[Biodevelopers] what databases are you using?

[Patrick McConnell]

For many applications, we are using MySQL.  It has proven to be quite
dependable and efficient.

For more complex data (e.g. blast results), we are moving towards using an
XML database.  The free XML databases (Xindice, and a couple others) do not
perform particularly well, and we found them to be undependable, often
hanging with frequent and simultaneous access.  Thus, we have invested in a
commercial product (Tamino), and have found it to be excellent.  Though we
are still in the development phase of our application, Tamino has worked
great.

I find the flexibility of XML to be essential to storing the often complex
biological data.  Also, several packages exist to automatically serialize
and deserialize Java objects to XML.  This has greatly sped development
time of our applications, as extremely complex data structures can be
mapped directly to XML and indexed in a database.

-Patrick McConnell
Duke Bioinformatics Shared Resource
mccon012 at mc.duke.edu





"Pawel Krasucki" <Pkrasucki at psstat.com>@bioinformatics.org on 07/11/2002
08:34:19 AM

Please respond to biodevelopers at bioinformatics.org

Sent by:    biodevelopers-admin at bioinformatics.org


To:    <biodevelopers at bioinformatics.org>
cc:

Subject:    RE: [Biodevelopers] what databases are you using?


I was going to setup a test environment and was trying to figure what db
to setup as well.  You mentioned using Postgres, have you ever worked
with MySQL?  Although I've installed Postgres, I haven't worked with it
at all, is it hard to pick up and work with?  I had it running on Linux,
and was using GUI utility with Linux to administer Postgres,  is that a
common way to administer that db?

Paul Krasucki
IT Supervisor
Professional Solutions STAT Inc.,
St. Louis, MO  63114
(314) 428-8335 ext 129


-----Original Message-----
From: biodevelopers-admin at bioinformatics.org
[mailto:biodevelopers-admin at bioinformatics.org] On Behalf Of Joe Landman
Sent: Wednesday, July 10, 2002 09:55 PM
To: biodevelopers
Subject: [Biodevelopers] what databases are you using?

A few years ago, the db of choice was some sort of Oracle implementation
for many people I spoke to/worked with at a variety of pharmas and
biotechs.  I am curious what people are using now (if anything).  I do
know people using flat files for a variety of reasons as well.

Just curious.  I use/like Postgres for my own development/testing.

--
Joe Landman,
email: landman at scientificappliance.com
web  : http://scientificappliance.com

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