Path: utzoo!attcan!uunet!bionet!AARDVARK.UCS.UOKNOR.EDU!BROE
From: BROE@AARDVARK.UCS.UOKNOR.EDU (Bruce Roe)
Newsgroups: bionet.molbio.genome-program
Subject: USENet and GenBank Updates
Message-ID: <9003171856.AA15058@genbank.bio.net>
Date: 17 Mar 90 18:57:00 GMT
Sender: daemon@genbank.BIO.NET
Lines: 87

Fellow netters, sequencers and assorted hacks...

Some very interesting stuff has recently been posted regarding USENET and
making computers easier to use for us poor, dumb, clones and sequencers.

The message from gilbertd@iubio.bio.indiana.edu 
Message-Id: <9003162052.AA04441@genbank.bio.net>

Containing "A brief guide to installing and reading Internet news from
 a networked Macintosh" was extremely useful and includes:

>>Macs that are connected to a network that includes tcp/ip links to the Internet
>>can be set up to let you easily read and post network news, including the
>>bionet.* newsgroups for research biologists.  The netnews reader stack is
>>easy to use, but requires some network knowledge to install.
>>Requirements:
>>*  Macintosh with an appletalk or ethernet connection
>>*  MacTCP software to provide the Mac with the tcp/ip communications link
>>*  Harry Chesley's netnews reader hypercard stack
>>*  A local area NNTP netnews server computer

and the message from genbank-bb@mcclb0.med.nyu.edu
Message-Id: <9003162115.AA05606@genbank.bio.net>

>>In order to use this data feed, software is needed to automatically extract
>>the news items (sequences) and load them into a database usable by the local
>>bank search software.  Two groups, one at the Public Health Research
>>Institute and the other at New York University Medical Center are
>>collaborating with Genbank to provide software to furnish this service.  We
>>expect to publish a short account of it in the near future.

are a great start on a system to provide first both a user friendly interface
and easily accessible network news, and second an automated method for
immediate database updates.

I do have some comments regarding the above and alternative approaches
to the problems they address.

   I just put up Dr. Clark's FAMAIL shells and they are fantastic.
This brings up the question, why should we clutter up our disk drives
with all the databases when GenBank has them easily accessible via the
Internet?  Is it because we want them here and do not want to depend
on a network??  I guess that's why.  I'd love to have daily database
updates on our VAX and take 5x more CPU time to search the databases
via WORDSEARCH or FASTA and bring every other user on our VAX to a
screeching halt while I search.  That gives me power. (is sarcasm
allowed on the net Dave??).

   Seriously though, as the databases grow in size, maintaining
them locally is going to be very difficult and searching them locally
is going to be very very slow.  So rather than having all of us deal 
with these databases locally, why doesn't the NIH think of funding
various sites located nation-wide to be mini-genbanks with the appropriate
access and searching programs?  I think this is called *distributive
computing* and it makes more sense to me than creating a local nightmare.

   What most users want is the ANSWER to the question they are
trying to ASK.  It is our responsibility to provide the tools to solve
the complex questions we are addressing by large scale sequencing and
not create a situation worse than what we now have.
 
  The idea is that with several computers containing the databases,
we could access one central server (maybe not the correct word) and
our search would be distributed to the least used computer at that
time and/or search several computers each containing a portion of the
database.  This idea is not new with me but is one which we should be
re-addressing.  Distributive computing and parallel processing may
provide a better and faster way of allowing us to obtain the results.

   As for making computer use easier. I think it's great that two of
my former students (Leslie and Chris Dow) should be advocates for this.
Both hated my Macs and loved PC's but that's another story.  It is,
as both Leslie and Chris have pointed out, very important for users
to have an understandable, easy to use, intuitive interface. The vast
majority of users do not care what computer is running what or what
operating system is being used and all this should be transparent to
the user.

Well, that's it from the home of the number one basketball team in the
USA.  In the words of a previous president of the University of Oklahoma,
"Lets create an academic environment our football (and now our basketball)
team will be proud of..."

Best to one and all,
Bruce A. Roe
Professor of Chemistry and Biochemistry
University of Oklahoma, Norman, OK 73019