Neuron (software)

Neuron is a simulation environment for modeling individual and networks of neurons. It was primarily developed by Michael Hines, John W. Moore, and Ted Carnevale at Yale and Duke.

Neuron models individual neurons via the use of sections that are automatically subdivided into individual compartments, instead of requiring the user to manually create compartments. The primary scripting language is hoc but a Python interface is also available. Programs can be written interactively in a shell, or loaded from a file. Neuron supports parallelization via the MPI protocol.

Neuron is capable of handling diffusion-reaction models, and integrating diffusion functions into models of synapses and cellular networks. Parallelization is possible via internal multithreaded routines, for use on multi-core computers. The properties of the membrane channels of the neuron are simulated using compiled mechanisms written using the NMODL language or by compiled routines operating on internal data structures that are set up with Channel Builder.

Along with the analogous software platform GENESIS, Neuron is the basis for instruction in computational neuroscience in many courses and laboratories around the world.

Neuron features a graphical user interace (GUI), for use by individuals with minimal programming experience. The GUI comes equipped with a builder for single and multiple compartment cells, networks, network cells, channels and linear electric circuits. Single and multiple compartment cells differ in that multiple compartment cells features several "sections", each with potentially distinct parameters for dimensions and kinetics. Tutorials are available on the Neuron website, including for getting basic models out of the cell, channel and network builders. With these builders, the user can form the basis of all simulations and models.

Cell Builder allows the user to generate and modify stick figure cell structures. These sections form the basis of functionally distinct areas of the neuron.

The user can define functionally distinct groups of sections. Sections branching from one another can be labeled "dendrites," while another, single section that projects from the same central one can be labeled as the "axon." The user can define parameters along which certain values are variable as a function across a section. For instance, path length along a subset can be defined as a domain, the functions along which can then be defined later.