codon.nih.gov

What is codon.nih.gov?

Codon is a Sun Enterprise 3000 UNIX server managed by the Research Services Branch (RSB), NIMH and the Instrumentation and Computer Section, NINDS. Services on Codon are available without charge to investigators and support staff in:

Primary Mission

Codon's primary mission is to provide a platform for the Genetics Computing Group molecular biology software suite. The package includes programs for sequence editing, mapping, translation, comparison, fragment assembly and database searching. To access the GCG package programs, type gcg.

User Environment

Codon is available for logins from anywhere on the Internet via Telnet, or dial-in access is available using Bullwinkle, RSB's remote access server.

Your default directory is your username on /u1 - for instance, /u1/ken is user ken's login directory. You have a 40 megabyte "soft" disk quota on /u1 , but you can temporarily use up to 50 megabytes - your "hard" quota - for up to 2 weeks. After that, the system will require you to delete some files before it will let you create more. To facilitate sharing files with your colleagues, the default file protection for new files you create will be readable by any user on the system, but you can change this if you wish with the umask command. Or you change the protection on individual files or groups of files after they are created using the chmod command. Several levels of file security are offered - you can restrict a file's readability to a specific group of users, or deny access to anyone but yourself. But Codon is NOT a secure site - you should not keep files on Codon relating to patient data, personnel matters or sensitive research data. Codon is to be used for official government business ONLY.

Please respect the privacy of other users on the system. Don't read or copy files that don't belong to you without the permission of the owner. Just because somebody leaves the door unlocked does NOT mean you have the right to rummage through their house.

Accidents happen. If you make a mistake and Codon crashes, don't feel too bad - the infallible computer hasn't been built yet, and scientists are forever pushing them beyond their limits. But deliberate crashing, file tampering, password-guessing on other user's accounts, E-mail or node "spoofing", creating computer "viruses" or "trojan horse" programs are all grounds for terminating your account.

Editing

To edit files, Codon offers the standard vi editor and the GNU emacs editor for old-timers who are not strangers to Unix. For "the rest of us," Codon offers pico, a simple, easy-to-use editor that comes with the pine mail program (see below).

Printing

Codon supports plain text and PostScript printing via the lpr command.

Graphics Output from GCG Programs

The GCG package programs can send graphics to several types of devices - see the Graphics section of the User manual. But I've defined several standard types as aliases for your convenience. The default is VersaTerm-Tek4105.

2Blaser Print output on the 2B07 laser printer
2Bcolor Print on the 2B07 color printer
myTek send graphics back to my screen, I'm a generic Tek4014 terminal
colorTek send graphics back to my screen, I'm a VersaTerm PRO terminal
smartTek send graphics back to my screen, I'm a SmarTerm terminal

Please NOTE the upper-case B's and T's. Unix is case sensitive!

Scripting and Programming

Codon runs under the Unix operating system, with access to most of the programs and utilities commonly available on Unix systems. By default the user's login shell is tcsh , but csh (c shell) and sh (Bourne shell) shells are also available. Users can write shell scripts to automate repetitive tasks, and users who are used to writing command files using DCL on the VAX can use vcl , a command-line interpreter that can emulate a large subset of DCL commands. Users interested in the new Pearl scripting language can develop programs on Codon, and Codon's full ANSI C compiler is available for the stout-hearted.

Electronic Mail

Codon uses the Unix mail utility as the default user interface for mail, but Codon also offers the pine mail program from the University of Washington, which is much easier to use. Our recommended solution is to use Codon as a POP3 mail server and to use Eudora POP mail client on the Macintosh or Windows-PC, Synergy Software's VersaTerm Link on the Mac, or any of several other POP3 client programs available both commercially or in the public domain - whatever works best for you. POP3 mail clients can be set up to remove the mail from Codon and store it on you own computer - providing a much higher level of mail privacy and security than you can get on a multi-user system like Codon.

Internet Access

Codon offers telnet for terminal emulation and ftp to exchange files with any of the million or so host machines on the world-wide Internet network.

Getting Help

Unlike the VAX, there is no standard "help" facility. But there ARE the manual pages. Most of the standard Unix commands have a manual entry, accessible by typing man , then the name of the command. You can search the manual pages if you don't know the command name by using man -k and a keyword.

If you are a user of the DCRT's Helix system you will find the "Convex Unix Primer" a helpful guide to the basic Unix commands like ls (List Files), cp (copy), and mv (move or rename a file).

"Learning the Unix Operating System" by Grace Todino and John Strang (O'Reilly & Associates, ISBN 0-937175-16-1) is another helpful beginner's book. It's written for users of the Bourne shell primarily, but most of the commands it describes are universally available and work just the same way under Codon's default tcsh environment.

The GCG package has its own on-line help system. For a description of the programs available, use the genhelp command. The Using the UNIX Version the GCG Package document provides an introduction to using some of the common Unix commands.

For information on using the Internet, one handy guide is The Whole Internet User's Guide and Catalog by Ed Krol, published by O'Reilly & Associates, ISBN 1-56592-025-2.

Finally, RSB computer specialists are available to answer your questions.

Ken Weeks - your system administrator.
ken@codon.nih.gov, 435-4538

If Ken's not available, try -

Wayne Rasband: wayne@codon.nih.gov, 435-4539
Brad Zoltic: brad@codon.nih.gov, 435-4533
Steve Ono: sgo@codon.nih.gov, 435-4530

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