Download Sequence Analysis Guide 2

Chapter 2
worthwhile to check the release numbers and dates every
once in a while to see if anything has changed since the
last time you used the system.
Wisconsin Package Basics
The GCG Philosophy
THE WISCONSIN PACKAGE
The Wisconsin Package is available on several operating
system platforms. The installation at UNMC is a Unix
version and is a Linux version at UNL. The Wisconsin
Package is accessible using the command-line, using an
X Windows interface (SeqLab) and using a Web browser
such as Netscape or Internet Explorer (SeqWeb). The
version available via the Web does not have all the
program features available in the other two versions of
GCG. Personal accounts for UNMC faculty, staff, and
students on the server gsaf.unmc.edu (gsaf for short) are
free. An online application form for new accounts may be
found at the GSAF web site (http://molbio.unmc.edu/).
Accounts at UNL are available through an application at
http://biocore.unl.edu/. When you log on to the remote
computer you get the Startup screen welcoming you to the
computer, as described in Chapter 1. At this point the
cursor awaits your input next to the prompt. To start using
any of the programs (tools) which make up the Wisconsin
Package you first need to initialize your session. This is
already done for you at UNMC and UNL. If you are able
to log onto gsaf or biocomp2, but GCG fails to start up for
some reason, contact the appropriate system
administrator.
The philosophy behind the Wisconsin suite of programs
is:
•
To provide a separate program for almost anything
you want to do.
•
Program options are always available at the
command line.
•
Results are sent to either a text file or to the
terminal screen.
•
Programs requiring intensive computation are run
in the background.
This philosophy can result in software that is not very
easy to use. However, this is not reason for despair. For
those with direct network connections, all of the GCG
programs can be used through an X Windows graphical
user interface called SeqLab.
Getting Help for GCG
After seeing the Startup screen a few times, you will
probably find that you tend to ignore it, but it is
All of the help files for the entire GCG set of program and
user manuals are loaded onto a Web server for you.
Currently, this site is http://molbio.unmc.edu/gcg-help/.
Since the primary interface to GCG is through graphical
methods, you can always run both the GCG graphical
interface (SeqLab) and your favorite Web browser at the
same time, viewing the help files for GCG and the actual
program interface simultaneously.
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