This directory contains scripts for various cell models which have been implemented with GENESIS. (Additional contributions are welcome!) Most of these models are in the form of a ".p" file, which may be used by the cell reader to create the cell, a file of functions to create the prototype channels which are used in the cell, and a "userprefs.g" file which may be used to read the cell into Neurokit. Other models may consist of scripts that define functions for creating the cells. Generally, there will be both a directory for the simulation that you can browse (along with README files describing the contents), and a compressed archive file that you can download.
Currently, it contains the subdirectories:
This simulation of the Aplysia ink motor neuron (L14) cell, contributed by Chris Butson, is modeled after the description by J. H. Byrne, J Neurophys, Vol. 43, pp. 630-650 and 650-669. The simulation consists of Ink_sim.g (main simulation script), ink_channels.g (ion channel descriptions) and ink_motor.p (cell description file).
This contains reduced neocortical pyramidal cells suitable for use in network models. The passive cell model parameter files layer5.p and layer2.p describe the reduced neocortical pyramidal cell models of Bush and Sejnowski (1993). The files layer5BDK.p and layer2BDK.p use the layer5.p and layer2.p morphologies to implement smaller versions of the Bernander et al. (1991) models. These use active channel model descriptions taken from Bernander, Douglas and Koch (1992). With these channels, the firing patterns under current clamp are very close to those of the larger models, with the spike adaptation typical of regular-firing pyramidal cells. The channels are defined and described in the file BDKchan.g. A userprefs.g file is included for use with Neurokit.
This simplified neuron model could be used to represent a fast spiking interneuron in a cortical network.
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).
The large (8 MB) tar file "jneurophys.jun93.tar.gz" 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, Journal of Neurophysiology 69:1948-1965
There are 4 basic mitral cell models, and a few variations on them with the electrode leak removed or TTX and TEA applied. There are 3 basic granule cell models, plus the usual variations, plus 2 more to illustrate that paramter searches can give multiple solutions. The ".p" cell parameter files to create the cells may be found in mit_classes and gran_classes. The channels are created from the prototypes in bulbchan.g. These simulations were programmed with GENESIS 1. A GENESIS 2 version of bulbchan.g may be found in the GENESIS 2 distribution as Scripts/neurokit/prototypes/newbulbchan.g, and GENESIS 2 scripts for the mitral cell are here, in mitral2.
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.
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.
This is a GENESIS model created by Pratik Mukherjee of slow oscillatory bursting in a thalamic relay cell. It is based upon the one by McCormick et al. (1991). This was converted to GENESIS 2 by Lauren Jones.
This contains scripts to create and test a GENESIS 2 implementation of the 1994 Traub et al. 64 compartment CA3 pyramidal cell [Journal of Physiology, Vol. 481.1, p. 79 (1994)]. This implementation was contributed by Pulin Sampat.
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 paper contained in the file menschik_finkel_1998.pdf.
Additional directories in the GENESIS distribution which contain cell models:
"Scripts/traub91" contains a tutorial based upon a GENESIS simulation of the hippocampal pyramidal cell model of Traub, et. al. [R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson, Journal of Neurophysiology, Vol. 66, p. 635 (1991)] This paper should be consulted while using the tutorial. The channels which are used by the "CA3.p" and "userprefs.g" file may be found in prototypes/traub91proto.g. The file "Scripts/neurokit/prototypes/traub91chan.g" is similar, except that it uses longer descriptive names for the channels.
"Scripts/burster" contains a tutorial on bursting molluscan neurons and the effects of the various types of ionic channels which are commonly found. The cell which is modeled is a "generic burster", loosely modeled after the Aplysia R15 cell, although it contains channel models taken from measurements on bursting neurons in Tritonia as well as Aplysia. Most of the channels are described in the review paper by David J. Adams, Stephen J. Smith and Stuart H. Thompson (Ann. Rev. Neurosci. 3, p.141 (1980). Further details of the tutorial and the channel models are given in Chapter 7 of "The Book of GENESIS".
"Scripts/piriform" contains an interactive tutorial version of the Wilson and Bower piriform cortex model. This model uses a simplified 5 compartment pyramidal cell and the two types of inhibitory interneurons.
"Scripts/purkinje" contains a tutorial version of the de Schutter and Bower Purkinje cell simulation. (De Schutter, E. and Bower, J. M. (1994) An active membrane model of the cerebellar Purkinje cell: II. Simulation of synaptic responses. J. Neurophysiol., 71: 401-419.)