MCell Quick Reference Guide (HTML) (PDF) A comprehensive guide covering all of the MDL commands that can be used in an MCell simulation.
Spatial Stochastic Modeling with MCell and CellBlender (PDF) This book chapter chapter provides a brief introduction to the theory and practice of spatial stochastic simulations with a focus on MCell and CellBlender.
MCell Reaction Syntax (PDF) A detailed guide to MCell's reaction syntax complete with diagrams and examples.
2015 MCell Workshop
- Welcome and Introduction to the Workshop (video)
- Overview of MCell Methods (video)
- Realistic Model of Synapses in Hippocampal Neuropil (video)
- Introduction to Rule-Based Modeling with BioNetGen and RuleBender (video)
- Weighted Ensemble Sampling in Spatial Stochastic Simulations (video)
- Introduction to Generative Modeling with CellOrganizer (video)
- Training Parametric Models (video)
- Diffeomorphic Modeling in CellOrganizer (video)
2014 MCell Workshop
- Welcome and Introduction to the Workshop (video)
- Overview of MCell Methods (video)
- Realistic Model of Synapses in Hippocampal Neuropil (video)
- Introduction to Rule-Based Modeling of Biochemical Systems with BioNetGen and RuleBender (video)
- Specifying a Rule-Based Model (video)
- Image-Derived Spatiotemporal Models of Subcellular Organization, Differentiation and Perturbation (video)
- Diffeomorphic Modeling in CellOrganizer (video)
- Training Parametric Models (video)
2013 MCell Workshop
- Welcome and Introduction to the Workshop (PDF, video)
- Introduction to Microphysiological Simulations Using MCell (PDF, video)
- Introduction to CellBlender and Model Geometry Creation (video)
- Introduction to Monte Carlo Methods for Diffusion and Reaction in Solution (PDF, video)
- Introduction to Rule Based Modeling with MCell (PDF, video 1, video 2)
2012 MCell Workshop
Book Chapter on Model Creation with Blender Supplemental material for a 2009 book chapter entitled Rapid Creation, Monte Carlo Simulation, and Visualization of Realistic 3D Cell Models.
