Introduction

This tutorial is intended to be a "quick start" to creating simulations with GENESIS. It should give you enough information to let you quickly begin creating cells and small networks with GENESIS. One way to use the tutorial is to go through it at a leisurely pace, exploring all the links to detailed information and documentation as you create models and perform the exercises. Another way is to take the most direct path, creating models without always understanding the details of what you have done. If you opt for this path, be sure to return to pick up the details when your lack of understanding makes progress difficult. Take your pick!

The tutorial makes frequent references and links to sections of the GENESIS Reference Manual. This is primarily a summary of the syntax used by the GENESIS Script Language Interpreter, the commands which it recognizes, and of the GENESIS ``objects'' that are available for constructing simulations. It also refers to chapters in The Book of GENESIS, by James M. Bower and David Beeman (published by TELOS/Springer-Verlag), familiarly called "The BoG".

The BoG gives a detailed coverage of realistic neural modeling from the subcellular to the network level, and provides the detailed guide to the construction of GENESIS simulations that is missing from the Reference Manual. This tutorial is constructed to minimize your need for the BoG -- it isn't an attempt to sell you our book! Nevertheless, this short tutorial can't possibly go into all the detail of a 482 page book, so you may wish to acquire a copy if you later decide to do some serious work with GENESIS.

GENESIS Scripting

If you have read the Introduction to GENESIS, you will be familiar with the rich variety of graphical user interfaces (GUIs) that are possible with GENESIS. In fact, it is possible to create and run GENESIS simulations with little or no programming, by using Neurokit (for single cells) or Kinetikit (for biochemical reactions). But, sooner or later, you will want the flexibility of creating your own GENESIS scripts.

The bad news is that to get the maximum benefit from GENESIS and from this tutorial, you will have to do some programming in the GENESIS scripting language. The good news is that the modular object-oriented nature of GENESIS makes it easy to modify existing scripts. Once you have learned a few basics of GENESIS scripting and have some good example simulation scripts to get you started, you can create most of your simulations by simple "hacking" of existing scripts. That is the approach taken in this tutorial.

Some preliminaries

Before you start, you will need a little background.

• You should have some basic knowledge of compartmental modeling, which is covered in detail in the BoG. You can get a brief overview in parts of the Lectures on Computational Neuroscience. The book Methods in Neuronal Modeling, by C. Koch and I. Segev (eds.) second edition, MIT Press, Cambridge, MA (1998), is another good reference. The Introduction to GENESIS will also be a good background for understanding what follows.

• You should have GENESIS installed, and know how to start it up. You will need to know where GENESIS is installed. There will be a directory genesis that contains the executable program "genesis" and other directories, such as Scripts, which contains the example and tutorial simulation scripts that are distributed with GENESIS. So, when we refer to genesis/Scripts, you will need to know the full path, e.g. /usr/local/genesis/Scripts, in order to locate these files. You will also need to know where these tutorials are installed, as they may refer to the "GENESIS Tutorials directory", or to a file such as cells/simplecell/simplecell.g. The "GENESIS Tutorials directory", which contains the cells directory and other directories used by the GENESIS tutorials is the directory above the gentut directory that contains this GENESIS Programming Tutorial. The location of these directories and other information about using GENESIS is given in the local README file.

• You will need to know how to get around in a unix command-line environment, and to use a text editor. Fortunately, you only need to know a little. You can learn most of what you need to know about UNIX in order to use GENESIS in this Quick Guide to Getting around in UNIX.

The two most common text editors for UNIX are 'vi' and 'emacs'. If you are not familiar with either editor, you may find it easier to learn emacs. For an even simpler text editor with built-in help, try 'pico' if it is installed. If you are using Linux with the GNOME or KDE desktop, try 'gedit' or 'kedit".