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    ByoDyn

    Category  Cross-Omics>Pathway Analysis/Tools

    Abstract  ByoDyn is a 'computational framework' that can be used to
    study the dynamical behavior of gene regulatory networks (GRNs) and
    for parameter estimation in uni- and multicellular models.

    Recent 'systems biology' approaches have given a second life to
    classical biochemical kinetics methods. It is becoming a routine task to
    build models of increasing complexity on a given gene regulatory,
    signal transduction or metabolic network or pathway of interest.

    One of the main problems in building such models is the determination
    of the parameters underlying each modeled equation or process.

    ByoDyn has been designed to provide an easily extendable
    'computational framework' to deal with the estimation of parameters in
    highly uncharacterized models.

    There are five (5) main features/capabilities of ByoDyn:

    1) Run quantitative simulations of unicellular or multicellular
    biochemical networks both deterministically and stochastically.

    2) Perform analysis of the sensitivity of the system with respect to the
    parameters of the model.

    3) Estimate the numerical values of the biochemical parameters that
    match a given set of experimental data along 'time' for any of the
    system's nodes.

    4) Use the Fisher information matrix to help in designing optimal
    experiments for the calibration problem.

    5) Determine the global shape of the parameter space thanks to Monte
    Carlo sampling coupled with cluster analysis and Principal Component
    Analysis (PCA).

    ByoDyn Simulations --

    ByoDyn uses Systems Biology Markup Language (SBML) format files to
    run unicellular systems or a homemade format for multicellular models.

    A parser based on libSBML has been developed to build the system of
    (nonlinear) ordinary differential equations (ODEs).

    Note: LibSBML is an open-source programming library to help you
    read, write, manipulate, translate, and validate SBML files and data
    streams.

    It is Not an application itself (though it does come with example
    programs), but rather a library you can embed in your own applications.

    ByoDyn uses several routines from SciPy (The SciPy library is built to
    work with NumPy arrays, and provides many user-friendly and efficient
    numerical routines such as routines for numerical integration and
    optimization) to solve the above problem.

    Also, the package LSODA (Livermore Solver for Ordinary Differential
    equations), is called because of its ability to switch automatically
    between both stiff and non-stiff integrators when necessary.

    As a secondary possibility ByoDyn can also make external calls to:

    a) Octave (Octave is a high-level language, primarily intended for
    numerical computations. It provides a convenient command line
    interface for solving linear and nonlinear problems numerically, and for
    performing other numerical experiments using a language that is
    mostly compatible with MATLAB);

    b) OpenModelica (OpenModelica is an object-oriented, declarative,
    multi-domain 'modeling language' for component-oriented modeling of
    complex systems);

    and c) XPPAUT (XPPAUT is a tool for solving differential equations,
    difference equations, delay equations, functional equations, boundary
    value problems, and stochastic equations);

    which is an advanced approach in order to solve other system
    equations such as differential algebraic equations (DAEs), events or
    delays via delay differential equations (DDEs).

    ByoDyn uses several functions to create PostScript or Portable Network
    Graphics (PNG) plots such as trajectories of the 'node concentration'
    along time for unicellular systems and cell matrices where the steady
    state node concentration is shown by color intensity.

    Sensitivity, identifiability, optimal experimental design and many other
    functions also render to appropriate graphs.

    ByoDyn Sensitivity analysis --

    The sensitivity analysis of the system along time with respect to a
    specific parameter is also performed.

    This step allows you to discriminate the parameters that are less
    affecting the dynamics of the system and that therefore might be
    excluded from the optimization routines.

    Global sensitivity can be explored thanks to the Monte Carlo sampling
    and principal component analysis (PCA) of the resulting cluster of
    solutions.

    ByoDyn Parameter estimation --

    If temporal quantitative data about the expression of the nodes is known
    along time, ByoDyn uses state of the art optimization algorithms to
    obtain the numerical values of the biochemical parameters that
    reproduce the given experimental behavior.

    The manufacturer has implemented different global and local
    optimization methods to obtain the best set of parameters in each
    particular case.

    ByoDyn Optimal experimental design --

    Analysis of the covariance matrix for the change in the fitness function
    with respect to the parameters has lead to the implementation of
    optimal experimental design approaches.

    Fisher information matrix analyses are executed to assess which point
    results are more informative for the ‘model calibration’ problem.

    System Requirements  

    ByoDyn is an object oriented (OO), Python based, program that makes
    use of several 'open source' libraries freely available for non-
    commercial use:

    The PORT library from Netlib for Newtonian optimizations; the SciPy
    package version 0.6.0 for scientific libraries in Python, including the
    ODE solvers; and the libSBML (Gnu LGPL) library version 3.2.0 for
    handling SBML files.

    The program has been tested on Linux Fedora Core 2 and 4 and on
    Mac OS X platforms and its migration to any other platform is
    straightforward.

    Manufacturer   

    Computational Biochemistry and Biophysics Laboratory (CBBL)
    Research Unit on Biomedical Informatics (GRIB)
    Barcelona Biomedical Research Park (PRBB)
    C/Doctor Aiguader, 88
    E-08003 Barcelona, Spain
    Tel: 34-93-3160504
    Fax: 34-93-3160550
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