NOTE: These scripts are for GENESIS version 1.4, and have not yet been converted to GENESIS 2 syntax. This would be done using the "convert" utility, followed by some editing of the graphics3.g script to adjust sizes of some XODUS widgets. (See genesis/Doc/Convert.txt.) This would make a nice student project for someone learning GENESIS. If you carry out the conversion before we do, please let us know, and submit your scripts to http://genesis-sim.org.
This directory contains a "user friendly" version of Jisoon Ihm's three neuron tritonia CPG simulation, based on an earlier GENESIS simulation by Sylvia Ryckebusch. The simulation closely follows the three neuron model of the tritonia CPG described in Chapter 6 (by Peter Getting) of "Methods in Neuronal Modeling", 1st editionn, edited by Christof Koch and Idan Segev.
This version has an improved graphical interface which allows all significant parameters to be modified. The tutorial may be run by typing "genesis T3". The HELP button allows you to view various "*.hlp" files and to view experimental results for comparison with the simulation. The file "program.notes" contains Dave Beeman's informal notes on the program.
The "Cell Parameters" buttons call up menus with buttons for the soma and the various channels for each cell. These can be used to call up submenus with dialog boxes for viewing or changing the soma or channel parameters. The channel names indicate the cells which give input to them. For example, the dsi channel "vsiK" is a potassium channel which receives input from the vsi neuron, and dsi channel "dsiNa2" is one of the two sodium channels to which the dsi neuron self-connects. Changing the weight for a given channel to zero gives a convenient way to see the effect of disabling the channel.
(At present there is no way to use dialog boxes to modify the single Hodgkin-Huxley channel (hh_K) which exists in the vsi. The "Reset Defaults" button also has not been implemented yet.)
As a compromise to speed up plotting, the spikes which are shown on the graphs with the cell Vm do not include all the spikes which appear in the larger "Spike Plot" graph. At the expense of slower execution time, this can be changed in T3.g by modifying changing "setclock 1 2.0" to "setclock 1 0.5".
Note on the help display:
The default width of the windows used to display the help files has been set to accomodate the large font used with X11 revision 4 ("R4"). When running the simulation on DECstations and other machines which use X11 R3 with its smaller font size, the windows will be wider than they need to be. Although they may be resized with the mouse, the easiest way to change them to an appropriate size is to edit the file "helpforms.g" and change the statement near the beginning, 'XREV = "R4"' to 'XREV = "R3"'.
Note on memory usage:
This simulation, with its many channels and plotting of individual spikes, has a voracious appetite for memory. On machines with a limited amount of memory, long simulation runs can result in a "core dump". To maximize the available memory, you should use a minimum number of terminal windows and have no other major processes running. When making another run after changing parameters, it may be necessary to first exit the simulation and then begin again.