[Biodevelopers] RDBMS and Bioinformatics

[Malay]

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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Hi Hari:

I am sure it is. There are several ways to store the data. Sometimes it 
makes sense in using simple flat files for storage and information 
retrieval and they can be quite fast. SRS comes in my mind.

Like any other cases of software engineering, academic world in 
dominated by open source software. MySQL dominates Internet and most of 
the times is used as the dominant storage of date. Though it lacks 
advanced features of high-end databases such as views, bioinformatics 
most of the time does not require such high-end features and you can 
simply mimic these features with some tricks. Use of expensive 
commercial databases such as ORACLE (leaving out MSSQL, which will tie 
you with particular platform) can not be justified for most situations.

I hope it gives some flavours.

Malay
mbasu(at)ncbi.nlm.nih.gov