smith@mcclb0.med.nyu.edu (11/24/90)
I heard that the decisions about which RDBMS to use with the new
GenBank were getting closer to an irrevocable decision. I think this is an
issue worth discussing, since I for one an unclear as to all the
ramifications of it. We do not have an RDVMS right now, but we are expect to
be under considerable pressure to get INGRES. However, the GenBank people
seem to be discussing Sybase adn Oracle.
I have nothing against these, of course, but we do not want to be in
the position to have to buy several of these: because we can not afford it,
for one. (Someone I spoke to recently said: 'No problem, in five years they
will all be the same'. Right.)
We use the GCG package. It would be nice to know what all the
implications are for the different users are.
+---------------------------------------------------------------------------+
|Ross Smith, Cell Biology, NYU Medical Center, 550 First Ave., NYC, 10016|
|Phone: (212) 340-5356: FAX: (212) 340-8139 (Alternate NYUMC) (212) 340-7190|
|E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+---------------------------------------------------------------------------+michael%domain@LANL.GOV (Michael J. Cinkosky) (11/25/90)
----- Begin Included Message -----
From BIOSCI-REQUEST@genbank.bio.net Fri Nov 23 16:39:47 1990
Received: from domain.lanl.gov by life.lanl.gov (4.1/5.17)
id AA09791; Fri, 23 Nov 90 16:39:46 MST
Received: from p.Lanl.GOV by domain.lanl.gov (4.1/5.17)
id AA05154; Fri, 23 Nov 90 16:40:10 MST
Received: from genbank.bio.net by p.Lanl.GOV (5.61/1.14)
id AA04667; Fri, 23 Nov 90 16:40:56 -0700
Received: by genbank.bio.net (5.61/IG-2.0)
id AA27965; Fri, 23 Nov 90 15:37:14 -0800
Received: by genbank.bio.net (5.61/IG-2.0)
id AA27931; Fri, 23 Nov 90 15:36:15 -0800
Message-Id: <9011232336.AA27931@genbank.bio.net>
To: genbank-bb@mcclb0.med.nyu.edu
From: smith@mcclb0.med.nyu.edu
Subject: RDBMS for GenBank sequence data...
Date: 23 Nov 90 21:17:53 GMT
Status: RO
I heard that the decisions about which RDBMS to use with the new
GenBank were getting closer to an irrevocable decision. I think this is an
issue worth discussing, since I for one an unclear as to all the
ramifications of it. We do not have an RDVMS right now, but we are expect to
be under considerable pressure to get INGRES. However, the GenBank people
seem to be discussing Sybase adn Oracle.
I have nothing against these, of course, but we do not want to be in
the position to have to buy several of these: because we can not afford it,
for one. (Someone I spoke to recently said: 'No problem, in five years they
will all be the same'. Right.)
We use the GCG package. It would be nice to know what all the
implications are for the different users are.
+---------------------------------------------------------------------------+
|Ross Smith, Cell Biology, NYU Medical Center, 550 First Ave., NYC, 10016|
|Phone: (212) 340-5356: FAX: (212) 340-8139 (Alternate NYUMC) (212) 340-7190|
|E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+---------------------------------------------------------------------------+
----- End Included Message -----
Ross,
Your message is a bit unclear to me. You seem to be saying that
GenBank is about to choose an RDBMS and that you are afraid that we
are going to make a choice that will have a negative impact on you
and others in the community.
The fact is, however, that we purchased an RDBMS (Sybase) several
years ago and have been using it to maintain GenBank internally for
several months now. We continue to produce the flatfile distribution
with which you are familiar. There are no plans to stop this form of
distribution at any time in the near future.
We are in the process of establishing a number of dynamic satellite
copies of our relational version of the database at remote sites. At
this time all of these sites are running Sybase as well, but our software
for maintaining these databases has been carefully designed to be RDBMS-
independent. (We have already done a port to Oracle, which we have a
trial copy of for this very purpose. As long as Ingres, or any other
RDBMS, supports a C-callable, run-time configurable SQL interface
there is no problem in porting our code to support it. There are some
RDBMS interfaces that we cannot use because they do not support true
dynamic SQL generation (e.g., Oracle's embedded sql interface seems
to suffer from some limitations of this sort). but most RDBMS's do
support a low-level C-callable interface that we can use in porting our
software.)
Given all of this, I do not see that there is any problem brewing,
but perhaps I am simply not understanding your questions. Does any
of this help? Are there other concerns?
Michael Cinkosky
Computation Domain Leader
GenBankMBCICERO%TWNAS886@PUCC.PRINCETON.EDU (11/25/90)
Agree!
smith@mcclb0.med.nyu.edu (11/25/90)
In article <9011241736.AA05688@domain.lanl.gov>, michael%domain@LANL.GOV (Michael J. Cinkosky) writes: > > Ross, > Your message is a bit unclear to me. You seem to be saying that > GenBank is about to choose an RDBMS and that you are afraid that we > are going to make a choice that will have a negative impact on you > and others in the community. Yes. > The fact is, however, that we purchased an RDBMS (Sybase) several > years ago and have been using it to maintain GenBank internally for > several months now. We continue to produce the flatfile distribution > with which you are familiar. There are no plans to stop this form of > distribution at any time in the near future. Thanks. > We are in the process of establishing a number of dynamic satellite > copies of our relational version of the database at remote sites. At > this time all of these sites are running Sybase as well, but our software > for maintaining these databases has been carefully designed to be RDBMS- > independent. This is really what I needed to know. > (We have already done a port to Oracle, which we have a > trial copy of for this very purpose. As long as Ingres, or any other > RDBMS, supports a C-callable, run-time configurable SQL interface > there is no problem in porting our code to support it....most RDBMS's do > support a low-level C-callable interface that we can use in porting our > software.) > Given all of this, I do not see that there is any problem brewing, > but perhaps I am simply not understanding your questions. Does any > of this help? Are there other concerns? I think this answers it very nicely. I was most concernend that there be a RDBMS-independant scheme, and a way to get code running using the system we may have to get. Thanks. +---------------------------------------------------------------------------+ |Ross Smith, Cell Biology, NYU Medical Center, 550 First Ave., NYC, 10016| |Phone: (212) 340-5356: FAX: (212) 340-8139 (Alternate NYUMC) (212) 340-7190| |E-Mail: SMITH@NYUMED.BITNET (BITNET), SMITH@MCCLB0.MED.NYU.EDU (Internet)| +---------------------------------------------------------------------------+