23. The Book of GENESIS

For an introduction to neural modeling, and a ``users guide'' to the construction of neural simulations with GENESIS, we recommend our book,

The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation System, Second Edition.

James M. Bower, California Institute of Technology, Pasadena, and David Beeman, University of Colorado, Boulder

This is the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator, which is provided on a CD ROM within the book. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences.

Part I, Neurobiological Tutorials with GENESIS, teaches concepts in neuroscience and neural modeling by means of eight interactive computer tutorials. These span the range from neuronal membrane properties to cortical networks, and may be used without any prior knowledge of the GENESIS simulator or computer programming.

Part II, Creating Simulations with GENESIS, is a practical guide to the programming of the GENESIS simulator for the construction of one's own simulations. The tutorials in this section progress from the construction of simple cell models to detailed cell and network models with a sophisticated graphical interface. The readers are instructed in the process of creating new simulations of their own interest, starting with existing simulations.

CONTENTS

Part I

Neurobiological Tutorials with GENESIS

Chapter 1 Introduction

James M. Bower and David Beeman - Caltech / Univ. of Colorado

Chapter 2 Compartmental Modeling

James M. Bower and David Beeman - Caltech / Univ. of Colorado

Chapter 3 Neural Modeling with GENESIS

James M. Bower and David Beeman - Caltech / Univ. of Colorado

Chapter 4 The Hodgkin-Huxley Model

Mark Nelson and John Rinzel - Univ. of Illinois / NIH

Chapter 5 Cable and Compartmental Models of Dendritic Trees

Idan Segev - Hebrew University

Chapter 6 Temporal Interactions Between Post-Synaptic Potentials

Idan Segev - Hebrew University

Chapter 7 Ion Channels and Bursting Neurons

James M. Bower and David Beeman - Caltech / Univ. of Colorado

Chapter 8 Central Pattern Generators

Sharon Crook and Avis Cohen - Montana State Univ./Univ. of Maryland

Chapter 9 Dynamics of Cerebral Cortical Networks

Alex Protopapas and James M. Bower - Caltech

Chapter 10 The Network Within: Signaling Pathways

Upinder S. Bhalla - National Centre for Biological Sciences, Bangalore

Part II - Creating Simulations with GENESIS

David Beeman - Univ. of Colorado, plus authors noted below

Chapter 11 Constructing New Models

James M. Bower - Caltech

Chapter 12 Introduction to GENESIS Programming

David Beeman and Matthew A. Wilson - Univ. of Colorado/MIT

Chapter 13 Simulating a Neuron Soma

Chapter 14 Adding Voltage Activated Channels

Chapter 15 Adding Dendrites and Synapses

Chapter 16 Automating Cell Construction with the Cell Reader

Chapter 17 Building a Cell with Neurokit

Chapter 18 Constructing Neural Circuits and Networks

Michael Vanier and David Beeman - Caltech/Univ. of Colorado

Chapter 19 Implementing Other Types of Channels

Chapter 20 Speeding up GENESIS Simulations

Erik De Schutter and David Beeman - Univ. of Antwerp/Univ. of Colorado

Chapter 21 Large-Scale Simulation using Parallel GENESIS

Nigel H. Goddard and Greg Hood - Pittsburg Supercomputing Center

Chapter 22 Advanced XODUS Techniques: Simulation Visualization

Upinder S. Bhalla - National Centre for Biological Sciences, Bangalore

Appendix A Acquiring and Installing GENESIS

Appendix B GENESIS Script Listings

Bibliography

Index of GENESIS Commands

Index of GENESIS Objects

Index

Originally published January 1998 by TELOS/Springer-Verlag -- ISBN 0-387-94938-0

Free downloadable edition available at http://www.genesis-sim.org/GENESIS/iBoG/index.html.