NEURON + Python Tutorial

A newer version of this tutorial is available

Thomas McTavish, Robert A. McDougal, N. Ted Carnevale, Michael L. Hines

Contents:

• Python Basics
  • Variables: Strings, numbers, and dynamic type casting
  • Lists
  • range()
  • For loops and iterators
  • Dictionaries
  • Functions
  • Classes
  • Importing modules
  • Pickling objects
• NEURON + Python Basics
  • What is NEURON?
  • Step 1: Import the neuron module into Python.
  • Step 2: Create a cell
  • Biophysical Mechanisms
  • Step 3: Insert a passive mechanism.
  • Step 4: Insert an alpha synapse.
  • Step 5: Set up recording variables.
  • Step 6: Run the simulation.
  • Step 7: Plot the results.
  • Step 8: Saving and restoring results.
• Ball-and-stick: 1 - Basic cell
  • Cell model design
  • Ball-and-stick model
  • Create our sections
  • Topology
  • Geometry
  • Biophysics
  • Instrumentation
• Ball-and-stick: 2 - Cell class
  • Ball and stick class
• Ball-and-stick: 3 - Basic cell
  • Extend BallAndStick with 3D location functions
  • Construct and layout our cells
  • Make a NetStim
  • Connect the cells
• Ball-and-stick: 4 - Ring Network Classes
  • Create a generic cell class
  • Define BallAndStick as an extension to the base Cell class
  • Make a Ring class
  • Test the network
  • Run a few networks
• Ball-and-stick: 5 - Parallel Net
  • Parallel communication in NEURON
  • Test MPI and Parallel NEURON
  • Import our modules
  • Parallelize Ring class
  • Test the net
  • Run parallel simulations
• SpikePlot Demo
  • Introduction
  • Import the module
  • Basic plot
  • SpikePlot variables
  • Multiple trains