NeuronC Neural Simulation Language

This page provides information about NeuronC, a neural circuit simulation language that allows a user to construct a realistic biophysically-based model of a neural circuit (1 to 10,000 neurons) and simulate a physiology experiment on it.

Features:

It's free (source code included).
Runs under virtually any Unix system.
Includes drivers for VGA, X11, PS.
Comes with programs for plotting and displaying data.
Manual comes with distribution.
New additions to the simulator.
NeuronC is described in a methods paper., J. Neurosci. Methods (1992) 43: 83-108.
Click here to receive the NeuronC distribution.

Click here for microcircuitry simulation projects:

Capabilities:

Neural elements:
- cable (a portion of a dendritic tree or axon)
- sphere (a neuron's soma)
- synapse (chemical synapse that transfers information from one neuron to the next.)
- channel (voltage-sensitive membrane channel)
  - Sodium
    - Hodgkin-Huxley (m3h).
    - Markov sequential-state (noise or macroscopic).
  - Potassium
    - Hodgkin-Huxley (n4).
    - Markov sequential-state (noise or macroscopic).
    - KA (fast inactivating).
    - Ih, slow inactivating.
    - KCa calcium-activated.
  - Calcium
    - Voltage-activated (m3h)
    - Calcium diffusion with shells.
- gap junction (electrical synapse)
  - voltage-gated
  - modulated by second messenger (cycA, cycG)
  - battery
  - resistor
- Conversion from branched cables to compartments.
  - automatic setting of compartment size, numbering.
  - automatic "condensation" of closely-coupled compartments according to criterion.
  - modifications allowed during the simulation.
- Numerical integration methods:
  - Euler integraion (explicit).
  - Fully-implicit.
  - Crank-Nicolson (combination of Euler, implicit: more accurate, faster).
Schematic of synaptic model in NeuronC:

A synapse is represented in NeuronC by a series of separable filters that define how the presynaptic voltage signal affects the postsynaptic membrane.

Speed

Measurements of simulation speed based on the number of compartments solved per second are usually inappropriate and can be incorrect. Read about the measurement of simulation speed. NeuronC was originally based on Mike Hines' "Cable" neuron simulator package which was an interpreted language that gave the user great flexibility. However, NeuronC has been greatly enhanced to allow the user to simulate a neural circuit, display it in 3D, and simulate a complete physiology experiment. Both interpreted and native C versions of NeuronC are included in the NeuronC distribution.

3-d visualization schemes

NeuronC can produce accurate 3D views of a neural circuit model. For more realistic perspective and surfaces, NeuronC creates a scene for rendering with the "Povray" ray-tracer. Neural elements can be displayed from different perspectives with a wide variety of lighting, surface color and texture. Povray is easily compiled and is available for many types of operating system.