MCell Documentation

 
  • 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.
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    • News and Events

      July 8, 2021: MCell4 & Cellblender Release

      A brand new release of MCell with CellBlender with many new improvements such as Python API, native BioNetGen lanuage support and integration with Blender 2.93 is available for download here.

      The 2021 Cell Modeling Workshop will be held as a virtual workshop on July 12th-16th, 2021.

      July 12-16, 2021: Cell Modeling Workshop

      The 2021 Cell Modeling Workshop will be held as a virtual workshop on July 12th-16th, 2021.

      June 22-26, 2020: Cell Modeling Workshop

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