Automating Cell Construction with the Cell Reader

Abstract

In the previous chapter, we created a simple multi-compartmental neuron with a dendrite compartment, a soma, and an axon. The dendrite contained a synaptically activated channel and the soma contained voltage-activated Hodgkin—Huxley sodium and potassium channels. The script tutorial4.g, listed in Appendix B, contains the function definitions and commands used to construct this neuron, provide synaptic input to the cell, and plot the results of the simulation. In this tutorial, we will modify the script in order to construct the same neuron from a data file, using the GENESIS cell reader. The cell reader, which is implemented in the readcell command, allows one to build multi-compartmental neurons by reading cell parameters from a cell descriptor file. This file contains the names and dimensions of the compartments that will be used in the cell, along with the names of the channels and other elements that are contained within each compartment. The cell reader then uses this information to put together a cell and to establish the necessary messages between the various elements. This can significantly reduce the effort needed to construct a complex cell with many compartments and channels.