Python Tutorials

These tutorials teach you how to build NEURON models in Python, progressing from the basics to a complete network simulation. If you are new to NEURON, start with the Scripting Basics tutorial, then work through the Ball-and-Stick series.

Python & NEURON Basics

A quick introduction for Python users new to NEURON: importing the module, creating sections, and running a simulation.

Introduction to Python

Scripting NEURON Basics

How to run Python scripts with NEURON, access HOC from Python, and use NEURON’s core objects.

Scripting NEURON basics

Basic Tutorials

• Introduction to Python
• Scripting NEURON basics

Ball-and-Stick Tutorial

Build a biophysically detailed neuron model step by step — from a single compartment to a multi-cell ring network:

1. Single compartment — create a soma with Hodgkin–Huxley channels

2. Add dendrite — attach a dendrite and observe signal propagation

3. Instrumentation — record, plot, and analyze results

4. Ring network — connect multiple cells into a network

Ball-and-Stick Tutorial

• Ball and stick 1: Basic cell
  • Load NEURON
  • Defining the cell morphology
  • Instrumentation
  • Run the simulation
  • Plot the results
  • Simulation studies
  • Exercise
  • Advanced exercise
• Ball and stick 2: Build a ring network of ball-and-stick cells
  • Generic cell class
  • Adjusting position and orientation
  • Construct and position our cells
  • A first synapse, and input via a NetStim
  • Running and plotting a simulation
  • Connecting the cells
• Ball and stick 3: Extensible network of cells
  • Loading libraries
  • Generic Cell class
  • Make a Ring class
  • Test the network
  • Explore effects of parameters
• Ball and stick 4: Parallel vs serial mode
  • Parallel communication in NEURON
  • Test MPI and Parallel NEURON
  • Back to the example
  • Test the model
  • Gathering spikes