 38330 Montbonnot France
    Tel. +33 4 76 97 10 70
    E-mail: info@genostar.com
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