The goal of this exercise is to create a simple network of two cells that fire in alternate bursts. To make it easy to get started, you have been given all of the scripts to create a simulation with a single cell:
simplecell.g - creates a simple cell with a soma and a dendritic compartment
cell.p - the cell parameter file for the cell, used by the readcell command
protodefs.g - makes the prototypes for the channels, compartments, and spike generator that readcell creates from the cell parameter file
graphics.g - provides the GUI for the simulation
xtools.g - defines some script functions that are usefull for making GUIs
The main script simplecell.g uses the readcell command to create the cell "cell1" from the cell parameter file, cell.p. Chapter 16 of the Book of GENESIS (BoG) and the documentation for the readcell command explain the details of creating a cell from a cell parameter file. The file protodefs.g, which is included by simplecell.g, includes files that are in the Scripts/neurokit/prototypes directory. This is possible because your .simrc file gives a path to that location. These files define the functions used by protodefs.g to create the elements that are named in the cell.p file. Finally, the graphical user interface is provided by the file grpahics.g. Most of the XODUS commands used in this file are explained in BoG chapters 13 and 14. The "scale" button in the upper left corner of the graph is made with the "makegraphscale" function that is defined in xtools.g.
The resulting cell has a soma compartment with squid-like Na and K channels, and a dendrite compartment with both an excitatory and an inhibitory synaptically activated channel, implemented with synchans. The soma receives a default injection current of 0.5 nA, and fires a regular train of spikes, much like the single compartment example in BoG chapter 14.
Spend some time running the simplecell simulation and understanding enough of the simulation scripts until you feel that you are ready to modify simplecell.g to make two coupled cells. Then, copy these files into your own directory, and make the changes necessary to create a second cell with no current injection, and plot its Vm on the graph in a different color. Of course, the plot will be a flat line, as it is receiving no stimulus. Now, use the information in BoG chapter 15 or the docmentation for synchan to connect the spike output of cell1 to the excitatory synchan of cell2, and the spike output of cell2 to the inhibitory input of cell1. Use an axonal propagation delay of 0.005 seconds for each connection. Finally, experiment with the synaptic weights for each synapse until you can achieve a pattern of alternate bursts of action potentials. To make it easy to change the weights, you may wish to add dialog boxes for entering weights to the control panel.