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    SYCAMORE

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

    Abstract  SYCAMORE (SYstems biology Computational Analysis and
    MOdeling Research Environment) is a web-based system that provides
    you with a facilitated access to a number of tools and methods in order
    to 'build models' of biochemical systems, view, analyze and refine them,
    as well as perform quick simulations.

    SYCAMORE integrates different online applications as well as locally
    installed software.

    It provides user guidance for the sequence of steps associated with
    model building (especially based on database knowledge), model
    checking, simulation and analysis of results.

    Moreover, it offers some unique features, e.g. access to protein
    structure-based parameter estimation.

    Thus, it does Not compete with web-based applications like WebCell
    (see G6G Product Number 20457), VCell (see G6G Product Number
    20440) or JSim which are online simulation and analysis tools, but
    rather should serve as a kind of 'expert system' facilitating the setting up
    of the models.

    To really analyze a final model in detail SYCAMORE interfaces with
    locally installed tools like COPASI (see G6G Product Number 20296)
    and does Not intend to substitute or compete with this class of tools.

    SYCAMORE aids the user in ensuring that their files are compatible with
    the Systems Biology Markup Language (SBML) file standard for
    biochemical models.

    This facilitates the exchange and re-useability of kinetic models in
    systems biology.

    SYCAMORE also facilitates the searching of enzymatic reaction kinetics
    databases such as BRENDA and SABIO-RK which contain kinetic
    parameters and kinetic equations that are required for setting up a
    kinetic model.

    SYCAMORE Use Case --

    Suppose the user is interested in simulating the first two (2) steps of
    glycolysis in human hepatocytes.

    First a model has to be set-up.

    For this, SYCAMORE provides an interface to the SABIO-RK database to
    permit the user to locate and select the relevant kinetic data for these
    two (2) reaction steps.

    Once the data have been selected and sent to SYCAMORE, the
    parameters can be adjusted in the SYCAMORE editor, e.g. to make the
    units used consistent.

    SYCAMORE also allows the user to add further reactions, e.g. to make
    the system open and define an influx of glucose and an efflux of
    fructose-6-phosphate.

    SYCAMORE will then enable the user to check the model for
    completeness as regards the kinetic equations and their parameters.

    If parameters are missing, SYCAMORE provides search tools to locate
    relevant data for parameter estimation and the ability to estimate
    parameters using protein structural data or perform a classical
    parameter estimation using experimental data and locally installed
    software.

    In the case of the protein structural data, electrostatic distances
    between related proteins are computed and the kinetic parameters for
    the electrostatically most similar protein can be chosen.

    A parameter sensitivity analysis can also be performed.

    Once the model is complete, a simulation can be carried out on the
    SYCAMORE server using COPASI with SYCAMORE displaying a plot of
    the resulting time course or by launching locally installed software, e.g.
    COPASI or ProMoT (see G6G Product Number 20332).

    System Requirements  

    SYCAMORE is a web-browser-based application running on Tomcat
    and currently supporting the Internet Explorer, Firefox, Mozilla web
    browsers running on Linux, Mac and Windows operating systems.

    It is mainly based on Java Server Pages (JSP) technology.

    Manufacturer   

    SYCAMORE is a joint project of the Molecular and Cellular Modeling
    Group (MCM) and Scientific Databases and Visualization Group (SDBV)
    at EML Research, as well as the department for Modeling of Biological
    Processes at the University of Heidelberg.

    EML Research gGmbH
    Villa Bosch
    Schloss-Wolfsbrunnenweg 33
    D-69118 Heidelberg
    Germany

    And

    Institute for Zoology
    BIOQUANT
    Im Neuenheimer Feld 267
    69120 Heidelberg
    Germany

    Manufacturer's Web Site   

    http://sycamore.eml.org/sycamore/

    Price   Contact manufacturer

    G6G Product Number  20456

    G6G Manufacturer Number 104083
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