ayout 1 - EMBL Grenoble

EMBL-EBI
The Microarray Software Development Team
Previous and current research
Our team has been developing software for ArrayExpress since 2001 (Sarkans et al., 2005). As of
October 2008 ArrayExpress holds data from almost 200,000 microarray hybridisations and is one
of the major data resources of EMBL-EBI. The software development team has built the following
components of the ArrayExpress infrastructure:
• Repository – the archival MIAME-compliant database for the data that support publications;
• Data Warehouse – a query-oriented database of gene expression profiles;
• MIAMExpress – a data annotation and submission system;
• Expression Profiler – a web-based data analysis toolset;
• components used internally by the ArrayExpress production team.
In 2008 we continued our efforts to rebuild the ArrayExpress infrastructure, with an emphasis on
simplification of data management tasks and software components, tighter integration of data submission
and management, and use of automated workflows for data processing.
Ugis Sarkans
PhD in Computer Science,
University of Latvia, 1998.
Postdoctoral research at the
University of Wales,
Aberystwyth.
Technical team leader at
EMBL–EBI since 2006.
The team is also working on data management and integration solutions for domains beyond microarray data. We participate in the MolPAGE
project, an integrated EU effort that aims to find biomarkers for genetic diseases, and type II diabetes in particular. Our team’s main achievements
in this project are: the basic principles and architecture of a framework for managing human sample information and output of highthroughput
analytical platforms; and a generic data reannotation, integration and warehousing solution.
We also participated in data standardisation efforts, in particular MAGE (Spellman et al., 2002) and MAGE-TAB (Rayner et al., 2006) and
regard this work as crucial for the successful development and support of a high-throughput data management infrastructure.
Future projects and goals
The main goal for 2009 is gradually rolling out the next-generation infrastructure for ArrayExpress. The main tasks of this project include:
• replacing the central databases of ArrayExpress with a single unified database;
• organising a system for synchronising the old and new databases, enabling testing and gradual switchover to the new infrastructure;
• porting the existing workflows to the new system;
• porting ArrayExpress interfaces to work with the new back-end.
There are significant changes planned also from the perspective of external users. There is a clear conceptual separation between ArrayExpress
Repository and ArrayExpress Warehouse/Atlas. The former serves the need to provide an archive of scientific record, working in tandem
with journal publications, while the latter provides researchers with biologically meaningful information about expression of genes in
various conditions – either in a more ‘raw’ form (as in the Warehouse), or already processed (as in the Atlas). However, there is no need to
maintain a distinction between these resources from the web access point of view. We plan to build a unified interface that, in response to user
queries, will provide information on all levels of granularity: whole experiments (Repository), sets of expression profiles (Warehouse), and
interesting facts about gene expression (Atlas), providing users with a choice for further investigation.
Selected references
Haudry, Y. et al. (2008). DXpress: a database for cross-species
expression pattern comparisons. Nucleic Acids Res., 36, D87-D853
Jones, A.R. et al. (2007). The Functional Genomics Experiment
model (FuGE): An extensible framework for standards in functional
genomics. Nat. Biotechnol., 25, 1127-1133
Rayner, T.F. et al. (2006). A simple spreadsheet-based, MIAMEsupportive
format for microarray data: MAGE-TAB. BMC
Bioinformatics, 7, 89
Sarkans, U. et al. (2005). The ArrayExpress gene expression
database: a software engineering and implementation perspective.
Bioinformatics, 21, 195-1501
Spellman, P.T. et al., (2002). Design and implementation of
microarray gene expression markup language (MAGE-ML). Genome
Biol., 3, RESEARCH006
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