[Biodevelopers] what databases are you using?

[Joe Landman]

I agree on the need for flexible XML databases.  

What has worried me is the serialization of objects.  The beauty of XML
is of course that it is a self descripted structured datatype.  Building
objects using XML to represent the data structures is a powerful
technique (been doing that with Perl for more than a year).  The problem
is storing the object in a DB.

Serialization has always bugged me as non-optimal approach...  using a
database as a file system rather than a database.  Are there any
non-serializing DB's for XML out there?  It doesnt seem like a hard
problem to solve...

Aside from that, the utility of the DB is significantly lowered as a
language independent persistant data object repository if you need to
deal explicitly with one languages serialization methods (e.g. no
language independent de-serialization methods).  This point has also
irked me, and I dont know of a good solution to serialization (apart
from not serializing).  Add to this the performance hit of walking a
complex data structure and formatting it for the serialization
process...


Joe

On Thu, 2002-07-11 at 08:57, Patrick McConnell wrote:
> 
> 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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Joe Landman,
email: landman at scientificappliance.com
web  : http://scientificappliance.com