UH Gene-Server Update (long)

Dan Davison dbd at THEORY.BCHS.UH.EDU
Fri Dec 20 13:13:21 EST 1991

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

Help and index files:
All help and index files have been either re-written or edited.


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
MOLEVOL old-molecular-evolution-list-archive1  omelarchive2

PIR-ENTRY pir-entry1 pir-entry2 pirentry3
PIR-LOCUS pir-entry1 pir-entry2 pir-entry3 (a synonym by popular demand)
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.


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, 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.


A WAIS service is available on ftp.bchs.uh.edu,,
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:

   :version  3 
   :ip-address ""
   :ip-name "ftp.bchs.uh.edu"
   :tcp-port 9000
   :database-name "Gene-Server"
   :cost 0.00 
   :cost-unit :free 
   :maintainer "davison at uh.edu"
   :description "Server created 12/91 edc at evolution.bchs.uh.edu"

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 at bchs.uh.edu
from the internet, or from BITNET
	gene-server%bchs.uh.edu at CUNYVM

The WAIS software for X, NeXT, and terminal use is available from
quake.think.com via anonymous FTP, but the hours are restricted.

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