Education

CVAPP is a morphology viewer/editor written in Java by Robert Cannon for converting between file formats. Dieter Jaeger has written these notes for using CVAPP with GENESIS in order to produce cell parameter (.p) files from Neurolucida reconstructions.

As computers are reaching the practical limit of CPU speed, it is becoming more common to
use multicore processors that effectively turn a PC into a parallel computer. This offers
the prospect of harnessing this power by using PGENESIS under Linux to turn an inexpensive
PC into a fast parallel computer for running large GENESIS simulations. This tutorial is
intended as supplementary material to guide you through the PGENESIS documentation and to
address specific issues encountered when using PGENESIS and MPI on PCs with Linux.

This Mini-Tutorial on installing GENESIS with Cygwin under Windows was
contributed by Avrama Blackwell at George Mason University. It gives a
concise description of the steps required, and has been updated to reflect
changes in Cygwin packaging since the original README files in the GENESIS
distribution were written.

In GENESIS, a gap junction between compartments in two different cells can be implemented
by passing an RAXIAL message directly from each compartment to the other, with the Ra
field replaced by a number representing the resistance of the gap junction. However, this
simple approach cannot be used with the hsolve method, normally making it necessary to use
a very small time step when implementing gap junctions on a detailed cell model with many
small compartments. Carson B. Roberts has contributed this tutorial with example scripts

This tutorial, given by Hugo Cornelis at GUM*02, discusses the use of
the hsolve method for faster and more accurate implicit solution of the
model equations. He discusses a number of internal secrets of hsolve
that explain how it gets its extra performance: examples of channel and
table rearrangements, updated simulation schedule, internal data
streams, interoperability with synchans via discrete events. It also
treats the use of findsolvefield and interactions with external objects.

view the tutorial

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