The Book of GENESIS: Exploring Realistic Neural Models with the GEneral NEural SImulation SystemThis is the second edition of a step-by -step tutorial for professionals, researchers and students working in the area of neuroscience in general, and computational neuroscience in particular. It can also be used as an interactive self-study guide to understanding biological neuronal and network structure for those working in the area of artificial neural networks and the cognitive sciences. The tutorials are based upon the GENESIS neural simulation system, which is now being used for teaching and research in at least 26 countries. The following chapters consist of a combination of edited contributions from researchers in computational neuroscience and current users of the system, as well as several chapters that we have written ourselves. This book, and the tutorial simulations on which it is based, grew out of a simulation laboratory accompanying the annual Methods in Computational Neuroscience course taught at the Marine Biological Laboratory in Woods Hole, MA from 1988 to 1992. Since that time, the tutorials have been further developed and refined while being used in courses taught at Caltech and several other institutions, including the Crete course in Computational Neuroscience. For this second edition, we have made many revisions and additions based on comments, suggestions and corrections from members of the GENESIS Users Group, BABEL, and from students and teachers who have used this book. |
Contents
| 4 | |
Single and Few Compartment Models | 9 |
Neural Modeling with GENESIS | 17 |
B GENESIS Script Listings | 33 |
4 | 35 |
1 | 51 |
5 | 65 |
1 | 78 |
5 | 251 |
Constructing Neural Circuits and Networks | 278 |
7 | 286 |
8 | 299 |
The Traub Model CA3 Pyramidal Cell | 300 |
Using Experimental Data to Make a tabchannel | 307 |
Implementing CalciumDependent Conductances | 314 |
NMDA Channels | 324 |
5 | 89 |
Ion Channels in Bursting Neurons | 97 |
5 | 118 |
7 | 127 |
8 | 131 |
3 | 138 |
Chains of Coupled Oscillators | 144 |
4 | 154 |
6 | 162 |
Signaling Pathways | 169 |
4 | 189 |
Introduction to GENESIS Programming | 202 |
5 | 211 |
Adding VoltageActivated Channels | 225 |
4 | 233 |
Adding Dendrites and Synapses | 242 |
Speeding Up GENESIS Simulations | 326 |
5 | 338 |
Experiments with the hsolve Object | 346 |
5 | 360 |
7 | 368 |
DrawPix Philosophy | 382 |
5 | 388 |
6 | 394 |
Bibliography | 402 |
About the Authors | 409 |
| 433 | |
| 436 | |
77 | 438 |
| 451 | |
| 454 | |
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Common terms and phrases
action potentials addmsg axon behavior Bower burst button Ca2+ cable calcium cell model cell reader cell/soma chanmode channel conductance Chapter command computational connections constant create delay dendrite compartment dendritic tree described dialog box display draw widget element enzyme equation EREST_ACT example excitatory feedback field float function Gbar GENESIS GENESIS simulation gmax graph hhchan.g Hodgkin and Huxley Hodgkin-Huxley hsolve inhibitory injection current interface ion channels ionic K_squid_hh Kinetikit labeled membrane potential menu msec neural Neurokit neurons node object option oscillators parameters pathways piriform cortex plot postsynaptic potassium protein prototype pyramidal cell randomspike reset resting potential reversal potential run the simulation scale setfield showfield sodium soma specify spike squid squid giant axon step synaptic conductance synaptic input synchan tabchannel toggle tutorial variable voltage clamp widget xform XODUS xview zero