A pre-publication copy of "The Book of GENESIS" will be on display at
both the Springer and Birkhauser booths during the November Neuroscience
Society meeting. The book is expected to be in print by mid-December.
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The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural
SImulation System.
James M. Bower, California Institute of Technology, Pasadena, and David Beeman,
University of Colorado, Boulder
This book introduces the GENESIS neural simulation system, as well as the
new interdisciplinary field of computational neuroscience. It is a
step-by-step tutorial for professionals, researchers and students working in
the area of computational neuroscience or neuroscience in general. Each
tutorial is accompanied by a number of suggested exercises, "experiments",
or projects which may be assigned as homework, or used for self-study. The
Preface and Introduction give suggestions for incorporating this material
into neuroscience courses with existing textbooks. It can also be used as
an interactive guide to understanding neuronal and network structure for
those working in the area of neural networks and the cognitive sciences.
Part I, Neurobiological Tutorials with GENESIS, teaches concepts in
neuroscience and neural modeling by means of seven interactive computer
tutorials. These 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.
The GENESIS software is UNIX-based and may be obtained at no cost by
following the procedure described in Appendix A. Further information about
GENESIS may be obtained from the WWW server,
http://www.bbb.caltech.edu/GENESIS, or by email requests to
genesis@cns.caltech.edu.
To be published December 1994 by TELOS/Springer-Verlag -- ISBN 0-387-94019-7
CONTENTS
Part I - Neurobiological Tutorials with GENESIS
Chapter 1 Introduction
James M. Bower and David Beeman - Caltech / University of Colorado
Chapter 2 Compartmental Modeling
James M. Bower and David Beeman - Caltech / University of Colorado
Chapter 3 Neural Modeling with GENESIS
James M. Bower and David Beeman - Caltech / University of Colorado
Chapter 4 The Hodgkin-Huxley Model
Mark Nelson and John Rinzel - University 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 / University of Colorado
Chapter 8 Central Pattern Generators
Sharon Crook and Avis Cohen - University of Maryland
Chapter 9 Dynamics of Cerebral Cortical Networks
James M. Bower and Alex Protopapas - Caltech
Part II - Creating Simulations with GENESIS
David Beeman - University of Colorado, plus authors noted below
Chapter 10 Constructing New Models
James M. Bower - Caltech
Chapter 11 Introduction to GENESIS Programming
David Beeman and Matthew A. Wilson - University of Colorado/MIT
Chapter 12 Simulating a Neuron Soma
Chapter 13 Adding Voltage Activated Channels
Chapter 14 Building a Multi-compartmental Neuron
Chapter 15 Automating Cell Construction with the Cell Reader
Chapter 16 Building a Cell with Neurokit
Chapter 17 Constructing Neural Circuits and Networks
Michael Vanier and David Beeman - Caltech/University of Colorado
Chapter 18 Implementing Other Types of Channels
Chapter 19 Speeding up GENESIS Simulations
Chapter 20 Advanced XODUS Techniques: Simulation Visualization
Upinder S. Bhalla - Mount Sinai School of Medicine
Appendix A Acquiring and Installing GENESIS
Appendix B GENESIS Script Listings
Bibliography
Index of GENESIS Commands
Index of GENESIS Objects
Index
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