==== 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: [[attachment:Glazier_Raleigh_Lecture_July_2012.pdf|PDF]] | [[attachment:Glazier_Raleigh_Lecture_July_2012.pptx|PPT]] Jim Sluka's CC3D Liver models slides (PPT): [[attachment:Sluka CC3D Liver Models.ppt|attachment:Sluka CC3D Liver Models.ppt]] Introduction to CompuCell3D (Maciej Swat): [[BinDoc/cc3d_binaries/Presentations/Introduction_To_CompuCell/CompuCell_intro_2012.pdf|PDF]] Introduction to Python Scripting in CC3D (Maciej Swat): [[BinDoc/cc3d_binaries/Presentations/Introduction_To_CompuCell/PythonScriptingInCompuCell_2012.pdf|PDF]] Merging CC3D and SBML: [[Workshops/Workshop12/Materials?action=AttachFile&do=get&target=MergingCC3DandSBWSBML.pdf|PDF]] | PPT (Updated) == Tutorials and Examples == !BacteriumMacrophage: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/BacteriumMacrophage.zip|ZIP]] !CellsortPython - simple cell growth : [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython.zip|ZIP]] Reaction-Diffusion example: [[attachment:FitzHughNagumo.zip]] !CellsortPython - cells growing in response to concentration: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython_1.zip|ZIP]] Cell growth in response to concentration, division and differentiation: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython_2.zip|ZIP]] Cell growth in response to concentration - cell dictionaries: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython_3.zip|ZIP]] Cell growth in response to concentration - scalr field visualization: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython_4.zip|ZIP]] Cell growth in response to concentration - external force: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellsortPython_5.zip|ZIP]] Measuring diffusion of cells : [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/CellDiffusion.zip|ZIP]] Cell Cycle Model: [[attachment:CellCycle.zip|zip]] Cell Cycle exercise solution: [[attachment:CellCycle2.zip|zip]] John Tyson's Model: [[attachment:CellCycle_TysonNovak2001.pdf|paper]] | [[attachment:CellCycleTyson.zip|solution]] Vasculogenesis 2D version 1: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/Vascular1.zip|zip]] Vasculogenesis 2D version 2: [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/Vascular2.zip|zip]] Average Concentration in Cells (Python solution) : [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/PixelTrackerExample.zip|zip]] Average Concentration in Cells (C++ steppable - nee to be compiled) :[[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/AverageConcentration.zip|zip]] Average Concentration in Cells (simulatio using C++ steppable ) : [[BinDoc/cc3d_binaries/Tutorials/HamnerWorkshop/PixelTrackerExample_c++.zip|zip]] -------- ===== CompuCell3D System Requirements: ===== '''Windows''' * [[SrcBin|CC3D Source and Binaries web page]] '''Mac OS X''' * [[SrcBin|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:'' -~ ~-[[http://sourceforge.net/projects/cc3d/files/3.4.2/mac/|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''' * [[SrcBin|CC3D Source and Binaries web page]] -------- ===== Useful 3rd-Party Software Links: ===== '''Python''' * [[http://www.python.org/|Main Python Website]] * [[http://www.python.org/download/releases/2.7.2/|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: [[http://sourceforge.net/projects/notepad-plus/|Notepad++]] * Mac OS X users: [[http://www.barebones.com/products/textwrangler/|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.