To run the leech heartbeat network simulations you must first compile a 
version of genesis that includes the necessary objects.  The instructions for
this are located in the README file in the top directory leech.  

The two cell, six cell, and eight cell simulations are started by typing 
"hn2", "hn6_4", "hn8" at the genesis prompt while in the appropriate
directory. The model will initially have the default parameters that are set 
in the .p files (e.g. Ek, gbar of channels etc.).  Default parameters can also
be loaded interactively by typing "include default_param.g" or by adding this 
line to the main script.

To start the simulation 
1) Press reset button or type "reset" 
2) Press the init button or type "restore start_state.bin". This restores the 
   state variables such as the membrane potential from a binary file.  It is 
   important to set the state variables to start in the middle of a cycle.  
   Unfortunately this may not work on all machines since the binary file 
   created by the restore command might not be readable on a machine with a 
   different version of Unix.  In this case the simulation can also be 
   started from an ascii file (eg. include start_state_asc.g).  The user may 
   create a new binary state variable file by typing 
   "start_state_bin start_state".  
3) Press the Run button or use the step command to run the simulation 
   eg. "step 10 -t" (runs a simulation for 10 sec)

To see graphics
uncomment lines under "// make control and graphs" in the main simulation 
script (eg. hn2.g, hn6_4.g or hn8.g) to show graphs.  The line 
make_scale_forms must be uncommented in order for the axis scaling to work 
within the graphs.

Some useful files you may want of modify:

output_asc_volt.g -contains the function output_asc_volt which sends the
              membrane potential of the cells to an ascii file.  
             - syntax output_asc {filename}


output_asc.g -contains the function output_asc which is similar to the function              above but sends additional to an ascii file.  
             - syntax output_asc {filename}

save_state_bin.g -contains the function save_state_bin which saves the state
                  variables to a binary file using the genesis command save.
		  This file can be used to restore a simulation with
    		  the saved states by typing "restore {filename}"
                  - syntax "save_state_bin {filename}"

save_state_asc.g -contains the function save_state_asc which saves the state
                  variables to an ascii file 
                  (eg. save_state_asc start_state_asc.g) This file can be used
                  to restore a simulation by typing including the .g file
                  (eg. include start_state_asc.g).  This method of saving and
                  restoring the state variables is not as accurate as the 
                  binary method because the state variables of the synchan 
                  are not saved (these are readonly or are hidden).

save_param.g  -contains the function save_param which saves the model 
               parameters (e.g. Ek and gbar for each channel etc.) to an ascii
               file.  The resulting file can be used to set the model 
               parameters with the include command.  The filename must end in
               .g
	       - synatax "save_param {filename}"

save_table_asc.g -contains two functions "save_table_X" and "save_table_XY"
                  which can be used to save tab chan parameters to an ascii
                  file for viewing.  The first function if for channels with
                  just an activation variable.  minf =X_A/X_B
                  tau = 1/X_B

Notes:
The HN3 and HN4 cells are identical in terms of the maximal conductances in 
the default configuration.  The gbar of the Na current is slightly higher in 
HN 1 cells than in HN 2 cells.  This was necessary so that the cells would 
spike at slightly different times.

There are also scripts which were taken from the squid tutorial for voltage
clamping.  These are not yet in a user friendly form.
                 



 



