contents

software

data

java models

Computational Neuroscience: Realistic Modeling for Experimentalists

Erik De Schutter (editor)
Robert Cannon (CD-ROM)
Published by CRC Press, Boca Raton, Florida, 2000

This CD-ROM contains images, data files, simulation scripts and models to accompany the book Computational Neuroscience: Realistic Modeling for Experimentalists. It is organised as a self-contained web site with one section for each chapter in the book, containing all material specific to that chapter.

The software and data sections hold copies of various public domain resources including the Neuron and GENESIS simulation environments and a cell archive with detailed reconstructions of hippocampal neurons.

External links are shown in orange and require internet access. All others are to material on the CD-ROM itself.

The web site www.compneuro.org has been set up to hold additions, corrections and updates to material on the CD-ROM. It has the most recent versions of the interactive java models, so if you experience problems running them form the CD-ROM try upgrading from www.compneuro.org/catacomb.

Contents

1
	Introduction to Equation Solving and Parameter Fitting ..........................................................................1
	Gwen LeMasson and Reinoud Maex
	Interactive demonstrations of numerical integration schemes, and parameter sensitivity for spiking neurons
2
	Modeling Networks of Signaling Pathways .........................................................................................25
	Upinder S. Bhalla
	Interactive Java demonstrations of the models in the text; GENESIS simulation scripts
3
	Modeling Local and Global Calcium Signals Using Reaction-Diffusion Equations .................................49
	Gregory D. Smith
	1-D calcium buffering and diffusion demos; sample Yorick code and tutorial for examples in the text, tables of parameters used in simulations
4
	Monte Carlo Methods for Simulating Realistic Synaptic Microphysiology Using MCell ........................87
	Joel R. Stiles and Thomas M. Bartol
	Movies and Model Description Language (MDL) input files for example MCell simulations in the text; OpenDX visual program for 3-D rendering of MCell output
5
	Which Formalism to Use for Modeling Voltage-Dependent Conductances? .......................................129
	Alain Destexhe and John Huguenard
	Models and data for most of the channels in the text; simulations showing differences in their behavior
6
	Accurate Reconstruction of Neuronal Morphology ............................................................................159
	Dieter Jaeger
	Supplementary images; Cvapp morphology conversion and editing software
7
	Modeling Dendritic Geometry and the Development of Nerve Connections .......................................179
	Jaap van Pelt, Arjen van Ooyen and Harry B.M. Uylings
	Interactive neuron growth model with examples of S1-rat cortical layer 2.3 pyramidal cell basal dendrites and guinea pig Purkinje cell denerites
8
	Passive Cable Modeling - A Practical Introduction ............................................................................209
	Guy Major
	Simulations of passive structures; linearity; recipricocity; propagation and attenuation; Neuron simulation scripts
9
	Modeling Simple and Complex Active Neurons ................................................................................233
	Erik De Schutter and Volker Steuber
	Passive spine model; movies; GENESIS tutorial and simulation scripts
10
	Realistic Modeling of Small Neuronal Circuits ...................................................................................259
	Ronald Calabrese, Andrew A.V. Hill and Steve D. van Hooser
	GENESIS tutorial on the leach heart network
11
	Modeling of Large Networks ...........................................................................................................289
	Michael E. Hasselmo and Ajay Kapur
	Interactive models of continuous firing rate networks and integrate-and-fire networks; Genesis scripts
12
	Modeling of Interactions Between Neural Networks and Musculoskeletal System .............................317
	Orjan Ekeberg
	Movie of lamprey swimming motion
software
	Copies of Public Domain Packages for Local Installation
	Robert C. Cannon
	Complete Neuron and GENESIS simulation environments; XPP dynamical systems package; Catacomb modeling tools; Cvapp morphology converter and editor
data
	Morphology Database and Links to External Resources
	Robert C. Cannon
	Archive of hippocampal neuronal morphology; Links to external resources