BioBit No 15 Genbank on-line Service (GOS)

ROBERT HARPER, FINLAND HARPER at finuh.bitnet
Thu Mar 22 03:25:00 EST 1990



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                               No 15
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      INDEPENDANT NEWSLETTER PRODUCED AT HELSINKI UNIVERSITY, FINLAND
                     << EDITED BY ROBERT HARPER >>
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     This edition of BioBit deals with GOS (GenBank On-line Service).
     Originally I wanted to do a session with Dave Kristofferson using
     IRC which is an INTERNET RELAY CHAT just to show that chatting is
     possible on Internet as well as on Bitnet. In actual fact we did
     have one IRC session between Finland and the USA, but a full
     example session will have to wait until a later date. Perhaps the
     scientific user community is still not ready for IRC.

     Just before Christmas the BIONET computer resource came to a
     halt, and GenBank On-line Service was the pheonix that was born
     out of the ashes. (Nice mythological reference there ED). I was
     interested to know what the change from BIONET to GOS would mean
     in practical terms, hence this short interview. Here are the
     questions that I posed.

Questions:-

****    GOS   *****

1) How does GOS compare to BIONET?
2) Has the changeover caused any confusion amongst users?
3) What is the most recent development in database distribution?

****  Electronic Communications and Bulletin Boards (Newsgroups) ****

1) How does GOS view the BIOSCI Bboards?
2) How would you like to see the Bboards develop?
3) What are the problems that exist with Bboards?

****    Connection  by Public Data Network or by Internet  ****

1) If I am on Internet can I FTP into GOS?
2) Do I pay anything to get into GOS?
3) Is anonymous FTP possible?
4) What other "free" services does GOS offer?

****     More information  ****

1) Where can one get more information about GOS?
2) E-mail address?
3) Postal address?

     It also seems that the word BIONET has been burned into the
     conciousness of networkers in the life sciences since references
     are still being made to the BIONET Bboards... and even the name
     of BIONET is still retained in the Usenet newsgroups even though
     BIONET as a functional entity really does not exist anymore.

     (Have you noticed that LISTSERV people talk about "Lists", Usenet
     folk have invented "Newsgroups", and BIONET people refer to
     "Bboards", when basically they are talking about the same thing.)

     The correct term to use when refering to the network for life
     scientists is BIOSCI, since this covers the European nodes,
     namely those nodes at DARESBURY, BMC and IRLEARN. But I suppose
     that the name BIONET will stick in the memory and become the
     stuff that legends spring from... and besides it would be such a
     hasssle to convert everything on Usenet from BIONET to BIOSCI.
     Anyway enough of this preamble, let's get on with the questions.

> Questions:-
> ****    GOS
> 1) How does GOS compare to BIONET?

     The main software in use on BIONET was the IntelliGenetics
     software. This is still available on the on-line service but all
     costs of providing access to that software now have to be born by
     the user instead of being defrayed by the NIH.

     Some of the other aspects of BIONET such as the contributed
     academic software and the contributed databases are gone (except
     for FASTA/TFASTA which are still available), but these features
     were not used as extensively as the IG software and their loss
     may not be a major inconvenience to the user community.

     However, on the plus side, BIONET was limping along on an old DEC
     2065 computer which we had a very hard time getting funds to
     replace.  The GenBank On-line Service has a very fast Solbourne
     superminicomputer with four 20 MIPS processors (compared to about
     one 1.5 MIPS processor for the Dec 20).  (This information should
     be of special interest to Dr. Stephen "GCG" Clark :-) ED)

     Although disk I/O and other factors also contribute to the
     overall speed of program execution, it is safe to say that the
     sluggish response on BIONET should be a thing of the past (at
     least until the databases mushroom quite a bit more and the user
     community reaches even larger numbers than on BIONET (937)).

     Another important plus is the availability of the latest data
     from GenBank, EMBL, and GenPept (a database of translated coding
     regions from GenBank).  These databases are updated on-line on a
     daily basis. The regular quarterly releases of the SWISS-PROT
     database are also available.  All of these are searchable (for
     entry retrieval) by the very fast IRX program from the National
     Library of Medicine.

     Access to electronic communications remains unchanged from BIONET
     and a new newsgroup about the HUMAN-GENOME-PROGRAM has been added
     to the BIOSCI set. Finally, the GenBank On-line Service is now
     open to commercial users whereas previously we were restricted to
     providing access only for non-profit users.

> 2) Has the changeover caused any confusion amongst users?

     I'm sure that it has caused some since everything didn't come
     together until the last minute, i.e., just a few weeks before
     BIONET was terminated.  Application and information packets were
     sent to all BIONET users so hopefully the confusion has abated.

> 3) What is the most recent development in database distribution?

     The latest GenBank daily updates are distributed via the USENET
     newsgroup bionet.molbio.genbank.updates.  Public domain software
     produced in collaboration with Roy and Ross Smith and colleagues
     is available for offloading these files.

     The software extracts the data from the news distribution and
     converts it into a useable format.  The software is available for
     UNIX machines by anonymous FTP from:

             goober.phri.nyu.edu  (128.122.136.10).

     Software for VMS is available by MAILSERVer from MAILSERV at NYUMED.BITNET
     or MAILSERV at mcclb0.med.nyu.edu with a single line in the body of
     the  message reading "SEND NIGHTLY.1" The distribution is VMS_SHAREd.

> *** Electronic Communications and Bulletin Boards (Newsgroups)

> 1) How does GOS view the BIOSCI Bboards?

     We are continuing on in our previous capacity as a BIOSCI node.
     Users on GOS use the "vnews" USENET news software for reading
     BIOSCI and other USENET newsgroups.  This is very convenient and
     easy to use.

> 2) How would you like to see the Bboards develop?

     I hope that the HUMAN-GENOME-PROGRAM newsgroup leads to an
     expanded role for BIOSCI in communications among scientists in
     this area. After all of the smoke clears and everything is in
     place for GOS my first item is to get back together with various
     journal editors and increase the number of Table of Contents
     submissions to BIO-JOURNALS.

> 3) What are the problems that exist with Bboards?

     The main technical difficulty is the necessity to bridge a number
     of different mail programs on different networks while avoiding
     mail loops and error messages.  This has been overcome to a large
     extent, but not completely.

     Ideally I would like to see the uniform adoption of USENET news
     software by all sites thus eliminating the need for BIOSCI nodes
     and effectively putting us out of a large part of our job.  I
     don't hesitate to add that the communications software needs to
     be made more user-friendly too, although it is not as bad as a
     few people like to make out.  The new on-line service manual
     (free with the subscription) shows how simple it is to use e-mail
     and newsreading software.

     The main human problem is still increasing people's awareness of
     the existence and utility of BIOSCI.  I am very optimistic that
     this goal will be met over the next several years with a little
     bit of patience and perseverance.

> ****  Connection  by Public Data Network or by Internet

> 1) If I am on Internet can I FTP into GOS?

     Yes.  Our host is GENBANK.BIO.NET.

> 2) Do I pay anything to get into GOS?

     Yes, but there are also some free services.  I can't use the
     network for distributing prices.  This information is included in
     our application packets which can be requested by sending one's
     regular postal address (snail mail, not e-mail) to:

                         gos at genbank.bio.net

     There are two types of accounts, class I and class II.

     Class I provides access to all of the GOS features except for the
     IntelliGenetics software.

     Class II, for an additional fee, provides class I access plus
     access to the IntelliGenetics software.  There are also limits on
     connect hours for the initial fee and an hourly charge for extra
     time unlike on BIONET.

     Since the NIH is underwriting considerably less of the service
     than it did for BIONET, it is necessary for us to pay for more of
     the costs with increased user fees.

> 3) Is anonymous FTP possible?

     Yes.  The latest sequence data can be retrieved by anonymous ftp
     to genbank.bio.net.  The old BIONET contributed software is still
     in place although we can no longer devote resources to supporting
     this.

     Before BIONET went under, as you well know, we transferred copies
     to both EMBL and the University of Houston who have included
     these programs on their software servers.  Spencer Yeh on BIONET
     as well as Ranier Fuchs and Dan Davison devoted a lot of effort
     in making sure that what had been created was not lost.

> 4) What other "free" services does GOS offer?

     Free limited-time sessions over Telenet to retrieve GenBank and
     EMBL entries with IRX.  Free e-mail FASTA database searches and
     retrieval of hits by locus name or accession number.  To get
     information on this, send a message containing just the word HELP
     (no subject line) to:

                     search at genbank.bio.net.

> ****     More information

> 1) Where can one get more information about GOS?

     Just send a request for an application to gos at genbank.bio.net and
     we'll promptly send one out to you.  We need a regular full
     postal address from potential applicants.  The application packet
     fully describes the service features and prices.

> 2) E-mail address?

     Same as the above

> 3) Postal address?

     GenBank On-line Service
     c/o IntelliGenetics
     700 E. El Camino Real
     Mountain View, CA  94040
     USA

     Phone: 415-962-7364
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          % Robert Harper        %    Internet: HARPER at CC.HELSINKI.FI  %
         % Helsinki University  %   Earn/Bitnet HARPER at FINUHA.BITNET  %
        % Finland              % Tel:358-0-7085300 Fax:358-0-7085011 %
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-=ROB=- % These opinions are shareware... if you like them send $5  %
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