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 parameters in order to faithfully reproduce the electrical responses of the larger models.
layer5.p has 9 compartments and represents a layer 5 pyramidal cell.
layer2.p has 8 compartments and represents the more compact layer 2/3 spiny stellate cell (modified superficial pyramidal cell).
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. Slightly different sets of channels have been used with these reduced morphologies by Bush and Sejnowski (1996) to model cortical networks.
The channels are defined and described in the file BDKchan.g. A userprefs.g file is included for use with Neurokit. The file BDK5cell.g and the included files graphics.g and protodefs.g may be run as a stand-alone GENESIS simulation of the layer5BDK.p model.
O. Bernander, R. J. Douglas, K. A. C. Martin and C. Koch, Synaptic background activity influences spatiotemporal integration in single pyramidal cells, Proc. Natl. Acad. Sci. 88:11569-11573 (1991).
O. Bernander, R. J. Douglas and C. Koch, A model of regular-firing cortical pyramidal neurons, CNS Memo 16, Caltech (1992).
P. C. Bush and T. J. Sejnowski, Reduced compartmental models of neocortical pyramidal cells, J. Neurosci. Methods 46:159-166 (1993).
P. C. Bush and T. J. Sejnowski, Inhibition synchronizes sparsely connected cortical neurons within and between columns in realistic network models, J. Comput. Neurosci. 3:91-110 (1996).
C. Koch, R. J. Douglas and U. Wehmeier, Visibility of synaptically induced conductance changes: theory and simulations of anatomically characterized cortical pyramidal cells, J. Neurosci. 10:1728-1744.