Worm Breeder's Gazette 12(5): 10 (February 1, 1993)

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Internet Network Access to the ACEDB Database

J. Michael Cherry

Department of Molecular Biology, Massachusetts General Hospital,
Boston, MA 02114 USA
e-mail: cherry@frodo.mgh.harvard.edu

Information from the Caenorhabditis database ACEDB, created and maintained by Richard Durbin and Jean Thierry-Mieg, is now available through the worldwide Internet computer network from Massachusetts General Hospital. The Caenorhabditis information is provided using the Gopher client/server software developed at the University of Minnesota. Gopher provides an easy to use menu interface and can display many types of information. However to increase the availability of the information contained in ACEDB we are currently only providing text. The overlapping physical map of cosmids and YACs has been converted to text pictures for this network version of the database. Genetic Map and DNA sequence graphic displays that are available with the ACEDB workstation version are not provided. However the underlying information used to create the graphic displays is provided. The Gopher services operate using specialized software on an Internet connected computer to link a variety of remote information resources. This software is available at no charge for most types of personal and workstation computers, as well as mainframes. Gopher software for Macintosh, DOS, Unix and VMS is available via Anonymous FTP from boombox.micro.umn.edu.

Searches of the ACEDB database through Gopher are done by querying with words that are present in the database. If more than one word is entered in a query the software will find all entries in the database that contain any of the input words. That is the software assumes there is an 'or' between multiple query words. The search can be made more specific by including 'and' or 'not' search modifiers between words, and the asterisk ('*') wild card can be added to the end of words, but not at the beginning, to extend the number of possible matches. Here are four example queries: dpy* and lin-1 ;supernumerary and neurons; homeobox* and 199*; DH#SL013 .

The ACEDB containing Gopher server is provided from weeds.mgh.harvard.edu, this is the host name to use when connecting directly. A public account with access to the Arabidopsis Research Companion service (which includes the network version of ACEDB) is provided by the Department of Molecular Biology at Massachusetts General Hospital, Boston. If the appropriate Gopher software cannot be obtained for your networked computer a special account on the computer named ochre.mgh.harvard.edu is available. A VT100 or better VT terminal emulator is required to properly interact with this public account. From most computers use the command "telnet ochre.mgh.harvard.edu" to connect with the MGH computer then enter the user name "gopher" and the password "thaliana. Telnet programs are usually standard on most computers connected to the Internet including Macintosh and PC compatibles. This public account should provide a useful service to the large amount of biological information that is becoming available via Gopher. There is no public modem access to this account.

It is recommended that the Gopher client software be obtained for your computer so that files can be retrieved, saved and printed on your locally. However, the software used on the public access account provides an option to mail a text file or an entry from one of the many databases available via Gopher. First view the file of interest or make a query to the database and view the information of interest. After viewing the file or database entry simply press the "m" key then the return key. You will be asked for an electronic mail address. Please type carefully. You should enter your full and complete Internet electronic mailing address. Note: UK users must reverse the host name portion of their Janet address, e.g. the Janet address 'user@uk.ac.cam.vax' converted to the Internet format is 'user@vax.cam.ac.uk'.

For a general overview of the Gopher and the wealth of Internet services that are becoming available the following book is recommended. "The Whole Internet User's Guide & Catalog" by Ed Krol, (1992) O'Reilly & Associates, Inc. Sebastopol, California. ISBN 1-56592-025-2