traub94 - hippocampal CA3 pyramidal cell

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

CHANGES FOR TRAUB94

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.
  3. Model is constrained using antidromic stimulation.
  4. Implementation of spines on dendritic compartments. This was done by doubling the area (in his paper). However, to incorporate this in GENESIS, I had to double CM, halve RM, and double the ionic conductance densities for each compartment.
  5. I have not yet implemented synaptic channels.
  6. Time step is 2.5 microseconds; much smaller than the 1991 paper. So the simulation is a lot slower, when used with non-hsolve methods.

There are other subtle changes; please refer to the paper for the differences.

Additional comments by Dave Beeman (dbeeman@dogstar.colorado.edu)

As this model has a large number of compartments, it should be run using one of the implicit integration methods (method 10 or 11), using hsolve. This will allow a step size of about 25 microseconds, instead of the 2.5 microsecond step required for the default method 0. This is illustrated in the script "traub94.g", which uses hsolve with chanmode 1, and method 11 (Crank-Nicholson). The "userprefs.g" file included here allows it to be used with Neurokit.

Files in this directory: 


README          This file

CA3.p           The cell parameter file for the model

traub94proto.g  File defining functions to create the library of channels

traub94.g       Script to run the model with chanmode 1 and method 11.
                At the cost of increased execution time, the "make_xcell"
                statement near the end of the script may be uncommented to
                create a display of the cell.  This requires GENESIS 2.1
                or later.

userprefs.g     Used to run the model under Neurokit.  NOTE: This requires
                the version of Neurokit provided with GENESIS 2.0.1 or later.

traub94.old.g   Version of traub94.g for GENESIS 2.0 - 2.0.2