NEURON Programmer’s Reference

This is the complete reference for NEURON’s Python and HOC programming interfaces. For hands-on introductions, see the Python tutorials or the NEURON scripting basics.

NEURON supports multiple programming languages. Most users work in Python, but HOC is also fully supported. See Accessing HOC from Python and HOC accessing Python for interoperability.

At a Glance

The most commonly needed classes and topics, organized by task:

Build Cell Morphology

Create and connect sections to define cell shape and topology.

Section — the fundamental building block
SectionList — group and iterate over sections
SectionRef — reference to a section
Topology — connecting sections
Geometry — length, diameter, 3-D points

Add Biophysics

Insert ion channels, set conductances, and define custom mechanisms.

Point Processes and Artificial Cells
insert(), range variables
MechanismType — enumerate available mechanisms
MechanismStandard — inspect mechanism parameters
KSChan — kinetic scheme channels
NMODL — the NMODL language

Stimulate & Record

Inject current, clamp voltage, and capture simulation output.

Vector — record(), play(), data storage
Standard Run Tools — finitialize, continuerun
CVode — variable time-step integration
SaveState / BBSaveState — checkpointing
FInitializeHandler — custom init actions

Build Networks

Wire cells together with synapses, spike detectors, and gap junctions.

NetCon — spike-triggered connections
ParallelContext — parallel and distributed simulation
ParallelNetManager — high-level network manager
LinearMechanism — linear circuit elements
StateTransitionEvent — discrete event models

Reaction-Diffusion

Model intracellular and extracellular chemistry.

Basic Reaction-Diffusion — overview of the rxd module
RXD Tutorials — hands-on examples
Impedance — frequency-domain analysis

Visualization & GUI

Plot results, display morphology, and build interactive interfaces.

Graph — time-series and X-Y plots
Shape / PlotShape — cell morphology display
RangeVarPlot — range variable visualization
Panel — custom GUI panels
Deck, VBox — GUI layout containers

Frequently Used Classes

Class	Purpose	Category
Vector	Record, store, and manipulate arrays of doubles	Data
NetCon	Connect a spike source to a synaptic target	Network
ParallelContext	Parallel and distributed simulation	Network
SectionList	Group sections for iteration	Morphology
CVode	Variable time-step integrator	Simulation
Random	Random number generation	Math
Matrix	Matrix operations	Math
Graph	Plot data	Visualization
Shape	Display cell morphology	Visualization
File	File I/O operations	Programming
MechanismType	Query available mechanisms	Model

Additional commonly used classes: Glyph, GUIMath, Impedance, KSChan, LinearMechanism, List, MechanismStandard, ParallelNetManager, PlotShape, Pointer, PtrVector, PWManager, RangeVarPlot, SectionBrowser, SectionRef, StringFunctions, SymChooser, TextEditor, Timer, ValueFieldEditor.

Commonly referenced topics: FunctionFitter, Printf (Formatted Output), Math.

See also the Index for a complete alphabetical listing.

Basic Programming

General-purpose programming facilities: math, strings, I/O, GUI design, dynamic code loading, and Python–HOC interoperability.

Model Specification

Define cell morphology, insert biophysical mechanisms, specify ions and channels, build networks, and model reaction-diffusion.

Simulation Control

Initialize, run, and manage simulations. Configure integrators, set environment variables, and control the interpreter.

Visualization

Plot simulation results, display cell morphology, and create interactive graphical interfaces.

Analysis

Programmatic and GUI-based tools for analyzing simulation output, including impedance analysis and curve fitting.