CellBlender Tutorial

From BioNetWiki

Jump to: navigation, search

This page contains materials used for a tutorial on using CellBlender and MCell given at the at the 2015 q-bio summer school (Albuquerque) on July 15, 2015.

Contents

Getting Started

  1. Download Blender from here and follow the installation instructions.
  2. Download and follow the MCell installation instructions.
  3. Download CellBlender from here and following the instructions here. (Note: Don't download the version listed on the installation page.)

Intro Materials

Tutorial Examples

  1. Freely diffusing molecule (zipped .blend file)
  2. Adding a mesh object and first order decay (zipped .blend file)
  3. Bimolecular reactions (zipped .blend file)
  4. Lotka-Volterra - reaction limited (zipped .blend file)
  5. Lotka-Volterra - diffusion limited (zipped .blend file)
  6. Reactions on surfaces

Reference Materials

  1. MCell FAQ - Confused about units? The answer is here.
  2. MCell Documentation - Comprehensive documentation on MCell use and extensive video lectures and tutorials.
  3. Bartol et al. (2015) - Short article on MCell/CellBlender.
  4. Kerr et al. (2008) - Detailed description of simulation algorithms used in MCell3
Personal tools