NEURON course exercises

These exercises are adapted from the 2018 NEURON summer course given in Atlanta, Georgia. You can also download the course archive.

 

  1. Introduction to the GUI
    Lipid bilayer model
     
  2. Interactive modeling
    Squid axon model
     
  3. The CellBuilder
    Constructing a ball and stick model, saving session files
     
  4. Using morphometric data
    The Import3D tool
     
  5. Scripting NEURON with Python
     
  6. Using NMODL files
    Single compartment model with HHk mechanism
     
  7. Using ModelDB and ModelView
    Neuroinformatics tools for finding and understanding models
     
  8. Reaction-diffusion
     
  9. Specifying inhomogeneous channel distributions
    with the CellBuilder
     
  10. Custom initialization
     
  11. Introduction to the linear circuit builder
    A two-electrode voltage clamp
     
  12. State and parameter discontinuities
     
  13. Bulletin board parallelization
    Speed up embarrassingly parallel tasks
     
  14. HOC exercises
    Introduction to the HOC programming language
     
  15. Multithread parallelization
     
  16. Networks: discrete event simulations with artificial cells
    Introduction to the Network Builder
     
  17. Networks: continuous simulation of nets with biophysical model cells
    Network ready cells from the CellBuilder
     
  18. Hopfield-Brody network in Python
     
  19. MPI Parallelization
     
  20. Using the Neuroscience Gateway Portal
     
  21. Numerical Methods Exercises