Some suggestions for using the material on this CDROM for self-paced
study
The genesis/Scripts directory in any of the unpacked GENESIS distribution
archive files contains several tutorial simulations (squid, cable, neuron,
burster, traub91, purkinje, piriform), described in Part I of "The BoG".
The Tutorials directory on this CDROM contains:
- PDF version of "The Book of GENESIS" (the "BoG"; Bower and Beeman, 1998).
Chapters 4, 5, 7, and 9 cover the basics of realistic neural modeling.
- Introduction to Realistic Neural Modeling -- The first part,
"Introduction to Realistic Neural Modeling for the Beginner" is a general
overview and introduction to compartmental cell modeling and realistic
network simulation for the beginner. Although examples are drawn from
GENESIS simulations, the tutorial emphasizes the general modeling approach,
rather than the details of using any particular simulator.
- Introduction to Computational Neuroscience -- HTML version of
introductory lectures on neural modeling for an introductory biomedical
engineering course. It has sections on the Hodgkin-Huxley model and
compartmental modeling that might be useful to those who are studying
them for the first time, or who need some review.
- Introduction to UNIX or Linux -- This is a short guide to getting around
in the UNIX command line environment for Windows and Mac users.
- Tutorials/README -- This README file tells you how to obtain and install
GENESIS and the Tutorials package, and how to run GENESIS simulations.
- Introduction to the Hodgkin-Huxley model. Chapter 4 of the
BoG provides the theoretical background and describes the use
of the genesis/Scripts/squid simulation. Try exercises 7 and 8
in this chapter. These will help you to understand the process
by which action potentials are generated, and the basis for
effects such as refractory period and post-hyperpolarization
rebound (anode-break). For help (or to peek at the answers),
see the Lectures on Computational Neuroscience section on
the Hodgkin Huxley model.
- The effect of active channels in the dendrites on burst
firing. The genesis/Scripts/traub91 directory contains a
simulation based on a 19-compartment hippocampal pyramidal
cell model. Run the simulation, following the instructions
in the README file, and bring up the HELP form. Perform
the suggested experiments in order to understand how calcium
channels and calcium-dependent potassium channels in the dendrites
produce burst firing. Chapter 7 of the BoG provides the background for
understanding the types of ionic conductances that lead to this behavior
in pyramidal cells. This simulation is also described in the
Lectures on Computational Neuroscience.
- The De Schutter and Bower Purkinje cell model.
The full De Schutter and Bower (1994) detailed Purkinje cell model is
available as a tutorial in the genesis/Scripts/purkinje directory.
The file help.txt (which can be viewed with the HELP button) describes
the model and the various types of synaptic input that you can apply.
- The Wilson and Bower piriform (olfactory) cortex model.
Run the simulation in the genesis/Scripts/piriform directory, following
the instructions in the README.1st file, after reading BoG Chapter 9.
Try some of the suggestions in the "help" window and the exercises at the
end of the chapter.
This multi-part hands-on tutorial in creating GENESIS simulations is the
main tutorial of the package, and is intended to be a "quick start" to
creating simulations with GENESIS. It should give you the tools and enough
information to let you quickly begin creating cells and networks with
GENESIS, making use of the provided example simulations. You will find
that the modular object-oriented nature of GENESIS makes it easy to create
new simulations using parts taken from existing simulations, such as the
example scripts in the directories Tutorials/cells and Tutorials/networks.
The Tutorials directory also contains a copy of the hypertext reference
manual for GENESIS commands and simulation object types (classes).
There are exercises throughout the GENESIS Modeling Tutorial. Here are
some more suggestions:
- A simple network model. To get started with network modeling, work
through enough of the tutorial to understand the section on "Creating large
networks with GENESIS". This section describes the construction of the
model in Tutorials/networks/RSnet. This is a simple network, consisting of
a grid of simplified neocortical regular spiking pyramidal cells, each one
coupled with excitatory synaptic connections to its four nearest neighbors.
This might model the connections due to local association fibers in a
cortical network. The example simulation was designed to be easily
modified to allow you to use other cell models, implement other patterns of
connectivity, or to augment with a population of inhibitory interneurons
and the several other types of connections in a cortical network. Try some
of the modifications suggested at the end of the tutorial section.
- Extending the RSNet model to include inhibitory interneurons.
This "extended version" of the Tutorials package has three extra
network models included in Tutorials/networks.
The Tutorials/networks/GENESIS_HH_benchmark directory contains a GENESIS
implementation of a 4000 neuron version of Vogels and Abbott (2005) model,
using neurons with Hodgkin-Huxley dynamics, instead of integrate-and-fire
neurons. This was used as a benchmark for a review of neural simulators in
a paper in preparation by Destexhe et al. (2006). The README file
describes how to run the dualexpVA-HHnet.g simulation, and some of the
experiments that can be performed with the GUI.
From the standpoint of realistic neural modeling with GENESIS, this is
not a very interesting simulation. The single compartment neurons have
only fast Na and delayed rectifier K conductances, and fire tonically,
much like the original integrate-and-fire neurons. The behavior of
the simulation is similar to the original, but runs much more slowly.
There is little point in using GENESIS for such a model.
However, this well-documented simulation is offered as a useful starting
point for those who would like to perform some "GENESIS script hacking" and
try some simple modifications to the script, to use more realistic neuron
models and to experiment with modifications of the network connectivity.
The README file lists some small modeling projects that could be carried
out with modifications to this simulation.
- Understanding a detailed network model.
The Tutorials/networks/hippo2 directory contains a small hippocampal
network model consisting of 72 pyramidal cells (Traub 1994 model) and
18 interneurons (Traub 1995 model) with realistic patterns of connections.
The directory contains detailed documentation and papers describing the
model, but this is not a tutorial simulation, and will take some work
to understand. It runs without a GUI and writes data (a lot!) to files.
The Tutorials/networks/TurtleVisCortex directory contains another large
research simulation, the Nenadic, Ghosh and Ulinsky large scale model of
turtle visual cortex. Although it was not intended to be a tutorial, it is
very well documented, with modular code. In this simulation, cells are not
located on a regular grid, but are placed according to coordinates that are
read from files. As an exercise, or the start of a different cortical
modeling proect, the simulation could be generalized by using the cell
reader to create cell prototypes, instead of creating cells "the hard way",
as in BoG Chapters 13-15.
The latest edition of the classic "Synaptic Organization of the Brain"
contains multi-authored reviews of our current understanding of the "wiring
diagrams" of different portions of the brain. It should be the starting place
for any modeling study of brain regions.
Shepherd, GM (2003) "The Synaptic Organization of the Brain", 5th ed,
edition, Oxford University Press, NY
The November 2005 special issue on Realistic Neural Modeling in the
electronic journal Brains, Minds, and Media contains published versions of
the modeling tutorials that were presented at the 2005 WAM-BAMM conference
and GENESIS users meeting. The Table of Contents for this issue with links
to view or download the articles can be found at
http://www.brains-minds-media.org/237/. Those who are interested in
learning the details of creating realistic single cell models using
experimental data may want to read the advanced tutorial by Dieter Jaeger
in this issue.
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Last updated on: Fri Jul 6 13:28:03 MDT 2007