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From: roy@phri.UUCP (Roy Smith)
Newsgroups: net.bio,net.std
Subject: Sequence analysis software standards committee forming
Message-ID: <247@phri.UUCP>
Date: Mon, 3-Jun-85 17:32:57 EDT
Article-I.D.: phri.247
Posted: Mon Jun  3 17:32:57 1985
Date-Received: Thu, 6-Jun-85 01:27:41 EDT
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Organization: Public Health Research Inst. (NY, NY)
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Xref: watmath net.bio:209 net.std:46


	For the past few months, Seth Pinsky at Rockefeller University
and I have been exchanging sequence analysis software and complaining to
each other about the lack of standardization in the programs.  We would
like to improve the situation.  Towards this end, we are trying to
enlist people who write sequence analysis software to form a standards
committee.

	After a bit of asking around, it seems that no such committee or
project already exists; if you are aware of such a body, please let me
know so we don't end up working against each other.  Also, if you know
of any large audience which isn't seeing this message (because they are
not on usenet) but should, let me know about that too.

	Note that we are primarily interested in talking to programmers
(rather than users).  This is intended to save time, not to offend.
Clearly, since scientists are the end-users of the programs us
programmers write, their input is vital towards making intelligent
scientific decisions.  However, the issues we intend to discuss are
primarily programming, not scientific problems, and we don't want to get
bogged down in arguing about what a good ribosomal binding site looks
like.

	It is also clear that the set of all scientists and the set of
all programmers are not mutually exclusive.  Just because you are one of
the former doesn't mean we don't want to talk to you.  In fact, the
people we want are probably the intersection of the above two sets.  If
you are from any of the established data-base groups (GenBank, EMBL,
NBRF, Bionet, etc.) we are particularly interested in hearing from you.

	Both Seth and I work on Unix machines.  We don't want to get
into Unix vs. VMS vs. TOPS-20 vs. IBM debates, but initially any
programming efforts will probably be confined to software which runs
under Unix, simply because that is what we are most familiar with.
Eventually, I think our goal is to come up with a comprehensive set of
programs which are portable to other operating systems and to hardware
from various vendors, but this may be more work than we are willing to
expend.

	Before we start writing any software, however, we want to come
up with standards for how the software should behave, rather than
actually worrying about specific implementations of algorithms (i.e.
RFC-style documents).  Even before that, the first step is to locate a
group of people who can give intelligent input into the whole process.
For more information, contact:

	Roy Smith
	Public Health Research Institute
	455 First Avenue
	New York, NY  10016
	(212)-578-0822
	{allegra, rocky2!cubsvax}!phri!roy
-- 
allegra!phri!roy (Roy Smith)
System Administrator, Public Health Research Institute