Workshop Resources for the "Developing Multi–Scale, Multi–Cell Biological Simulations with CompuCell3D and SBW" Joint Training Workshop - July 30th – August 3rd 2012, at the Hamner Institute for Health Sciences, Research Triangle Park, North Carolina

CompuCell3D Materials for the 2012 Workshop:

Presentations:

James Glazier's Talk: PDF | PPT

Jim Sluka's CC3D Liver models slides (PPT): attachment:Sluka CC3D Liver Models.ppt

Introduction to CompuCell3D (Maciej Swat): PDF

Introduction to Python Scripting in CC3D (Maciej Swat): PDF

Merging CC3D and SBML: PDF | PPT (Updated)

Tutorials and Examples

BacteriumMacrophage: ZIP

CellsortPython - simple cell growth : ZIP

Reaction-Diffusion example: FitzHughNagumo.zip

CellsortPython - cells growing in response to concentration: ZIP

Cell growth in response to concentration, division and differentiation: ZIP

Cell growth in response to concentration - cell dictionaries: ZIP

Cell growth in response to concentration - scalr field visualization: ZIP

Cell growth in response to concentration - external force: ZIP

Measuring diffusion of cells : ZIP

Cell Cycle Model: zip

Cell Cycle exercise solution: zip

John Tyson's Model: paper | solution

Vasculogenesis 2D version 1: zip

Vasculogenesis 2D version 2: zip

Average Concentration in Cells (Python solution) : zip

Average Concentration in Cells (C++ steppable - nee to be compiled) :zip

Average Concentration in Cells (simulatio using C++ steppable ) : zip

CompuCell3D System Requirements:

Windows

* CC3D Source and Binaries web page

Mac OS X

* Current CC3D versions are supported on Mac OS X 10.6.x ("Snow Leopard" 2009 release) and 10.7.x ("Lion" 2011 release), on 64bit intel hardware.

NOTE about older Mac OS X operating system releases - such as 10.5.8:

CC3D 3.4.2 is the last pre-compiled binary distribution of CompuCell3D to support Mac OS X 10.5.x (AKA Leopard). The CC3D 3.4.2 version is however lacking several features of the more current CC3D releases, such as TWedit++ to automatically generate working simulation code, parallel execution with OpenMP, CellDraw to graphically prepare the initial cell layout in simulations, etc.

To run the current CC3D versions such as 3.6.2, you may consider upgrading your Mac system to at least 10.6.x -- unless 10.5.8 is required for some other software that may not be compatible with more recent Mac OS X releases. But since Mac OS X 10.8 was just released a couple of days ago, more and more software updates will only be available for more recent Mac OS X versions.

For users who are very proficient with compiling software libraries for Mac OS X, it may be possible to compile CC3D 3.6.2 for Mac OS X 10.5.8. This is however quite a complex process, since it'll require installing not only Apple's Xcode developer tools, but also an up-to-date GCC compiler distribution (which may have to be first compiled itself, if there are no available GCC precompiled distributions for 10.5.8); and then all the required 3rd party libraries such as Qt, PyQt, VTK, etc.

Linux

* CC3D Source and Binaries web page

Useful 3rd-Party Software Links:

Python

* Main Python Website

* Python 2.7.2 download page

Text Editors

* Twedit++ - simple but powerful and cross platform programmer's editor, bundled with current CC3D versions.

* Windows users: Notepad++

* Mac OS X users: TextWrangler

* Linux users: Linux has many programmer's editors and they are almost always bundled with your Linux distribution. Our favorite is Kate editor. GEdit is not bad either.