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    JigCell

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

    Abstract  JigCell is a suite of ‘cell cycle modeling’ tools. It is also an
    effort to develop and maintain an ‘open source modeling’ environment
    for computational biology.

    JigCell's goal is to support building and testing models for studying
    complex ‘biochemical regulatory’ systems in general, and the cell cycle
    control system in particular.

    JigCell currently includes a 1) Model builder, 2) Run manager, 3)
    Comparator, and 4) Automatic parameter estimator.

    The manufacturers hope to soon add a numerical bifurcation analysis
    package.

    1) JigCell Model Builder --

    The JigCell Model Builder (JCMB) aides the modeler in defining a
    system to be modeled using Systems Biology Markup Language
    (SBML). JCMB uses a spreadsheet interface, allowing a large amount
    of data to be displayed in an organized manner.

    In addition to allowing the modeler to define chemical species,
    equations, and relationships, JCMB also provides the ability to define
    events that occur when a user-defined condition is met.

    The models created with JCMB can be used in conjunction with the
    other JigCell tools to simulate the behavior of the model, and to
    evaluate the ability of the model to match the phenomena the model is
    meant to represent.

    The JCMB allows the user to define a 'regulatory network' model using a
    spreadsheet interface. The JCMB provides a number of functionalities
    for both a first-time user and an expert modeler.

    The first of these is the ability to define all the necessary components of
    a regulatory network model. JCMB allows the user to specify the
    reaction equations, functions, rate laws, and conservation relations that
    define a complete model.

    In addition, JCMB also allows the modeler to specify units and events.
    An event, such as cellular division, can be defined by specifying a
    condition that must be met to trigger the event, and the changes that
    result due to the event.

    A major goal of JCMB is to minimize the time and errors associated with
    translating a 'wiring diagram' for a regulatory network to a set of
    equations. JCMB accomplishes this through its spreadsheet interface.

    As the user enters reaction equations, rate laws, and functions into their
    respective spreadsheets, several other spreadsheets are updated to
    track the species, parameters, equations [Ordinary Differential
    Equations (ODEs) and rule equations], and conservation relations
    associated with the model.

    After the user has finished defining a model using JCMB, this model
    can be used with the other JigCell tools to simulate the response of the
    model to given conditions.

    The JigCell Model Builder uses SBML Level 2 to define a model based
    on the data the user provides.

    There are 10 different spreadsheets for model data; each spreadsheet
    is associated with a particular tab. There are eight (8) tabs for the
    different SBML components in a model (reactions, functions, rules,
    compartments, species, parameters, units and events).

    There is one (1) tab for the Conservation Relations that exist in a model,
    and one (1) tab for the equations, both ODEs and rule equations.

    2) JigCell Run Manager --

    The JigCell Run Manager (JCRM) allows a user to specify a set of
    specifications for simulation runs using a spreadsheet interface. Each
    row of the spreadsheet describes the information necessary for a
    single simulation run.

    JCRM serves two (2) chief purposes. The first is to organize related
    simulation runs, allowing the user to run and view the results of either
    the entire ensemble or of a single simulation. The second is to provide
    the specifications needed to run a simulation that matches a particular
    experiment.

    This specification allows for another program such as the JigCell
    Comparator (see below...) to generate an assessment of how well
    experimental data matches simulation output.

    To specify a simulation run, the user must provide a model, a
    parameter set, an initial condition set, and a simulator parameter set.
    These are all specified using a spreadsheet interface. These sets are
    called 'basal settings' and the three (3) types are parameter, initial
    condition, and simulator.

    a) Basal ‘parameter sets’ are initially derived from the parameters of an
    existing model. The user may then use an editor to derive new
    parameter sets from these and any subsequently derived sets.

    b) Basal ‘initial condition’ sets are initially derived from the 'initial
    conditions' of an existing model. The user may then use an editor to
    derive new initial condition sets from these and any subsequently
    derived sets.

    c) Basal ‘simulator parameter’ sets are initially discovered through
    Open Agent Architecture (OAA) calls to find available simulators. The
    user may then user an editor to derive new simulator parameter sets
    from these and any subsequently derived sets.

    3) JigCell Comparator --

    The Comparator is an integrated package of Java tools for performing a
    quantitative analysis on a collection of data sets. 'Core tools' for the
    system are focused around data entry, transformation, and analysis.

    Additional tools can be created and linked with the Comparator. Domain
    users customize the Comparator by adding and removing tools.

    JigCell is a suite for 'cell cycle modeling' that includes the Comparator.

    The 'cellcycle module' is the collection of Comparator tools used by
    JigCell.

    This module customizes entry of experimental data, supports dynamic
    data collection from models using the JigCell Model Builder and Run
    Manager, and performs ‘objective-based comparisons’.

    4) JigCell Automatic parameter estimator --

    Parameter Estimation (both in terms of allowing the user to search for
    good parameter values to a model by hand and allowing the computer
    to perform automated searches for good parameter values) is a major
    focus of the JigCell project.

    The manufacturers have done extensive work toward building tools to
    support both user-based and automated parameter estimation.
    However, at this time the parameter estimation tools are Not integrated
    with the other components of the JigCell system.

    A parameter estimator takes a biological model, experimental data, and
    the relationship between the model and data.

    Using this information the parameter estimator uses numerical tools to
    vary the parameters to the model looking for the parameters that best fit
    the experimental data.

    The manufacturer’s most current parameter estimation software is PET
    (Parameter Estimation Toolkit). PET is a graphical user interface (GUI)
    for discovering rate constants, of molecular network models, that fit
    experimental data.

    It is designed for use by ‘theoretical biologists’ to build ‘regulatory
    network’ models and compare the models to experimental results.

    PET contains many features intended to ease and quicken the model
    building process. To do this PET:

    a) Provides a GUI for entering a mathematical model [using the JigCell
    Model Builder (see above...)];

    b) Stores multiple sets of parameters and initial conditions (basal sets);

    c) Provides means for users to define changes to the model
    parameters and initial conditions (called simulation definitions) to
    mimic experiments;

    d) Simulates models using one or more basal set and simulation
    definition;

    e) Estimates parameters using a global or local parameter search
    algorithm;

    f) Plots simulations and experimental data in a grid of plots for visual
    comparison; and g) Provides undo/redo functionality.

    System Requirements  

    Contact manufacturer

    Manufacturer   

    JigCell is a joint effort by members of the Departments of Biology and
    Computer Science at Virginia Tech.
    Their goal is to advance the state of the art for modeling in Systems
    Biology.
    Virginia Polytechnic Institute and State University
    Blacksburg, VA 24061-0002

    Manufacturer's Web Site   

    http://jigcell.biol.vt.edu/software.php

    Price   Free for use under the DARPA BioSPICE user license.

    G6G Product Number  20471

    G6G Manufacturer Number 104096
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