Spatial Rule-based Modeling of Cellular Biochemistry with MCell/ BioNetGen/ CellBlender

glbio mcell tutorial 2013

James Faeder and Markus Dittrich (MMBioS) 

Great Lakes Bioinformatics Conference 2013
May 14, 2013


In this tutorial we will introduce several simulation tools for the modeling of complex and spatially realistic biochemical and cellular systems: BioNetGen, MCell and CellBlender.

See the tutorial:

BioNetGen is a software for the specification and simulation of rule-based models of biochemical systems, including signal transduction, metabolic, and genetic regulatory networks; MCell (Monte Carlo cell) is a simulation package that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate the movements and reactions of molecules within and between cells — cellular microphysiology. Its companion program CellBlender is an integrated MCell model development, simulation and analysis package.

During the workshop we will introduce the relevant background and theory of biochemical modeling and then demonstrate how to use BioNetGen, MCell and CellBlender to create and run biochemical models.


Slides for the talk are linked below. The first set of slides covers

  • Multiscale Challenge (Dittrich)
  • Introduction to National Center for Multiscale Modeling of Biological Systems (Faeder)
  • BioNetGen Motivation and Intro (Faeder)

The second set of slides covers

  • Introduction to Microphysiological Simulations Using MCell (Dittrich)