A Library for the Compartmental Simulation of Neurons

J. Strout, Department of Neuroscience, University of California, San Diego

Send correspondence to:

J. Strout
Department of Neuroscience,
University of California, San Diego
La Jolla, CA 92093-0608 (USA)
jstrout@ucsd.edu

KEY WORDS: neural simulation, compartmental modeling, C++, class library

Abstract
(Neuroscience-Net, Volume 2, Article #10013; August 25, 1997)

A programming library ("CONICAL") is presented which assists in the construction of compartmental models of neurons. The library consists of approximately 20 classes in the C++ programming language. Standard input and output are used, and the code has been co-developed under several operating systems, to ensure maximum portability. The library is non-monolithic, i.e. portions of it may be used as needed without the entire library present. Complex classes were derived from simpler ones in several steps to provide flexible opportunities for customization; and as a C++ library, the simulation code may be readily embedded in larger applications. Documentation, including introductory material and examples, is provided in hypertext format and can be viewed with any tables-capable World-Wide Web browser. Classes provided include cylindrical compartments, passive and active ion channels, and synapses, including one based on Markov kinetic models. Performance of the library was compared to the Genesis and Neuron neural simulators on a simple action potential simulation. The CONICAL program required less user-written code and much less memory than the equivalent Genesis script, and ran more than twice as fast; it was also significantly faster and more memory-efficient than the comparable Neuron script. CONICAL provides an alternative simulation environment which may be useful when portability, extensibility, or efficiency is needed, especially on personal computers or single-processor workstations.

Key words: neural simulation, compartmental modeling, C++, class library