= Workshop 11: CompuCell3D Workshop Materials =
== Agenda ==
[[attachment:Workshops/Workshop11/CompuCell3DCourse2011.pdf|PDF]]

== Presentations ==
Introduction to multi-cell, multi-scale modeling - Introductory talk by James Glazier - [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/lectures/IntroductionToCompuCell/Glazier%20q-Bio%20Tutorial%20August%202011.pptx|PowerPoint]]| PDF

Introduction to CompuCell3D (Maciej Swat)  - [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/lectures/IntroductionToCompuCell/CompuCell_intro_2011.ppt|PowerPoint]] | [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/lectures/IntroductionToCompuCell/CompuCell_intro_2011.pdf|PDF]]

Initial Conditions in CompuCell3D: PIFF files and CellDraw (Mitja Hmeljak) - 
[[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/lectures/CellDraw_1.5.0_presentation_2011.pdf|PDF]]

Introduction to Pythion scripting in CompuCell3D -[[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/lectures/IntroductionToCompuCell/PythonScriptingInCompuCell_2011.pdf|PDF]]

Bioprinting video - [[http://www.youtube.com/watch?v=wtVvbzgW_gs|YouTube link]]

Merging CC3D and SBW/SBML (Julio Belmonte) - [[attachment:MergingCC3DandSBWSBML.pptx|PowerPoint]] | [[attachment:MergingCC3DandSBWSBML.pdf|PDF]] | [[attachment:MergingCC3DandSBWSBML.zip|Videos]]

== Examples: ==
=== Michael Rountree Files ===
 * [[attachment:RountreeInitializerPresentation.py]]
 * [[attachment:RountreeSteppablePresentation.py]]

=== Abbas's How To ===
 . '''[[Workshops/Workshop11/Materials/AbbasHowTo|Abbas's How to Simulate Using CC3D]]'''

 * [[attachment:Adhesion Parameter Values.doc]]

 * [[attachment:CNV-P-T1-T2 .pptx]]

 * [[attachment:CellDiffusionCalculatorSteppable.py]]

 * [[attachment:cellsort2D_negative_J.py]]

=== MiniCC3D ===
Set of Python script demonstrating how CC3D really works at the Python level. [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/MiniCC3D/|Download]]

=== Calculating Cell Diffusion Constant ===
Simple simulation demonstrating how to calculate diffusion constant of cells - the slope of the <r^2>/4 (as a function of time) is average diffusion constant of  cells - [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/CellDiffusion.zip|Download]]

=== Bacterium Macrophage Simulation ===
This is an attempt to simulate famous experimental movie in CC3D - [[http://www.youtube.com/watch?v=NN9EHZugwl8|movie link]]

CC3D simulation done by workshop participants assumes bacterium secretes chemical which attracts Macrophage - [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/BacteriumMacrophage.zip|Download]]

=== Morphogen-dependent cell growth - aka AdvancedCellsort ===
[[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/AdvancedCellsort.zip|Download]]

=== Cancer Stem Cells ===
Exercise - [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/Cancer%20stem%20cells.pdf|download assignment]]

CC3D model [[attachment:Heiko3_O2_ps.zip|Download]]

=== Vascular Tumor simulation (Abbas Shirinifard) ===
This is a simplified version of a simulation presented in this [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/Abbas_Paper.pdf|paper]].

Simulation code [[http://code.compucell3d.org/svn/cc3d/branch/Workshop08/Exercises/2011/VascularTumor.zip|Download]]

=== CC3D-SBW ===
Simple Oscillator  - [[attachment:SimpleOscillator.jan|Jarnac]]  | [[attachment:SimpleOscillator.sbml|sbml]]

ChemotaxisDemo

{{{
    PluginElmnt_2=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Chemotaxis"})
}}}
{{{
    ChemicalFieldElmnt=\
}}}
{{{
    PluginElmnt_2.ElementCC3D("ChemicalField",{"Name":"FGF","Source":"FlexibleDiffusionSolverFE"})
}}}