Workshop 11: CompuCell3D Workshop Materials

Agenda

PDF

Presentations

Introduction to multi-cell, multi-scale modeling - Introductory talk by James Glazier - PowerPoint| PDF

Introduction to CompuCell3D (Maciej Swat) - PowerPoint | PDF

Initial Conditions in CompuCell3D: PIFF files and CellDraw (Mitja Hmeljak) - PDF

Introduction to Pythion scripting in CompuCell3D -PDF

Bioprinting video - YouTube link

Merging CC3D and SBW/SBML (Julio Belmonte) - PowerPoint | PDF | Videos

Examples:

Michael Rountree Files

• RountreeInitializerPresentation.py

• RountreeSteppablePresentation.py

Abbas's How To

• Abbas's How to Simulate Using CC3D

• Adhesion Parameter Values.doc

• CNV-P-T1-T2 .pptx

• CellDiffusionCalculatorSteppable.py

• cellsort2D_negative_J.py

MiniCC3D

Set of Python script demonstrating how CC3D really works at the Python level. 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 - Download

Bacterium Macrophage Simulation

This is an attempt to simulate famous experimental movie in CC3D - movie link

CC3D simulation done by workshop participants assumes bacterium secretes chemical which attracts Macrophage - Download

Morphogen-dependent cell growth - aka AdvancedCellsort

Download

Cancer Stem Cells

Exercise - download assignment

CC3D model Download

Vascular Tumor simulation (Abbas Shirinifard)

This is a simplified version of a simulation presented in this paper.

Simulation code Download

CC3D-SBW

Simple Oscillator - Jarnac | sbml

ChemotaxisDemo

    PluginElmnt_2=CompuCell3DElmnt.ElementCC3D("Plugin",{"Name":"Chemotaxis"})

    ChemicalFieldElmnt=\

    PluginElmnt_2.ElementCC3D("ChemicalField",{"Name":"FGF","Source":"FlexibleDiffusionSolverFE"})