Tutorials/cells

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/

Directories:

simplecell

- 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.

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simplecell2

- 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 simulation.

FScell

- This simplified neuron model could be used to represent a fast spiking interneuron in a cortical network.

RScell

- 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.

corticalcells

- 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.

new_mit

- This contains mitral cell scripts by U. S. Bhalla.

traubcell

- 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.

traub94

- The 1994 Traub model is a more detailed version of the 1991 model, with 64 compartments.

traub95

- 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 directory.

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