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

Abbas's How To

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"})

Workshops/Workshop11/Materials (last edited 2011-09-10 20:45:04 by 149-159-1-113)