QBI NEURON Tutorial

An introductory NEURON tutorial for neuroscientists

Introduction to NEURON

NEURON is an advanced simulation environment for realistic modeling of biological neurons and neural circuits

NEURON was first developed in the early 1990’s and has been increasingly used by neuroscientists world-wide as a tool for single neuron and network simulation, with 1840 publications as of 31st December, 2016.

Many aspects of neural behaviour can be demonstrated with NEURON, for example, the influence of different channel types in the production or prevention of action potential generation. It is a powerful neuronal simulator that is able to mathematically compute the activation of many conductances simultaneously and describe the resulting electrical outcome both spatially and temporally within the neuron. Further, intra- and extra-cellular conditions such as temperature and ion concentration can be modelled effectively; the flexibility and detail NEURON provides can be adapted to many biological conditions.

Several predefined features are provided with NEURON, some of which we will use, are:

Additional standard mechanisms included in NEURON are:

There is an active community for NEURON who contribute a wide range of models and components shared on the NEURON database, ModelDB, for anyone to use (with appropriate citation).

Overview of the tutorial

The main aim of this course is to understand how you can produce a simulated electrophysiological response with the NEURON application.

  1. Simple Model: We will start with a simple model of a soma and single dendrite, commonly known as a “Ball and Stick” model and cover the basics of running a simple simulation.
  2. Complex Model: To provide a more realistic scenario, we will load actual Neurolucida data and create a model from experimental data.
  3. Synaptic Model: We will introduce NEURON’s own integrative language called HOC and then create a model with a simple synaptic input.
  4. Network Model: We will then proceed to the establishment of a simple network model.

Background knowledge

NEURON models electrophysiological data and a good background understanding of neuronal electrophysiology is essential for creating accurate models. This tutorial is a practical guide on how to input data into NEURON to create models so it will not cover any of the theories behind the algorithms. The major aspect of NEURON to be aware of, is that the basic building block is the segment component, which is a cylinder of uniform conductance based on cable theory.

Getting started

The tutorial assumes you have already installed NEURON on your system. If not, please go to Setup.

So let’s go!

STEP 1: Launch the GUI version of NEURON with nrngui

From your NEURON folder created during installation, click on nrngui. For those preferring the commandline, type the following from the NEURON directory:

load_file(“nrngui.hoc”)

You will get a tiny window called NEURON Main Menu mainmenu

Don’t lose this window! We will be using it to launch:

  1. Cell Builder
  2. Current clamp processes
  3. Simulation controls
  4. Output graphs
  5. Save our files
  6. Load our saved files

STEP 2: Setup your NEURON project

It is recommended to create a project to keep your model files together.

  1. Create a folder on your computer
  2. From the File menu, select working dir
  3. In the Directory text box, enter or select the project folder you created
  4. Click on Move To
  5. When you re-open NEURON at a later date, from the File menu, select recent dir to quickly find your folder again

Resources

What is NEURON

NEURON’s HH defined

Neuronal Cable Theory

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