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. All of Upi's original scripts, along with simulation results and figures from the paper are in the jneurophys.jun93.tar.gz file in the BABEL cells/mitral_granule directory.
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 chan_kinetics/smit.p in not having the synaptically aactivated channels. Also has the fix for the soma RM.
newbulbchan.g - a corrected version of the neurokit/prototypes/newbulbchan.g file for the channel prototypes
userprefs.g - lets you run Neurokit in this directory to experiment with smit2.p and mit.p. This is the easiest way to experiment with the models when developing things to try for the tutorial. Start by recording from the soma and one of the distal denrites, with 0.5 nA injection to the soma.
injtut.g - This is a general-purpose current injection demo for experimenting with different kinds of file output, xcell display, etc., by setting some flags at the start of the script. It was designed to be the basis for code that is used to initialize the GENESIS server when used with the Modeler's Workspace. It contains no model-specific code, but can be used to run any model with a .p file and a channel prototypes file.
protodefs.g - this is included by injtut.g, and contains the model-dependent statements. This version is a copy of protodefs.mit.g or protodefs.smit2.g. It makes the channel prototypes and sets some global variables used by injtut.g. A lot of this would be replaced by files created by, or commands sent by the client program in the Workspace.
cellview.g - is included by injtut.g to provide the xcell display.
inj2.g - The GENESIS 2 version of Upi's mit_curr_inj/inj.g script, used for creating the simulations plot in FOg. 4.
inj2.gif/inj2.ps.gz - display created by inj2
Fig4A.data - experimental data file (Upi's correct.block) for Fig. 4A current injection with blocking of Na and Kfast (K2_mit_usb) and partial blocking of K channels.
Fig4D.data - experimental data file (Upi's correct.noblock) for Fig. 4D current injection with no channel blocking.
experiment.gif - screen grab of Fig. 4D. without any axes or scales shown.
For details on the output of Vm of all compartments to a file, and the blocking of Na and K channels to produce Fig. 4 B, see the notes at the end of "Notes".
The calcium-dependent K channel Kca_mit_usb requires a two-dimensional funtion of both voltage and concentration. This is implemented in newbulbchan.g with a clever combination of vdep_channel, table, and tabgate objects. The vdep_channel is not supported for hsolve chanmodes greater than 1. In principle, the implmentation could be changed to use a tab2Dchannel (not available when the simulation was written). This would allow the use of chanmode 3, but requires the use of very large tables.
Dave Beeman