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    CompuCell3D

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

    Abstract  CompuCell3D is an open source modeling environment and
    partial differential equation (PDE) solver, primarily used to study 'cellular
    behavior'.

    CompuCell3D was initially developed to help researchers (biologists
    and physicists) model materials and tissues without having to dedicate
    resources to developing code that will reproduce existing software.

    CPM - Foundations for Tissue --

    CompuCell3D is based on the Cellular Potts Model (CPM).

    While the Potts model was originally developed to study ferromagnetic
    and crystalline systems; in the late 80's and 90's, Francois Graner and
    James Glazier extended the Potts model to study the coarsening of
    foam and sorting of biological cells.

    Since then modelers have continued to use the CPM to study foam,
    morphogenesis, biofilms, cancer, as well as many other biological and
    physical systems.

    CompuCell3D developed as a framework --

    The manufacturer developed CompuCell3D as a framework for Glazier-
    Graner-Hogeweg (GGH) model aka Cellular Potts Model (CPM)
    simulations.

    Unlike specialized research code, CompuCell3D is a 'simulation
    environment' that allows researchers to rapidly build and run shareable
    GGH-based simulations.

    It greatly reduces the need to develop custom code and its adherence to
    open-source standards ensures that any such code is shareable.

    CompuCell3D supports non-programmers by providing visualization
    tools, an eXtensible Markup Language (XML) interface for defining
    simulations, and the ability to extend the framework through specialized
    modules.

    The C++ computational kernel of CompuCell3D is also accessible
    using the open-source scripting language Python, allowing users to
    create complex simulations without programming in lower-level
    languages such as C or C++.

    Unlike typical research code, changing a simulation does Not require
    recompiling CompuCell3D.

    Users define simulations using CompuCell3D XML (CC3DML)
    configuration files and/or Python scripts.

    CompuCell3D reads and parses the CC3DML configuration file and
    uses it to define the basic simulation structure, then initializes
    appropriate Python services (if they are specified) and finally executes
    the underlying simulation algorithm.

    CompuCell3D is modular: each module carries out a defined task.

    CompuCell3D terminology calls modules associated with index copies
    or index-copy attempts 'plug-ins'.

    Some plug-ins calculate changes in effective energy, while others
    (lattice monitors) react to accepted index copies, e.g., by updating
    generalized cells’ surface areas, volumes or lists of neighbors.

    Plug-ins may depend on other plug-ins. For example, the Volume plug-
    in (which calculates the volume-energy constraint) depends on
    VolumeTracker (a lattice monitor), which, as its name suggests, tracks
    changes in generalized cells’ volumes.

    When implicit plug-in dependencies exist, CompuCell3D 'automatically
    loads' and initializes dependent plug-ins.

    In addition to plug-ins, CompuCell3D defines modules called
    'steppables' which run either repeatedly after a defined intervals of
    'Monte Carlo Steps' or once at the beginning or end of the simulation.

    Steppables typically define initial conditions, alter cell states, update
    fields or output intermediate results.

    CompuCell3D includes a Graphical User Interface (GUI) and
    visualization tool, 'CompuCell Player' (also referred to as Player).

    From Player the user opens a CC3DML configuration file and/or Python
    file and hits the “Play” button to run the simulation.

    Player allows users to define multiple 2D or 3D visualizations of
    generalized cells, fields or various vector plots while the simulation is
    running and save them automatically for post-processing.

    Integration with SBW --

    The manufacturer has conducted a preliminary integration of
    CompuCell3D with the Systems Biology Workbench (SBW) (see G6G
    Product Number 20453) to link to Subcellular models.

    As a result users can select the level of detail in their models while
    working within a single integrated framework.

    System Requirements  

    Contact manufacturer

    Manufacturer   

    CompuCell3D was created in collaboration between groups at IU and
    Notre Dame.

    Indiana University Bloomington
    107 S. Indiana Ave.
    Bloomington, IN 47405-7000
    USA
    Tel: (812) 855-4848
    And
    The Biocomplexity Institute
    Indiana University
    212 S. Hawthorne Drive
    Bloomington, IN 47405-7105 USA
    Tel: 812.855.1304
    Fax: 812.855.5533
    E-mail: bioc@indiana.edu

    And

    CompuCell Team
    Dr. Jesus Izaguirre
    Laboratory for Computational Life Sciences
    Department of Computer Science and Engineering
    University of Notre Dame
    325 Fitzpatrick Hall of Engineering
    Notre Dame, Indiana 46556 USA
    E-mail: compucell@cse.nd.edu

    Manufacturer's Web Site   

    http://www.compucell3d.org/

    Price   Open source

    G6G Product Number  20452

    G6G Manufacturer Number 104079
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