cells

This directory contains simulations and figures from the publication:

'Exploring parameter space in detailed single neuron models:
simulations of the mitral and granule cells of the olfactory bulb'
Upinder S. Bhalla and James M. Bower
Division of Biology, California Institute of Technology.
Journal of Neurophysiology Vol 69 No. 6, June 1993 pp 1948-1965

You are welcome to use the models for your own work, provided we
are cited appropriately. The final versions of the figures themselves
are copyrighted by the Journal of Neurophysiology, who should be contacted

This directory (mitral2) has some of Upi Bhalla's mitral cell scripts
converted to GENESIS 2, and some new mitral cell simulation scripts based
on these.

Some relevant files:

Notes - my notes on jneurophys.jun93 contents and the development of my
versions of the simulation scripts.

mit.p - the original mit.p file for the 286 compartment mitral cell model with
Upi's hack for the soma leakage resistance replaced by having a different
SOMA Vm

smit2.p - A smaller 53 compt mitral cell model - differs from

This is a very 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. This model is based on
the paper and simulation by

Destexhe, A., Rudolph, M., Fellous, J. M. and Sejnowski, T. J.
Fluctuating synaptic conductances recreate in-vivo-like activity in
neocortical neurons. Neuroscience 107: 13-24 (2001).

The simplicity of the cell model makes it suitable for use in large network

This simplified neuron model could be used to represent a fast spiking
interneuron in a cortical network. However, the model was created to
provide an example of GENESIS scripting, rather than to fit the current
clamp firing patterns of typical cortical inhibitory interneurons. Some
parameter adjustments are likely to be necessary before it is used in a
realistic cortical network model. The single-compartment RScell model with
the muscarinic current removed would also be a good starting point for a
parameter search over passive cell parameters and the conductance densities

This is a version of Traub's 51-compartment hippocampal interneuron,
contributed by Eliot Menschik. This, and the traub94 model pyramidal
cell were used in the papers:

Menschik, E. D. and Finkel, L. H. (1998) Neuromodulatory control of
hippocampal function: Towards a model of Alzheimer's disease. Artificial
Intelligence in Medicine 13:99-121.

Menschik, E.D. and Finkel, L.H. (1999) Cholinergic neuromodulation and
Alzheimer's disease: from single cells to network simulations. Progress in
Brain Research, 121:19-45.

Contributed by Lauren Jones: ljones@wesleyan.edu

This is a model of slow oscillatory bursting in thalamic relay cells in
GENESIS, based on one by McCormick et. al. (1991). This is a single
compartment lumped-soma model which includes four active membrane
conductances: a fast Na+ current, a delayed rectifier K+ current, a
low-threshold Ca+2 current (T-current), and a hyperpolarization-activated
K+ current (H-current). The interaction of these last 3 conductances
produces oscillatory bursting at 2-5 Hz when the resting membrane potential

The Traub'94 simulation has been implemented by Pulin Sampat
(Brandeis University) and by Patricio Huerta (MIT) with
help from Dr. Roger Traub.

The Traub91 simulation has been modified to incorporate the new
model by Traub, et. al. [Journal of Physiology, Vol. 481.1, p. 79
(1994)]. Basically, the new model should replicate (almost exactly)
the '91 results. Some of the new features of the model are:

1. Implementation of dendritic branching. The model now has
sixty-four soma-dendritic compartments.

2. Implementation of an axon initial segment, and an axon compartment.

The large (10 MB) tar file "jneurophys.jun93.tar" extracts to the directory
"jneurophys.jun93". This directory contains simulations and figures from
the publication:

'Exploring parameter space in detailed single neuron models:
simulations of the mitral and granule cells of the olfactory bulb'
Upinder S. Bhalla and James M. Bower
Division of Biology, California Institute of Technology.
Journal of Neurophysiology Vol 69 No. 6, June 1993 pp 1948-1965

This directory contains a hippocampal granule cell model implemented by Erik
De Schutter. This was used in his model of Ca diffusion in the hippocampus
granule cell, which was described in:

E. De Schutter and J.M. Bower: Sensitivity of synaptic plasticity to the
Ca2+-permeability of NMDA-channels: a model of long term potentiation in
hippocampal neurons. Neural Computation 5: 681-694 (1993).

ABSTRACT

We have examined a model by Holmes and Levy (1990) of the induction of

GENESIS implementation by D. Beeman, January 1998.

The passive cell model parameter files layer5.p and layer2.p describe
the reduced neocortical pyramidal cell models of Bush and Sejnowski (1993).

These are simplified (8-9 compartment) models of much larger (about
400 compartment) models of pyramidal cells from area 17 of cat visual
cortex (Koch, Douglas and Wehmeier 1990; Bernander, Douglas, Martin
and Koch 1991). A collapsing method was used that conserves the axial
resistance and makes some adjustments in the passive membrane