[Biodevelopers] Re: [Bioclusters] RDBMS and Bioinformatics

[Glenn T. Colby]

On Mon, 15 Mar 2004, Hong Zhang wrote:

> Most people may not choose ORACLE due to its price.

I concur, but many people do not realize that Oracle comes in several
editions -- Many features of the Enterprise Edition (very expensive) may
not be necessary for your application.  In our case, the Standard Edition
has met our needs well for a fraction of the cost.  If you intend to put
up a very large publicly-available database that requires
parallel-processing, hot-backups, etc., then sure, you would need
Enterprise edition.  I would be interested in hearing what others have to
say about the Standard vs. Enterprise Edition issue.

I used Sybase before (for the Mouse Genome Database) and found it performs
well, but nothing can match Oracle's proprietary PL/SQL language.  If you
intend to write a lot of code at the DB level (stored procs, triggers,
etc.), then Oracle is the way to go, IMHO.  If you are going to write your
business logic at a higher level, then Sybase may meet your needs for a
lower cost.

Sybase *does* offer *huge* discounts to non-profits, which I believe is
why many of the publicly-available biological databases started using it
back in the 90s.  If they had it to do over again, I suspect they would
bite the bullet and go for Oracle.

I was also told that the newest release of Oracle (10g) has built-in BLAST
support of some type.  We will see how that turns out...

--Glenn

       ,----------------.   ,-------.   ,--------.   ,-----------.
      /  Glenn T. Colby  \ /  Zappa  \ /  Brahms  \ /  Ellington  \
,----'                    `----------------------------------------.
| gcolby at mdibl.org                   MDI Biological Laboratory     |
|   Information Systems Specialist   Department of Bioinformatics  |
|   tel: (207) 288 9880 x110         Salsbury Cove, ME  04672  USA |

>
> On Mon, 15 Mar 2004, Dr. Hari Koduvely wrote:
>
> > Hi, I would like to know if RDBMS (Relational Data
> > Base Management Systems) is extensively used in
> > Bioinformatics Data Bases. If it indeed true, what is
> > the most suited RDBMS, Oracle?
> >
> > Regards
> > -Hari
> >
> > =====
> > Dr. Hari Koduvely, Ph.D.
> > Research Scientist
> > Unilever Research India
> > 64 Main Road, Whitefield
> > Bangalore 560066, INDIA
> > Ph:+91 80 5139 5629 (Office)
> >      +91 80 5221790 (Res)
> >
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> >
>
> --
> Hong Zhang, MIS
> Bioinformatics Analyst
> Dana Farber Cancer Institute
> Harvard Medical School
> 44 Binney St, D1510A
> Boston MA 02115
> Email: hong.zhang at research.dfci.harvard.edu
> Phone: 617-632-3824
> Fax: 617-632-3351
>
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