Neuron (software)

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Neuron
Basic data

developer Michael Hines, John W. Moore, and Ted Carnevale
Current  version 7.3
(April 3, 2013)
operating system Cross-platform
programming language C , C ++ , FORTRAN
category Neuron simulation
License GNU GPL
http://www.neuron.yale.edu/neuron/

NEURON is a simulation environment for models of individual neurons and neural networks . The program was essentially developed by Michael Hines, John W. Moore, and Ted Carnevale at Yale and Duke Universities in the USA . NEURON is optimized for the calculation of cable equations and therefore particularly suitable for neuron models with several compartments . Since version 7.3 it is also possible to simulate diffusion-reaction equations with NEURON and to incorporate these into the neuron and synapse models.

The program is primarily controlled using the HOC scripting language ; there is also a Python interface. The programs can be written interactively in a shell environment or loaded from a file. NEURON has a graphical user interface (GUI) that can be operated even without programming knowledge. The GUI can be used to construct cells with one or more compartments, networks, ion channels, and linear electrical circuits . In the case of more complex cells, individual parameter values ​​can be defined for each of the compartments, for example for the dimensions or the kinetics of the channels. The ion channels of the neuron model are simulated by precompiled mechanisms that are either written in NMODL programming language or defined by data structures created by a GUI tool (the Channel Builder).

NEURON supports parallel programming using the MPI protocol. Since version 7.0, parallelization can also be performed by internal multithreading routines to support computers with multiple cores .

NEURON is used worldwide for research and teaching in the field of computational neuroscience .

Application example

The following sample code creates a simple neuron model with a single compartment as the soma and multiple compartments as the axon . The dynamics of the membrane potential are described by the classical Hodgkin-Huxley equations . The program continues to generate an electrical stimulus and runs the simulation for 50 ms. 

//Erzeuge zwei Abschnitte, den Zellkörper und ein sehr langes Axon
create soma, axon

soma {
	// Die Länge des Somas ist 100 Mikrometer
	L = 100
	// Der Durchmesser ist ebenfalls 100 Mikrometer
	diam = 100
	// Füge die klassischen Hodgkin–Huxley-Kanäle ein
	insert hh
	// Füge die passiven Eigenschaften der Zellmembran hinzu
	insert pas
}
axon {
	L = 5000
	diam = 10
	insert hh
	insert pas
	// Unterteilt das Axon in 10 Kompartimente. Standardmäßig wird nur eins simuliert.
	nseg = 10
}

// Verbinde das proximale Ende des Axons mit dem distralen Ende des Somas
connect axon(0), soma(1)

// Deklariere den Stimulus (ein konstanter Strom) und setze ihn in die Mitte des Somas
objref stim
soma stim = new IClamp(0.5)

// Definiere einige Stimulusparameter: Verzögerung und Dauer (beide in ms), sowie Amplitude (in nA)
stim.del = 10
stim.dur = 5
stim.amp = 10

// Lade NEURONs Standard-Bibliothek, die die "run"-Routine enthält
load_file("stdrun.hoc")
// Lege eine Simulationszeit von 50 ms fest
tstop = 50

// Lass die Simulation laufen
run()

The result of this simulation can be displayed in the form of a plot showing the membrane potential as a function of time. Since the soma has been stimulated, the action potential appears there earlier than at the distal end of the axon.

Web links

Individual evidence

  1. ^ Romain Brette et al .: Simulation of networks of spiking neurons: A review of tools and strategies. In: Journal of Computational Neuroscience. 23, 2007, pp. 349-398, doi: 10.1007 / s10827-007-0038-6 .
  2. ↑ neuron.yale.edu
  3. ↑ neuron.yale.edu