Constructing Neural Circuits and Networks

Abstract

In this chapter, we demonstrate how to use GENESIS to set up a simple network of biologically realistic neurons. This will not be a “neural network” in the usual sense of a network of highly abstract units with no direct connection to biological neurons (such as a backpropagation network). Rather, the approach we take is to simulate a group of biological neurons at a moderate level of detail and then connect them in a network. In the process we discuss a number of GENESIS functions that are used for this purpose, as well as a few script commands that have not been described earlier in this book. Our examples are taken from a tutorial simulation called Orient_tut, which is a simplified model of orientation selectivity originally written by Upinder S. Bhalla. This tutorial contains several script files, of which about half deal with setting up the XODUS graphical user interface. We do not discuss these scripts in this chapter; the GENESIS commands used to set up the interface are described in Chapter 22, “Advanced XODUS Techniques.” The emphasis in this chapter is on showing you how to use GENESIS commands whose primary purpose relates to simulation of networks of neurons. Commands that have been discussed in detail in other chapters are mentioned only briefly here. Another example of a large network simulation in GENESIS is provided in Chapter 9, on the piriform cortex simulation.