www.compucell3d.org; python mac OSX, windows; open source software modeling environment and pde solver

http://www.compucell3d.org/

CompuCell is an open source software modeling environment and pde solver. It is largely used for cellular modeling (foams, tissues, etc.), however, efforts are being made to include fluid simulation capabilities. Created in collaboration between groups at IU and Notre Dame, CompuCell provides an easy user interface for complex cellular modeling.
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Integration with SBW

We have conducted a preliminary integration of CompuCell3D with Systems Biology Workbench (SBW) 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.

see : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007190

Binaries

Source Code and ChangeLog

SVN Repository

To download from our repository, use your favorite svn client and download from:

http://trac.compucell3d.net/svn/cc3d_svn/trunk/core

Known Issues and Requirements

  • Python 2.5
  • Ubuntu users must install python-qt4
  • ———
  • Python and MAC OSX

    Python comes pre-installed on Mac OS X, but due to Apple’s release cycle, it’s often one or even two years old. The overwhelming recommendation of the « MacPython » community is to upgrade your Python by downloading and installing a newer version from the Python standard release page.

    If you are using Mac OS X 10.5, see the Leopard wiki page for detailed information.

    If you’re just curious…

    You don’t have to download anything. You can run a Python interpreter by double-clicking on Applications / Utilities / Terminal (here’s a picture), then typing « python » into the window that opens up.

    You’ll see a prompt that looks like this:

    Python 2.3.5 (#1, Mar 20 2005, 20:38:20)
    [GCC 3.3 20030304 (Apple Computer, Inc. build 1809)] on darwin
    Type "help", "copyright", "credits" or "license" for more information.
    >>>
    

    (On Mac OS X 10.3 (Panther), it will say « Python 2.3.0 », an older version.)Try typing « 2 + 2 » and hit « Enter »:

    >>> 2 + 2
    4
    >>>
    

    You’ve just evaluated your first Python expression. It’s a simple environment, but good enough to work through the Python tutorial.By the way, if you download the recommended upgrade mentioned at the top of this page, the « IDLE » development environment will make working through the tutorial a bit easier.

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