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Neuron Software Package: A Basic Introduction. NMD Lab Jose M. [email protected] What is Neuron . Neuron is a simulation environment designed for modeling neurons and networks of neurons, developed by Yale University, Scientists.

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Neuron software package a basic introduction

Neuron Software Package:A Basic Introduction


Jose M.

[email protected]

What is neuron
What is Neuron.

  • Neuron is a simulation environment designed for modeling neurons and networks of neurons, developed by Yale University, Scientists.

  • Neuron provides tools for building, managing and using models specifically for the neuronal system.

Installation guide
Installation Guide

  • Visit:

  • Select your relevant operating system and install to selected location on your hard-drive.

Utilizing neuron single compartment cell
Utilizing Neuron:Single Compartment Cell

  • The neuron software architecture works off of .hoc files that define the majority of the parameters of the neuronal cell environment.

  • Our first example is that of an isopotential spherical cell with Hodgkin-Huxley currents, the surface area of the cell is 100um^2

A single compartment spherical cell
A single compartment Spherical Cell

  • We will learn how to

    • Create the model

    • Attach a stimulating electrode

    • Evoke an action potential

    • Show the time course of V_m

Step 1 build the interface required for simulation
Step 1: Build the Interface Required for Simulation

  • We will need 4 controls:

    • Controls for running simulation

      • This is the Neuron Main Menu, it controls all major facets of the environment

    • Controls for adjusting model parameters

      • Tools-> RunControlcreates a window that determines the parameters of how the simulation is run temporally.

    • Graphical Display of the simulation result

      • Graph-> Voltage Axis

    • Stimulation of the Model

      • Tools-> Point Processes-> Managers-> Point Manager

      • Here we define an Iclamp (current clamp)

Step 2
Step 2

  • Generate the geometry of the cell via the gui:

    • Build single compartment

    • Here we add HH, these are the Hodgkin-Huxley gating regime.

Step 3
Step 3

  • Once we have the cell geometry defined and the stimulation electrode. We can begin to perform experiments!

Step 4 using the interface we just built
Step 4: Using the Interface we Just built

  • Setting Stimulus Parameters:

    • Point process manager allows for modification of the stimulating process:

      • Use the spinner to increase and decrease “del” in ms.

      • Use direct entry to enter a value into the “dur” field in ms.

      • Type a mathematical expression into the “amp” 0+1 and then enter.


  • We now have:

    • RunControl Window: that delieneates the parameters of the simulation.

    • Graph Window: that serves to display the dependence of voltage on time.

    • PointProcessManagerWindow: that serves to modify the parameters of the process driving the simulation, in the current case a current clamp


  • First part:

    • Brief analysis on Nernst Potentials of most relevant ions.

  • Second part:

    • Linearized GHK Equation, solve for the relation algebraically.

  • Third part Neuron Simulation:

    • Simulate the Neuron for 100 ms with varying amplitudes.

    • Set the time via Tstop (100ms), this is total simulation time.

    • Set the duration of the Iclamp to (50ms)

    • Vary the current from 0.001 nA to the threshold where the cell can no longer respond (oscillations, no AP’s)