
	    		  Operation Manual

			    July 1, 1992

	  Institute for New Generation Computer Technology


1. Introduction

 This document describes operations for Experimental Sequence
Analysis System.

2. Start up the system

  Execute the following command in the simpos debugger.
 
      :demo(#demo). 

After a new window is opened, execute the following command
in the pimos listener.

      ga:go.

Then the system is started.

3. Operations

 Operations are executed by menu selection.
There are six menus : main menu, control menu,
protein data setup menu, GA parameter setup menu, display parameter
setup menu and structure operation menu.

1) Main menu

$B!!!!!!(BMenu		Explanation

$B!!!!(B Protein         : Open the protein data setup menu.

     Parameter       : Open the GA parameter setup menu.
                       
     Display         : Open the display parameter setup menu.
                       
     Execute         : Open the control menu.

$B!!!!(B Exit            : Quit the system.

                                +--------------+
                                |   Protein    |
                                |  Parameter   |
                                |   Display    |
                                |--------------|
                                |   Execute    |
                                |--------------|
                                |     Exit     |
                                +--------------+

		            Figure 1 Main menu

2) Control menu

      Menu		Explanation

     Graph           : Raise the graph window.
     Dlgraph         : Raise the performance meter window.
     3D Protein      : Raise the structure window in non-pause state.
		       Raise the structure window and
		       the structure operation menu in pause state.
     Rule            : Raise the rule window.
     Sequence        : Raise the sequence window
     Pause           : Suspend or restart display.
     Stop            : Stop the execution.

                                +--------------+
                                |    Graph     |
                                |   Dlgraph    |
                                |  3D Protein  |
                                |    Rule      |
                                |   Sequence   |
                                |--------------|
                                |    Pause     |
                                |    Stop      |
                                +--------------+

				Figure 2 Control menu

3) Protein data setup menu

 Setup a superfamily of proteins for the motif extraction.
This release allows you to setup only cytochrome c.

4) GA paramter setup menu

      Menu		Explanation

     PE              : Setup a number of processors
     generation      : Setup a number of generations(fixed to infinite)
     population      : Setup a number of individuals per one processor
     crossover       : Setup the same crossover rate for all processors
     mutation        : Setup the same mutation rate for all processors
     exchange        : Setup an exchange rate
     initialize      : Setup initial population(fixed to random)
     crossover       : Setup a crossover rate for each processor
     mutation        : Setup a mutation rate for each processor
     show            : Show the parameter window
     hide            : Hide the parameter window
     exit            : Exit

5) Display parameter setup menu

 This menu arranges the display speed of each window.

	Menu		Explanation

     graph width     : Setup a scale of the horizontal axis
		       of the graph window.
     max dl num      : Setup a scale of the vertical axis of the graph window.
     interval        : Setup parameters for the graph window.
     dl term         : Setup parameters for the performance meter window.
     rule term       : Setup parameters for the rule window.


6) Structure operation menu

	Menu		Explanation

     Rotate Object   : Rotate proteins.
     Move Viewpoint  : Move the viewpoint.
     Rotate Viewpoint: Rotate the viewpoint.
     Translation     : Move proteins.
     Extension       : Extend/Shrink proteins.
     Clear           : Initialize the window.
     [Close]         : Close this menu.
     Angle           : Setup a rotation angle.
     Distance        : Setup a movement distance.
     Coordinate      : Setup a rotation axis.
     Direction       : Setup a movement direction.
     Three Dimension : Change to stereoscopic display
     Coordinate Axis : Display coordinate axes.
     Protein Display : Display proteins.
     Protein Data    : Select proteins.

