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Bioinformatics Advance Access originally published online on November 25, 2004
Bioinformatics 2005 21(8):1495-1501; doi:10.1093/bioinformatics/bti157
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

The ArrayExpress gene expression database: a software engineering and implementation perspective

Ugis Sarkans *, Helen Parkinson , Gonzalo Garcia Lara , Ahmet Oezcimen , Anjan Sharma , Niran Abeygunawardena , Sergio Contrino , Ele Holloway , Philippe Rocca-Serra , Gaurab Mukherjee , Mohammadreza Shojatalab , Misha Kapushesky , Susanna-Assunta Sansone , Anna Farne , Tim Rayner and Alvis Brazma

EMBL Outstation—Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed.

Motivation: The lack of microarray data management systems and databases is still one of the major problems faced by many life sciences laboratories. While developing the public repository for microarray data ArrayExpress we had to find novel solutions to many non-trivial software engineering problems. Our experience will be both relevant and useful for most bioinformaticians involved in developing information systems for a wide range of high-throughput technologies.

Results: ArrayExpress has been online since February 2002, growing exponentially to well over 10 000 hybridizations (as of September 2004). It has been demonstrated that our chosen design and implementation works for databases aimed at storage, access and sharing of high-throughput data.

Availability: The ArrayExpress database is available at http://www.ebi.ac.uk/arrayexpress/. The software is open source.

Contact: ugis{at}ebi.ac.uk


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