Information for new GCG Users on cancercenter:

Richard Friedman,Ph.D.
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Facility
Columbia Presbyterian Medical Center
130 Black Building, 5-6901
friedman@cancercenter.columbia.edu
September 5, 2005


To learn GCG we recommend that you use the following manuals,
published by ourselves as well as GCG.


Tutorial manuals from the Oncoinformatics Core, $60.

-	Introduction to Computing on the Herbert Irving Comprehensive
	Cancer Center Oncoinformatics Core Compaq-Alpha.
-	Tutorial Introduction to the GCG Software Package for
	Biological Sequence Analysis.

GCG manuals from GCG

-	GCG Program Manual, Unix Version.  
-	GCG User's Guide, Unix Version.

These are available as HTML at

http://cancercenter.columbia.edu/genhelp/

These manuals are available as PDF files at

http://www.accelrys.com/doc/bioinformatics/index.html   

In addition to these manuals, users will also need to obtain specific
software to run GCG.  GCG has traditionally been accessible only
through a text based interface.  However,  a graphical user interface
is now available that makes GCG as easy to use as a Macintosh or
Windows program. This interface, called Seqlab, not only makes GCG much
easier to learn and to use, but also contains a new cut-and-paste
sequence editor.  Using Seqlab requires X-Windows Server software for
your Macintosh or PC.  A three button mouse is useful with X-Windows
(a 2 button mouse has most of the functionality).


Software recommended for access to GCG from a Macintosh OSX:

-	Terminal  (Comes with macintosh)
-	Fugu, a file transfer program is available for free from 
        http://www.columbia.edu/acis/software/fugu/

and if you are using Seqlab, the following is also necessary

-	X11 for Mac OSX (available on Mac OSX (10.3 or higher) systems disk 
-	Any 3 or 2 button USB mouse 

Software recommended for text based access to GCG from a Windows
machine:

-	Teraterm, a terminal emulation program is available for free from
	http://www.ayera.com/teraterm/`
-	WinSCP, a file transfer program is available for free from 
        /www.columbia.edu/acis/software/winscp/

and if you are using Seqlab, the following is also necessary:

-	X-Win32. If your department has a license, you can obtain a copy
	of the program for free from your departmental computer
	administrator. If your department doesn't have a license,
	you can obtain a license at a cost of $59.95 for students,
	or $115 for faculty at 

	http://www.starnet.com/licenses/education.htm


To use Seqlab better (see previous paragraph), you need to obtain the
following in addition to the software and manuals already mentioned.

SEQLAB manuals from GCG

-	Seqlab Guide    (PDF Only)
-	Seqlab Tutorial (PDF Only)