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    PROTON

    Category  Cross-Omics>Agent-Based Modeling/Simulation/Tools

    Abstract  PROTON (PROTotyping Object Networks) is an Integrative
    Modeling System (IMS).

    The purpose of the system is to support the modeling of large-scale
    systems by using integrative methods. Each installation of PROTON
    supports multiple users and it accesses different data-sources.

    The models are stored in separate services which are transparently
    managed by the system.

    The manufacturers approach includes models for the design of
    biochemical networks as objects, processes and systems.

    At the start, information from dynamically adopted data-sources are
    extracted and fused as molecular objects.

    In the second step, biochemical processes are identified interactively
    and large-scale state charts are automatically constructed from
    integrated data.

    Finally, networks of reactions are detected in the state charts and they
    are used to step wisely build the structure of the dynamic systems.

    PROTON Data-sources --

    PROTON is using content from molecular databases for the integrative
    modeling of biochemical networks. To extract information from data-
    sources you must have a login for each system.

    Without any further tools PROTON is only able to access relational
    databases (MySQL, Oracle, PostgreSQL) for the extraction of
    information.

    If you want to access non-standard databases (flat-files, websites etc.)
    the mediator BioDataServer (BioDataServer is an integrated information
    system of molecular and clinical data that integrates various
    databases) has to be plugged between PROTON and the data-source.

    For evaluation purposes, the manufacturer installed several molecular
    databases at their site related to the topic of gene regulatory networks, e.
    g. BIND, DIP, Ecocyc (see G6G Product Number 20231), MINT,
    RegulonDB, TRANSFAC (see G6G Product Number 20121), and
    UniProt using the manufacturers local relational database system.

    Furthermore, BioDataServer is providing a virtual relational access to
    the ‘molecular databases’ KEGG, BRENDA, MD-Cave and OMIM.  

    Note: PROTON is Not providing the molecular databases.

    PROTON Objects --

    The object layer of PROTON is an object-oriented modeling system.
    Because modeling is user-centric, each user has to be enabled to
    dynamically define his own types of molecular objects which should be
    part of a metabolic network.

    In addition, the flexible extraction, integration and fusion of information
    from different molecular data-sources lead to an automated
    construction of object-oriented metabolic networks.

    These on-the-fly generated networks are analyzed using interactive ad
    hoc queries.

    For the specification of the model the manufacturer uses the 'static
    classes' diagram which is part of the Unified Modeling Language (UML)
    standard. Internally the manufacturer uses the CORBA IDL specification.

    This is the reason why the structure and the content of each model can
    be easily integrated into object-oriented (OO) applications.

    PROTON Processes --

    'State charts' provide a dynamic view of biochemical networks.

    In the process layer of PROTON only the structure of state charts have to
    be modeled. Then using a specific view concept, state charts are
    automatically constructed from the objects formerly integrated into the
    model.

    Each view represents a different interpretation of the integrated
    information.

    Different implemented graph-based queries are used to search for
    networks inside the automatically generated state charts.

    The pathways found can then be exported to different formats, e.g.
    Graph Modeling Language (GML), MetaTool and Systems Biology
    Markup Language (SBML).

    PROTON Systems --

    The modeling of mechanistic systems requires the definition of the
    systems structure.

    Using the manufacturer's integrative approach, large-scale networks
    stemming form molecular databases are automatically included in
    models of biochemical systems.

    By assigning functions to each reaction, defining initial states and
    computing time courses the dynamic behavior of a biochemical
    systems is made available.

    The manufacturer's simulation model computes 'continuous
    processes' as well as 'discrete events'.

    Models can be save in the SBML format for further computing, e.g. for
    the optimization or the structural analysis of a system.

    System Requirements  

    Contact manufacturer

    Manufacturer   

    PROTON has been initiated by the MARG project, sponsored by the
    German Research Council (DFG).
    Andreas Freier
    Bioinformatics and Medical Informatics Department
    Technical Faculty
    Bielefeld University
    Germany
    E-mail: afreier@techfak.uni-bielefeld.de

    Manufacturer's Web Site   

    http://tunicata.techfak.uni-bielefeld.de/proton/web/main.jsp?dir=Overview

    Price   Contact manufacturer

    G6G Product Number  20454

    G6G Manufacturer Number 104081
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