October 20, 2008: Important announcement: July 1st, 2009 end-of-life for GCG and SeqWeb
February 2007 - GCG is now version 11.1.3, and SeqWeb is now version 3.1.2. The GCG/SeqWeb server, watson.achs.virginia.edu, has been upgraded to a new Dell PowerEdge 1950 (dual, 3.0GHz, dual-core Intel Xeon cpu's, 8GB RAM, and approximately 3TB of Apple Xserve RAID storage for databases.
Details of the new features can be found at Accelrys' web site
Access to GCG requires an account on the server, watson.achs.virginia.edu. If you do not have an account on this machine, email accounts@virginia.edu and request an ACHS UNIX account (i.e. an ACHS account for access to GCG on watson.achs.virginia.edu).
To run the command-line version of GCG logon to watson.achs.virginia.edu, and type: gcg
You must use a SSH2 compatible client to connect to watson - telnet is disabled.
(SSH is a secure shell, so your connections to watson are encrypted).
Manuals for GCG programs are available on this web site - full manual, abbreviated help guides
Windows users may use SecureCRT, available from the ITC downloads section. Mac OS X users can use the OS X Terminal application - openSSH is built into the OS X system. Mac OS 9 users should try MacSSH (also available from sourceforge)
SeqLab: To use the UNIX X Window graphical interface to GCG, SeqLab, you will need an X Window client package on your local computer:
Mac OS X 10.4 (Tiger) users - on your install DVD, there is a master install package named "Optional Installs.mpkg" which you can use to install the Tiger version of Apple's X11, as explained in Apple Knowledge Base article 301229 (note that the version of X11 available on apple.com's download site will NOT run under OS X Tiger).
Mac OS X 10.3 (Panther) users - CD #3 of your installation disks includes a package installer for Apple's X11 program. Install this package, start the X11 program from your "Applications/Utilities" folder, and use the following command to connect to watson:
ssh -X -l your_UVa_user_id watson.achs.virginia.edu
The "-X" sets up X Window forwarding (ie. of the watson X display to your local machine's screen), and the "-l" simply tells watson to log you on using the user_id you supply and not the account id of the local machine you are connecting from (if these id's are identical, you do not need to use the -l switch). To start the GCG package, simply type gcg. Once the package initializes, your prompt will change to >GCG>. Type seqlab to start up the X Window graphic interface.
Mac OS X 10.2 (Jaquar) users - Apple's X11 application will not run on 10.2.x systems. However there is a open source X Window project known as XFree86, which has an Apple port known as XDarwin. XFree86 is most easily installed using the package management tools built into the FINK project.
Windows users will need to obtain eXceed in order to run X Window sessions on watson. eXceed is an UNIX X-client for windows, available under site license from UVa. Instructions on obtaining and configuring eXceed for use with GCG/SeqLab are here.
The seqlab manual is available on this web site
SeqWeb version 3.1.2 - The Web interface to GCG (access via http://gcg.med.virginia.edu).
In order to use SeqWeb, you must be a current GCG user, and have a SeqWeb server account. GCG accounts are obtained by contacting ITC-accounts and requesting an ACHS account (i.e. an account for access to GCG on watson.achs.virginia.edu). SeqWeb accounts may be obtained using the form available on this website or emailing mblack@virginia.edu.
Make sure you have JavaScript enabled on your browser and set your cache size to 4096 KB or greater. You must also enable cookies.
The current version of SeqWeb (ver. 3.1.2) should work with most current web browsers (IE 7 and FireFox 1.5.x and 2.x on Windows machines, Safari 1.2+, FireFox 1.5.x or 2.x, and Camino 1.0.3 on OS X machines)
SeqWeb help is available from within the web application - click on the link, "Help Topics | Support" in the upper right of the SeqWeb browser window
On Line Manuals and help
The complete gcg manual is available on line for users of this site.
GCG Manual - Program descriptions arranged according to function
Researchers wishing their own copy of GCG manuals can obtain pdf-format files from Accelrys' web site (in the Bioinformatics section)
GCG Help - Programs listed alphabetically.
Tutorials and Handouts
Short descriptions of GCG commands A useful reference guide to all GCG programs and databases.
SeqLab and Xwindows documents SeqLab provides a graphical interface for all GCG programs through Xwindows. Instructions for installing Xwindows on a Mac or PC is also provided.
Introduction to GCG using Seqlab If you have eXceed or MacX running in the lab, this is an excellent way to get started. If you just want to ges started with using a basic terminal, use Introduction to GCG .
Multi sequence analysis tutorial A step by step guide to sequence alignment.
Advanced GCG This shows you how to run GCG from the command line as well as tips and tricks to make you more productive and put you in control.
Classes - Classes covering the same topics as the tutorials are scheduled throughout the year.
Support ranging from classes and handouts to personal instruction is available.
A mailing list is maintained to provide information on important changes in software and databases
Computers where GCG is installed
GCG command line and SeqLab access is by SSH logins to watson.achs.virginia.edu. As SSH connections are securely encrypted, you can access watson.achs.virginia.edu via SSH connections from anywhere. SeqWeb runs on the same machine, accessed by pointing your web browser to http://gcg.med.virginia.edu. You should be able to access seqweb from anywhere. If you encounter problems from off-grounds access, you can try a UVa secure connection, either via a Proxy account or using the "UVa Anywhere" VPN connection.
GCG/Wisconsin package Home Page
This site contains information on GCG products, plans, and copies of their newsletter.
Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.
Academic Computing Health SciencesBox 800555
Charlottesville, VA 22908
(434) 982-4025