This directory contains the documented GENESIS cell model simulations,
used in the GENESIS Modeling Tutorial. See the README files in the
directories below for more details.
Contents of cells/
- - This uses the cell
reader to create a simple two-compartment neuron with a dendrite
compartment, a soma, and an axon. The dendrite contains synaptically
activated excitatory and inhibitory channels and the soma contains
"squid-like" voltage-activated Hodgkin-Huxley sodium and potassium
channels, plus a spikegen element that acts like the intial part of an
axon. This may be used to provide synaptic input to another cell.
- - This implements the same model neuron as simplecell, but provides a
fancier graphical interface with controls to allow pulsed injection
current, synaptic input from spike trains, and random Poisson-distributed
background synaptic activation. It also provides user-defined string
variables in the main script that you can change to use with different cell
models. The README file for the simplecell2 model tells more about the
- - This manual
parameter search example shows how to use a custom XODUS GUI for
adjusting channel parameters. The example cell model is a version of
the layer 4 pyramidal cell from the ACnet2 network model.
- - This simplified neuron
model could be used to represent a fast spiking interneuron in a cortical
- - This is a simple one-compartment model of a neocortical regular
spiking pyramidal cell that, in addition to a fast sodium current and
delayed rectifier potassium current, uses a Muscarinic potassium current
(KM) in order to achieve spike frequency adaption.
- - These are simplified (8-9 compartment) models of much larger (about
400 compartment) models of pyramidal cells from area 17 of cat visual
cortex, derived from models by Bush and Sejnowski. A collapsing method was
used that conserves the axial resistance and makes some adjustments in the
passive membrane parameters in order to faithfully reproduce the electrical
responses of the larger models.
- - This contains mitral cell
scripts by U. S. Bhalla.
- - This uses a simple
script (traubcell.g) to create the 1991 Traub model 19-compartment CA3
region pyramidal cell from the CA3.p cell parameter file and the channel
prototypes file traub91proto.g.
- - The 1994 Traub model is a more detailed version of the 1991 model,
with 64 compartments.
- - This is a version of Traub's 51-compartment hippocampal interneuron.
- Purkinje_tutorial- This is a newer 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. In the new version, multiple cell views are now possible via the
output menu, and a configuration layer on top of the tutorial allows you to
restrict the GUI to the things that you think are important. The files
README and help.txt (which can be viewed from within the simulation by
using the HELP button) describe the model and the various types of synaptic
input that you can apply. The file archive file purkinje.Release2-2.16.tar.gz
included here extracts to the directory "Purkinje_tutorial", so that it
will not overwrite the older version, if it is unpacked in the genesis
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