MCell Documentation

 
  • 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.
  • 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.
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    • News and Events

      June 22-26, 2020: Cell Modeling Workshop

      The 2020 Cell Modeling Workshop will be held as a virtual workshop from June 22nd-26th, 2020.

      May 6, 2019: CellBlender for Windows 10 Release

      CellBlender for Windows 10 is available to download for the upcoming 2019 Cell Modeling Workshop.