Education

This is the latest version of a complete self-paced GENESIS modeling course that has been packaged for distribution on a CDROM, or installation on a hard drive. It brings together material that is available as separate downloads from the GENESIS web site and through the GENESIS Users Group. It includes several simulator-independent tutorials on biologically realistic neural modeling, as well as both tutorial and research simulations that have been implemented with GENESIS.

The GENESIS Neural Modeling Tutorials are an evolving package of HTML tutorials intended to teach the process of constructing biologically realistic neural models with the GENESIS simulator. The most recent versions are derived from the supplementary material provided with the introductory GENESIS modeling tutorials at WAM-BAMM*05, and further refined during the 2006 Latin American School on Computational Neuroscience (LASCON).

View the Genesis Modeling Tutorials

This gzipped tar archive contains the latest version (Release 2-2.16) of the Purkinje cell tutorial, and can be used to replace Release 2-2.11, which is included in the GENESIS 2.3 genesis/Scripts/purkinje directory. The tutorial implements the full De Schutter and Bower (1994) detailed Purkinje cell model. It extracts to the directory "Purkinje_tutorial", so that it will not overwrite the older version, if it is unpacked in the genesis directory.

The goal of this tutorial is to set up a two-dimensional array of model neurons with local excitatory and long-range inhibitory connections. This is easily accomplished using GENESIS by creating prototype elements with cell bodies, ion channels, and spike-generating elements which are duplicated, assigned positions in a two-dimensional grid, and graphically displayed. The text of the tutorial is given in tutorial7.text, and the script used to run the tutorial is tutorial7.g.

The simulation CPG_Rev, contributed by Joseph Aulenbrock, is a modification of the CPG tutorial, intended to extend its use to the study of simple idealized Hebbian reverberations. The documentation, in the text file reverb.txt and the postscript file reverb.ps, explores the behavior of some examples.

An improved version of revpac. The postprocessing has been simplified, and references have been added in the documentation.

The following files were submitted by Ed Vigmond (ed@gut.rose.utoronto.ca), and
were used in a biomedical engineering bio-electricity course at the University
of Toronto. This course is under the supervision of Dr. Berj L. Bardakjian
(blb@ecf.utoronto.ca).

hh.ps - Instructions and exercises to accompany the Squid tutorial on the
Hodgkin-Huxley model. (Stored as the compressed postscript file hh.ps.Z)

prop96.ps - Experiments on the propagation of neuronal electrical activity,
with an explanation of the theoretical background, instructions, and

Here are a few things to be aware of when setting up voltage clamp
circuitry ala the Squid model:

1) diffamp elements and the PID element have a "saturation" field that
limits the absolute magnitude of their output. Unfortunately this
field defaults to 0, which isn't very useful. Be sure to set it to
some large value (in the squid scripts it's set to 999, but you may
have to use a larger value if you're using some other set of units).

2) The tuning of the PID (proportional-integral-derivative) controller
involves balancing the quality of the voltage clamp against the size

In this tutorial we adapt the network in tutorial 7 to solve a famous optimization problem, the eight queens problem. This is done with a network of simple, but biologically realistic spiking neurons. The text of the tutorial is given in tutorial8.text, and the script used to run the tutorial is tutorial8.g.