NEURON Course Exercises

These exercises are adapted from the 2018 NEURON summer course given in Atlanta, Georgia.

  1. Introduction to the GUI

    • Lipid bilayer model
  2. Interactive Modeling

    • Squid axon model
  3. Using the CellBuilder

    • Constructing a ball and stick model, saving session files
  4. Working with Morphometric Data

    • The Import3D tool
  5. NEURON scripting exercises

  6. Using NMODL files

    • Single compartment model with HHk mechanism
  7. Using ModelDB with NEURON

    • Neuroinformatics tools for finding and understanding models
  8. Reaction-Diffusion Exercises

  9. Inhomogeneous Channel Distribution

  10. Custom Initialization

  11. Introduction to the Linear Circuit Builder

    • A two-electrode voltage clamp
  12. State and parameter discontinuities

  13. Batch runs with bulletin board parallelization

    • Speed up embarrassingly parallel tasks
  14. HOC Exercises

    • Introduction to the HOC programming language
  15. Multithreaded paralellization

  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 (NSG) portal

  21. Numerical Methods Exercises

  22. Electrotonic Analysis with NEURON