[Bioclusters] RDBMS and Bioinformatics

Tim Cutts bioclusters@bioinformatics.org
Mon, 15 Mar 2004 18:54:58 +0000

On 15 Mar 2004, at 18:28, Matthew Laird wrote:

> If you have money.... sure.  But most people tend to use MySQL, and 
> most
> Bioinformatics packages are designed with MySQL in mind.

The Sanger Institute uses both MySQL and Oracle.  Oracle gets used for 
heavily transaction-oriented work, such as laboratory entity tracking, 
and hence also for the sequencing efforts here.

Ensembl, which is hosted on our hardware is, as others have pointed 
out, run off MySQL - mostly because of Ensembl's open source nature, 
but also because read query performance on MySQL is pretty good, when 
you don't need transactions, and so can use the MyISAM table format.


Dr Tim Cutts
Informatics Systems Group
Wellcome Trust Sanger Institute
Hinxton, Cambridge, CB10 1SA, UK