From bioserv-owner@nic.funet.fi Fri Dec 20 13:12:50 1991 Received: from IUBIO.BIO.INDIANA.EDU by sunflower.bio.indiana.edu (4.1/9.5jsm) id AA04995; Fri, 20 Dec 91 13:12:46 EST Date: Fri, 20 Dec 1991 20:13:21 +0200 From: dbd@theory.BCHS.UH.EDU (Dan Davison) Message-Id: <9112201813.AA14850@theory.BCHS.UH.EDU> To: bio-software@GENBANK.BIO.NET Subject: UH Gene-Server Update (long) Cc: bionews@GENBANK.BIO.NET, bioserv@nic.funet.fi, dbd@theory.BCHS.UH.EDU, edc@theory.BCHS.UH.EDU Status: R The UH Gene-Server is feeling much better after a complete re-write of some shell programs. This note describes the changes, a new FTP address, and new WAIS service. Brief instructions for accessing the Gene-Server are included at the end of this note. 1) The following changes were made: Multiple requests now handled correctly: It now *correctly* handles multiple requests. Before, sometimes they would work, other times not. Now they will work correctly. File size limit changed: The mailing limit for requests has been raised to 1 megabyte (Internet only). Anything larger will take a long time to get to you, if it arrives at all -- many internet mailers silently enforce a limit of 1MB on file size. Help and index files: All help and index files have been either re-written or edited. COMMANDS CHANGES: HELP now sends only a HELP message and nothing else, on the assumption that if you want help you shouldn't be getting anything else back... INDEX by itself also sends the HELP message The following are valid "send" commands: ACCESSION gb-accession-number1 gb-accession-number2 gb-accession-number3 LOCUS gb-locus-name1 gb-locus-name2 gb-locus-name3 GB-LOCUS (a synonym for LOCUS) gb-locus-name1 gb-locus-name2 gb-locus-name3 GENBANK (a synonym for locus) gb-locus-name 1gb-locus-name2 gb-locus-name3 KEYWORD onekeywordonly (NOTE: NO "and", "or", or multiple keywords!) <====== AUTHOR author-last-name1 author-last-name2 author-last-name3 GB-INDEX index-name1 index-nam2 index-name3 SOFTWARE (anything else on the line will be ignored) DOS filename1 filename2 filename3 MAC filename1 filename2 filename3 UNIX filename1 filename2 filename3 VMS filename1 filename2 filename3 MATRIX biomatrixfile1 biomatrixfile2 biomatrixfile3 RENZDATA RENZREFS MOLEVOL old-molecular-evolution-list-archive1 omelarchive2 PIR-HELP PIR-ENTRY pir-entry1 pir-entry2 pirentry3 PIR-LOCUS pir-entry1 pir-entry2 pir-entry3 (a synonym by popular demand) PIR-RELEASE PIR-INDEX pir-index-1 pir-index-2 pir-index3 *************************************************************************** About AUTHOR and KEYWORD searching: This is a very primitive facility ("grep -i $1 file" for you Unix fans). It doesn't know multiple keywords or author names. If you ask for "human ribosomal dna" you will get a 6 MB file back in the mail, which will make you and your system adminstrator very unhappy. It doesn't know author's first names or initials. SEND ONE WORD ONLY FOR AUTHOR AND KEYWORD SEARCHING! BTW, if you want full keyword searching and are on the Internet, use the IRX facility at genbank.bio.net, which is free but limited to a 10 minute connection. Because of the demand, we will add multiple implicit "and" of keyword searching as soon as a shell problem can be worked around. "human ribososomal dna" will then do what you expect. This is NOT yet avaiilable. **************************************************************************** 2) FTP Site Change: First, remember that a complete collection of software is available from ftp.bio.indiana.edu, Don Gilbert's archive site. FTP is provided at the Gene-Server for deposition of programs and to provide access to recently added software. The contents here are neither complete nor carefully maintained. The new address is ftp.bchs.uh.edu, 129.7.2.43. The same directory structure and files as on menudo.uh.edu apply. The menudo archive will disappear without warning...they want their disk space back. 3) WAIS A WAIS service is available on ftp.bchs.uh.edu, 129.7.2.43, which consists of all the index and help files on the Gene-Server. Yes, this includes the GenBank and PIR locus/entry names as well as all the software. This is an approximation of the source file: (:source :version 3 :ip-address "129.7.2.43" :ip-name "ftp.bchs.uh.edu" :tcp-port 9000 :database-name "Gene-Server" :cost 0.00 :cost-unit :free :maintainer "davison@uh.edu" :description "Server created 12/91 edc@evolution.bchs.uh.edu" :) USE: The Gene-Server is funded by NSF grant DIR-9111695, and is free to all. To get started, send the word "HELP" to gene-server@bchs.uh.edu from the internet, or from BITNET gene-server%bchs.uh.edu@CUNYVM The WAIS software for X, NeXT, and terminal use is available from quake.think.com via anonymous FTP, but the hours are restricted.