NEURON is a simulation environment for modeling individual neurons and networks of neurons.
It was primarily developed by Michael Hines, John W. Moore, and Ted Carnevale at Yale
YALE
RapidMiner, formerly YALE , is an environment for machine learning, data mining, text mining, predictive analytics, and business analytics. It is used for research, education, training, rapid prototyping, application development, and industrial applications...
Duke University is a private research university located in Durham, North Carolina, United States. Founded by Methodists and Quakers in the present day town of Trinity in 1838, the school moved to Durham in 1892. In 1924, tobacco industrialist James B...
.
NEURON models individual neurons via the use of sections which are subdivided into individual compartments by the program, instead of requiring the user to manually create the compartments. The primary scripting language that is used to interact with it is hoc
Hoc (programming language)
hoc, an acronym for High Order Calculator, is an interpreted programming language that was used in the 1984 book The Unix Programming Environment to demonstrate how to build interpreters using Yacc....
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
interface is also available. The programs for it can be written interactively in a shell, or loaded from a file. NEURON supports parallelization via the MPI
Message Passing Interface
Message Passing Interface is a standardized and portable message-passing system designed by a group of researchers from academia and industry to function on a wide variety of parallel computers...
protocol. Also, starting with NEURON 7.0 parallelization is possible via internal multithreaded routines, for use on computers with multiple cores. The properties of the membrane channels of the neuron are simulated using compiled mechanisms written using the NMODL language.
NEURON along with the analogous software platform GENESIS
GENESIS (software)
GENESIS is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including subcellular processes, individual neurons, networks of neurons, and neuronal systems.GENESIS was developed in the Caltech laboratory of Dr. James M...
Computational neuroscience is the study of brain function in terms of the information processing properties of the structures that make up the nervous system...
in many courses and laboratories around the world.
Example
This example will create a simple cell, with a single compartment soma
Soma (biology)
The soma , or perikaryon , or cyton, is the bulbous end of a neuron, containing the cell nucleus. The word "soma" comes from the Greek σῶμα, meaning "body"; the soma of a neuron is often called the "cell body"...
The squid giant axon is the very large axon that controls part of the water jet propulsion system in squid. It was discovered by English zoologist and neurophysiologist John Zachary Young in 1936...
kinetics. Then, it will stimulate it using a stimulus, and run for 50 ms.
//create two sections, the body of the neuron and a very long axon
create soma, axon
soma {
//length is set to 100 micrometers
L = 100
//diameter is set to 100 micrometers
diam = 100
//insert a mechanism simulating the standard squid Hodgkin–Huxley channels
insert hh
//insert a mechanism simulating the passive membrane properties
insert pas
}
axon {
L = 5000
diam = 10
insert hh
insert pas
//the axon shall be simulated using 10 compartments. By default a single compartment is used
nseg = 10
}
//connect the distal end of the soma to the proximal end of the axon
connect soma(1), axon(0)
//declare and insert a current clamp into the middle of the soma
objref stim
soma stim = new IClamp(0.5)
//define some parameters of the stimulus: delay, duration (both in ms) and amplitude (in nA)
stim.del = 10
stim.dur = 5
stim.amp = 10
//load a default NEURON library file that defines the run routine
load_file("stdrun.hoc")
//set the simulation to run for 50 ms
tstop = 50
//run the simulation
run
If run from the GUI, a plot can be generated showing the voltage traces starting from the soma and the distal end of the axon. As expected, the action potential
Action potential
In physiology, an action potential is a short-lasting event in which the electrical membrane potential of a cell rapidly rises and falls, following a consistent trajectory. Action potentials occur in several types of animal cells, called excitable cells, which include neurons, muscle cells, and...
at the end of the axon arrives slightly later than it appears in the soma at the point of stimulation. The plot is membrane voltage versus time.
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