MCell4 and CellBlender Usage
MCell3 Documentation (for the previous MCell version)
- MCell Quick Reference Guide (HTML) (PDF)
- A comprehensive guide covering all of the MDL commands that can be used in an MCell simulation.
- MCell Reaction Syntax (PDF)
- A detailed guide to MCell's reaction syntax complete with diagrams and examples.
2021 Cell Modeling Workshop
- All Workshop Videos on YouTube (below are only those specific to MCell) (list)
- Particle-based spatial reaction/diffusion modeling with MCell (video)
- Building a complete spatial model of intracellular, inter-organelle transport using MCell - part 1 (video)
- Building a complete spatial model of intracellular, inter-organelle transport using MCell - part 2 (video)
- Model import and export, full circle between CellBlender and BioNetGen (video)
- MCell4 Python API tutorial (video)
- Spatial vs nonspatial models; CaMKII complex modeling (video)
2020 Cell Modeling Workshop
- All Workshop Videos on YouTube (below are only those specific to MCell) (list)
- Introduction to 2020 Cell Modeling Workshop (up to 24:40) (video)
- Particle-based Spatial Reaction/Diffusion Modeling with MCell (video)
- Starting with CelBlender, Modeling Diffusion and Reactions - part 1 (video)
- Modeling Diffusion and Reactions - part 2 & Building a Complete Spatial Model of Intracellular, Inter-Organelle Transport - part 1 (video)
- Building a Complete Spatial Model of Intracellular, Inter-Organelle Transport - part 2 (video)
- Movie Rendering with Blender (video)
- Geometry Import with Neuropil Tools - part 1 (from 2:05:45) (video)
- Geometry Import with Neuropil Tools - part 2 (video)
- Geometry Import with Neuropil Tools - part 3 & MCell4 Overview (video)
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.
