This is ACHS' main server for molecular biology analyses, and runs the Accelrys GCG package of programs (accessed either via the command line in an ssh terminal session, via SeqLab, an X windows based graphical interface, or SeqWeb, a web browser interface). Additional programs are also available, such as the EMBOSS suite of programs, Phylip, T-Coffee, and ClustalW/ClustalX. Watson is a Dell poweredge 1950 server (dual 3.00GHz, dual-core, Intel Xeon cpu's) with 8GB RAM. Local copies of popular databases are maintained on a ~3TB Apple XServe RAID array.
Connecting to watson - see instructions under accessing GCG
you must use a secure shell connection (SSH) to watson - telnet is disabled Windows users - use secureCRT or eXceed
Apple OS X users - use ssh in terminal, or Apple's X11 application as explained under accessing GCG
Watson mounts your home directory space, so you can access your watson files at any time from your ITC home directory
You can move files to and from your home directory on watson using ITC's home directory login application to mount your home directory to your local machine's desktop (this ITC application is available for both Windows and Apple OS X).
You may also use secure FTP to move files to and from your local machine and watson. Windows users may download and use SecureFX for SFTP transfers. Apple OS X users may use sftp from the command line in the terminal application, or use the graphic application Fugu (also available from ITC software downloads). CyberDuck is another free application for OS X users, and supports directory as well as file transfers.
Your account
If you do not have access to watson.achs.virginia.edu, send e-mail to accounts@virginia.edu to request an ACHS UNIX account. If you wish access to SeqWeb you must request it after accounts has confirmed your ACHS account is active.
Running GCG from the command line
If you run GCG from the command line, you do not have to do anything. Simply log in to watson (you must use ssh - telnet is not available on watson) and run GCG the same way as you would on crick. Everything will be exactly the same--except your programs will run much faster! Windows users needing an ssh client can download secureCRT from ITC. Mac OS X users can simply use ssh from a terminal session.
Running Seqlab on Watson
Seqlab will run on watson exactly the same as on crick. In order to access SeqLab, you must logon to watson using an X client which supports ssh connections. Windows users may obtain eXceed for PC's (note you will also need the security pack addon). Apple OS X 10.3.x users may use Apple's X11 application (available for download from Apple for OS X 10.3.x, or included with your Panther/10.3 CD's). OS X 10.2.x (Jaguar) users would do best to install the FINK package managment system and use it to install XFree86 (an open source X Window project).
General file tools on watson
Text editors:
nano - a basic command line text editor
pico - another basic command line text editor, very similar to nano (see nano documentation for commands)
Graphic file editors:
nEdit - this is an X application, so you will need to connect to watson via a secure Xwindows session (see instructions about connecting to use the UNIX X Window graphical interface to GCG).
Need Help?
If you need any assistance with your account on Watson, send e-mail to the ITC Help desk (or call 4-3731) .
If you need assistance with running GCG or migrating list files, send e-mail to Michael Black.
Please email comments or suggestions about the ACHS MolBiol pages to mblack@virginia.edu.
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