Exons:
Relevant bits of information for using the MUSC Shared Resource,
the BioMolecular Computing Resource (BCR).

Exon_14 The GCG Graphic User Interface SEQLAB.

Summary: a) start it! erg 2% setgcg
                      erg 3% gcg
                      erg 4% seqlab   or seqlab -small
          b) set things up: select working directory
          c) set things up: select a working list
          d) set things up: open the Output manger
          e) do something! select a function from the function menu

 Details below:

Version 9.0 of the GCG sequence analysis software has their first
production release of a graphic user interface referred to below as
Seqlab. Seqlab is the successor to WPI.  Seqlab is a SIGNIFICANT 
advance for the occasional user.  SeqLab is presently
available only to users communicating with the UNIX servers via an 
SGI workstation or from a PC or MAC equipped with functioning  
x-server software. Suitable x-server software includes eXodus from 
White Pine software or MAC-X or Hummingbird eXceed for WINDOWS. 

Initializing the Wisconsin Package Interface (SeqLab) is simple.  FIRST 
initialize the GCG suite by typing "setgcg", hit return. Next type 
"gcg" and type return. Next type "seqlab" and hit return if you have a 
16-20" or larger display or type "seqlab -small" and hit return if you 
have a 12-16" display.

The large "SeqLab Main List Window " opens and a smaller "About SeqLab "
window  appears on top of the larger window. Read the disclaimer 
and click the OK button to get rid of the "About.." window

The SeqLab Main List Window is the entry point for the GCG programs. 
Several pull-down menus are arrayed across the top of the window. 
Positioning the cursor over any of these and pressing the left button 
will display the pull-down menu. By again positioning the cursor over 
one of the cells and pressing the left mouse button again, one of two 
things occur. 1) A new small window appears specific for a program 
or function or 2) a secondary pull-down menu appears. The secondary
pull-downs work like the primary ones. The new windows require 
input from the user in order initiate a process.

The FIRST thing you need to do is to select a working directory.  Go 
to the "OPTIONS" pull-down menu. Select  "Working Directory"  and 
a new window appears which displays sub-directories of your  main 
UNIX directory. Make a selection and click on the OK button.

The SECOND thing you need to do is to select or create a working list.  
Go to the "Files"  menu to open a list or go to the "Sequences/Add" to 
select individual sequence files from your working directory. Any 
selected files are added to the current working list and may be saved 
as "working.list" or any other appropriate name in any other 
appropriate directory. Files MUST be placed into in the current working 
list before they are recognized by ANY other program for action.
The large window of the SeqLab MAIN List Window shows all of the 
current sequences.

The THIRD thing to do is to go to the Window menu and open the 
OUTPUT manager window. This creates a small window where the 
names of the  output files from computations completed in the current 
session will be written. Such output files may be viewed with the 
"display" button. Additionally, output files from previous sessions 
may be added to the current output list.
 
A word about OSF windows etiquette and standard operating procedures.
In the upper right-hand corner of every OSF window are two symbols. 
Clicking the large square will re-draw the window to full-screen. Clicking
the square in the full-screen mode re-sizes the screen to the smaller 
mode. The "period" or "dot" collapses the screen to a small icon  
which can be moved to a convenient place on screen while the user 
works with other windows to achieve some analysis. 

The fourth thing to do is to click on the "function" menu to select which 
GCG program you wish to run. Each has its own specific window. 
Programs requiring sequences as input or queries will direct you to
the current working list to select the file as query if you have not 
already done so. The remainder of the window will allow you to select 
various options for each program. At the bottom of each program window are 
four buttons, "close", "run", "background" and "help".  When you have 
configured the page to setup an analysis click on "run" and the program 
will execute. Use the "dot" to collapse the window and click on the 
output manager icon . When the job finishes, the output file's name 
appears in the Output manager's window listing. Highlighting a file 
and clicking on the Output manager's DISPLAY button will open
another window where the file may be viewed regardless of whether 
it is text or graphic in content. You then have the opportunity to save 
the files or re-name and save them or even to print the files or to 
copy/paste them into a buffer for transfer to other programs.