2 - The Neuron Simulation Environment in Epilepsy Research

Abstract

NEURON has long been recognized for its facility with mechanistic models of single cells that involve complex anatomical and biophysical properties. Where models of individual neurons are concerned, NEURON's domain extends “down” to the level of subcellular mechanisms including ion accumulation, diffusion and transport; chemical reactions; deterministic and stochastic gating of voltage- and ligand- dependent ion channels. Its domain extends “up” to the level of the extracellular milieu close to the cell membrane, i.e. local concentrations and electrical field, which is sufficient for modeling phenomena such as extracellular ion accumulation and extracellular stimulation and recording. NEURON has a special programming language called NMODL that can be used to enlarge its library of biophysical mechanisms (active currents, buffers, diffusion, exchange/pumps etc.) and also to define new types of synapses and artificial spiking cells that can interact with NEURON's event delivery system. NMODL offers many examples of how NEURON allows modelers to work with familiar concepts and focus on the biology, while shielding them from computational details. Its notation for specifying dynamics is very similar to kinetic schemes or differential equations.