22.
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
Published November 1997 by TELOS/Springer-Verlag -- ISBN 0-387-94938-0
($59.95)
Send orders to:
Springer-Verlag New York, Inc.
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You may find further information at the TELOS WWW site
<http://www.telospub.com/catalog/BIOLOGY/genesis.html>.