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Some suggestions for self-paced study or use in a course
Getting Started with GENESIS
- You have probably already downloaded the "The Ultimate GENESIS 2.4
Tutorial Distribution" from
genesis-sim.org/GENESIS/UGTD.html
- Unpack it into a location of your choice and set some browser bookmarks:
- Install Linux - If you are using this in a course, the tutors will
be your best source of information and help for installing Linux on a Windows
laptop or the local computer lab. There are good tutorials on installing Linux
at http://www.linux.org/, and in the
documentation with your chosen Linux distribution. Mac users should be familiar
with using command line unix commands under MacOS. For some rather outdated Linux
information see:
Some suggestions for installing Linux on a PC
. This has information on repartitioning Windows disks and
installing Linux. Any modern Linux distribution will have tools and
documentation for doing this.
Introduction to UNIX or
Linux and the graphical desktop This gives basic information on
command line unix commands for the beginner.
- Install GENESIS following the instructions in
distributions/ for
compiling and installing genesis-2.4beta-src.tar.gz. The Makefile
has options for PC Linux and MacOS platforms as well as many older
Unix Machines. The included binary versions for GENESIS 2.3 were
compiled on old 32 bit processors but may work on modern PCs with
32 bit libraries installed. Cygwin32 offers a way to experience
GENESIS under MS windows, but for serious work it is not a
satisfactory substitute for installing GENESIS in a Linux
partition. Modern "virtual machine" environments such as VMware
or VirtualBox are an alternative to using Cygwin.
GENESIS usually installs without problems under modern versions of
Linux. Most questions related to installation have been answered in
the archives of the 'genesis-sim-users' mailing list, which are
available from the GENESIS 2 Sourceforge page at
http://sourceforge.net/projects/genesis-sim/.
The multi-part hands-on GENESIS Modeling
Tutorial 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 Tutorials directories
cells and
networks .
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 expanded Tutorials directory in this package contains:
- The 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 with GENESIS -- The section "Brief Overview of
Realistic Neural Modeling Techniques" 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. It is followed by a
quick overview of how GENESIS is used to create these models.
- 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.
- 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.
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 multipart GENESIS Modeling Tutorial.
The exercises directory of this expanded
Tutorials package has additional GENESIS exercises from past neural modeling
courses. 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 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 networks/Vogels-Abbott_net
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 Brette et al.
(2007). 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 network 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 also lists some small modeling projects that could be carried
out with modifications to this simulation.
Be sure to read the description of the
VAnet2 model in the networks directory. This illustrates
how the use of hsolve in a large network model can speed simulation
times by factors of ten to twenty.
- Understanding a detailed network model.
The 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 networks/TurtleVisCortex
directory contains a 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. In addition to the
documentation provided with the model, there is a description of the model
and a video clip of the simulation in the final section of the Lectures on Computional Neuroscience.
As a simple excercise, follow the instructions in the documentation or the
comments in the main simulation script to make the simple edits needed to
vary the type of stimulus that is presented to the model. As an more
advanced exercise, or the start of a different cortical modeling proect,
the simulation could be generalized by using the cell reader to create cell
prototypes of any specified type, instead of creating cells "the hard way",
as in BoG Chapters 13-15.
- The networks directory has new
cortical network models, including the
ACnet2
and VAnet2 models and
tutorials with suggested exercises and projects.
- The GENESIS
Exercises collection contains many new exercises and project suggestions.
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 18 22:55:36 MDT 2014