8.4. Rat Neuromuscular Junction


The simulations and visualizations in this tutorial were generated using Blender 2.67 and CellBlender 1.0 RC. It may or may not work with other versions.

This tutorial is simply a follow-up to Section 4.5, Example Model: Acetylcholine Exocytosis and Miniature Endplate Current Generation at a realistic Neuromuscular Junction of Computational Neuroscience: Realistic Modeling for Experimentalists, ed. Dr. Erik Schutter.

The MCell MDLs and Blend file for this model are available here as a ZIP archive. The MDLs in this project required some hand-editing, because release patterns are not yet supported in CellBlender. As such, we have to be careful we don’t overwrite these hand-edited changes. Normally, when a user hits the Run Simulation button, it is actually exporting the MDLs and then running the simulation. However, there is an advanced option called Decouple Export and Run under the Preferences panel that is very useful for exactly this situation (i.e. when you need to run a simulation, but you don’t want to overwrite your existing MDLs).


Do not hit the Export Project button, unless you know what you are doing. Otherwise, you will overwrite hand-edited changes made to the MDLs.

After extracting the zip file, open rat_nmj.blend. First, we need to tell CellBlender where MCell is located. Under Project Settings, hit Set Path to MCell Binary, navigate to where you have downloaded MCell, select it, and hit the Set MCell Binary button. Next, hit the Run Simulation button. Once the simulation has completed, hit the Read Viz Data button. Hit Alt-a to play through the visualization data.