The NEURON Book神经元手册 mobi 下载 fb2 夸克云 azw3 网盘 pdf pmlz

　　The authoritative reference on NEURON, a software program used by neuroscientists to create computer models used to study the function of biological neurons and neural networks. Written by the creator of the NEURON program, its main purpose is to teach readers how to use NEURON. Without assuming any previous computer-programming knowledge, it provides practical advice and full working examples to help users get the most out of NEURON. It will be an essential handbook for anyone working with NEURON in computational neuroscience, theoretical neuroscience, neurophysiology, and neuroscience.

Preface

Acknowledgments

1 A tour of the NEURON simulation environment

1.1 Modeling and understanding

1.2 Introducing NEURON

1.3 State the question

1.4 Formulate a conceptual model

1.5 Implement the model in NEURON

1.5.1 Starting and stopping NEURON

1.5.2 Bringing up a CellBuilder

1.5.3 Entering the specifications of the model cell

1.5.3.1 Topology

1.5.3.2 Subsets

1.5.3.3 Geometry

1.5.3.4 Biophysics

1.5.4 Saving the model cell

1.5.5 Executing the model specification

1.6 Instrument the model

1.6.1 Signal sources

1.6.2 Signal monitors

1.7 Set up controls for running the simulation

1.8 Save model with instrumentation and run control

1.9 Run the simulation experiment

1.10 Analyze results

References

2 The modeling perspective

2.1 Why model?

2.2 From physical system to computational model

2.2.1 Conceptual model: a simplified representation of a physical system

2.2.2 Computational model: an accurate representation of a conceptual model

2.2.3 An example

3 Expressing conceptual models in mathematical terms

3.1 Chemical reactions

3.1.1 Flux and conservation in kinetic schemes

3.1.2 Stoichiometry, flux, and mole equivalents

3.1.3 Compartment size

3.1.3.1 Scale factors

3.2 Electrical circuits

3.3 Cables

References

4 Essentials of numerical methods for neural modeling

4.1 Spatial and temporal error in discretized cable equations

4.1.1 Analytic solutions: continuous in time and space

4.1.2 Spatial discretization

4.1.3 Adding temporal discretization

4.2 Numerical integration methods

4.2.1 Forward Euler: simple, inaccurate and unstable

4.2.1.1 Numerical instability

4.2.2 Backward Euler: inaccurate but stable

4.2.3 Crank-Nicholson: stable and more accurate

4.2.3.1 Efficient handling of nonlinearity

4.2.4 Adaptive integration: fast or accurate,occasionally both

4.2.4.1 hnplementational considerations

4.2.4.2 The user's perspective

4.2.4.3 Local variable time step method

4.2.4.4 Discrete event simulations

4.3 Error

4.4 Summary of NEURON's integration methods

4.4.1 Fixed time step integrators

4.4.1.1 Default: backward Euler

4.4.1.2 Crank-Nicholson

4.4.2 Adaptive integrators

……

5 Representing neurons with a digital digital computer

6 How to build and use models of individual cells

7 How to control simulations

8 How to initialize simulations

9 How to expand NEURON's library of mechanisms

10 Synaptic transmission and artificial spiking cells

11 Modeling networks

12 hoc,NEURON's interpreter

13 Object-oricnted programming

14 How to modify NEURON itself

Appendix A1 Mathematical analysis of IntFire4

Appendix A2 NEURON's buist-in editor

References

Epilogue

Index

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作者简介

　　Nicholas T. Carnevale is Senior Research Scientist in the Department of Psychology at Yale University. He also directs the NEURON courses at the annual meetings of the Society of Neuroscience and the NEURON Summer Courses at the University of California, San Diego and University of Minnesota, Minneapolis.

　　Michael L. Hines is Research Scientist in the Department of Computer Science at Yale University. His work is embodied in a program, NEURON, which enjoys wide use in the experimental and computational neuroscience community.

书籍介绍

The authoritative reference on NEURON, the simulation environment for modeling biological neurons and neural networks that enjoys wide use in the experimental and computational neuroscience communities. This book shows how to use NEURON to construct and apply empirically based models. Written primarily for neuroscience investigators, teachers, and students, it assumes no previous knowledge of computer programming or numerical methods. Readers with a background in the physical sciences or mathematics, who have some knowledge about brain cells and circuits and are interested in computational modeling, will also find it helpful. The NEURON Book covers material that ranges from the inner workings of this program, to practical considerations involved in specifying the anatomical and biophysical properties that are to be represented in models. It uses a problem-solving approach, with many working examples that readers can try for themselves.