Prof. Idan Segev

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Methods in Neuronal Modeling: From Ions to Networks

edited by

Christof Koch and Idan Segev

2-nd edition. MIT Press, Cambridge, MA, 1998. 687 pages.
ISBN 0-262-11231-0

This work is the standard handbook of computational and numerical methods and techniques for modeling nervous systems at various levels of resolution, from individual channels to single neurons, from small groups of neurons to neural networks. The second edition is completely updated from the first edition (originally published in 1989), with 7 new chapters and 7 completely revised chapters. The book was published in summer of 1998. For more information (and to order the book) please contact The MIT Press . You can also order it directly (at a discount) via www.amazon.com . We here provide a list of further computational resources, tutorials for the various computer simulators, software packages and data referred to in the handbook.

Table of content

Chapter 1: "Kinetic Models of Synaptic Transmission" by Alain Destexhe, Zachary F. Mainen and Terrence J. Sejnowski. Tutorial simulations that illustrate the use of kinetic models for building network simulations.
Chapter 2: "Cable Theory for Dendritic Neurons" by Wilfried Rall and Hagain Agmon-Snir. For a more complete historical account and compilation of the relevant papers see Segev, I., Rinzel, J. and Shepherd, G.M., The Theoretical Foundation of Dendritic Function: Selected Papers of Wilfrid Rall with Commentaries. MIT Press: Cambridge, Massachusetts (1994).
Chapter 3: "Compartmental Models of Complex Neurons" by Idan Segev and Robert E. Burke with an appendix by Michael Hines. A detailed description, tutorials and source files for the neurosimulator NEURON. The home page of a dedicated single-cell simulator written by Lyle Borg-Graham.
Chapter 4: "Multiple Channels and Calcium Dynamics" by Walter M. Yamada, Christof Koch and Paul R. Adams. For much, much more details see the textbook "Biophysics of Computation: Information Processing in Single Neurons" written by Christof Koch, and published by Oxford University Press in 1998.
Chapter 5: "Modeling Active Dendritic Processes in Pyramidal Neurons" by Zachary F. Mainen and Terrence J. Sejnowski. A directory that includes code used to generate the models illustrated in the chapter in addition to links to other simulators.
Chapter 6: "Calcium Dynamics in Large Neuronal Models" by Edik De Schutter and Paul Smolen.
Chapter 7: "Analysis of Neural Excitability and Oscillations" by John Rinzel and Bard Ermentrout. The XPP program used in this chapter to analyze bifurcations and plot the phase space diagrams. An extensive tutorial on XPP, geared toward neurobiology.
Chapter 8: "Design and Fabrication of Analog VLSI Neurons" by Rodney Douglas and Misha Mahowald. The ANALOG circuit simulator for analog CMOS integrated circuit. The complete layout for a silicon neuron.
Chapter 9: "Principles of Spike Train Analysis" by Fabrizio Gabbiani and Christof Koch. Detailed tutorials and MATLAB programs to analyze spike trains, compute the optimal reconstruction filter and so on.
Chapter 10: "Modeling Small Networks" by Larry F. Abbott and Eve Marder. A color version of Fig. 10.X.
Chapter 11: "Spatial and Temporal Processing in Central Auditory Networks" by Shihab Shamma.
Chapter 12: "Simulating Large Networks of Neurons" by Alexander D. Protopapas, Michael Vanier and James M. Bower. The home page (including tutorials, code and so on) of the subcellular, cellular and neural network simulation system GENESIS.
Chapter 13: "Modeling Feature Selectivity in Local Cortical Circuits" by David Hansel and Haim Sompolinsky.
Chapter 14: "Numerical Methods for Neuronal Modeling" by Michael V. Mascagni and Arthur S. Sherman. Links to numerical software referred to in the chapter and other numerical analysis resources. A. Sherman's Woods Hole lecture notes, which parallel the chapter and include exercises, can also be downloaded from there.