ayout 1 - EMBL Grenoble

EMBL Research at a Glance 2009
Weimin Zhu
MSc, 1993, University of
Toronto.
Project Manager, GDB
Project, Toronto, until 2000.
Head of Bioinformatics,
Synax Pharmar, Toronto,
Canada, until 2002.
Team leader at EMBL-EBI
since 2002.
Database Research and Development Group
activities
Previous and current research
In February 2008, the Database Applications team was reorganised to form the Database Research
and Development group due to the creation of the PANDA group.
As the Database Application team, the team’s main functions were to provide software/tool development
and maintenance support for the EMBL Nucleotide Sequence Database, and Oracle
database support for all the Oracle databases in the PANDA group. The team also coordinated
hardware resources with the EBI’s Systems and Networking team to ensure the hardware requirements
for the projects within PANDA were met.
The group’s new mandate is to conduct research and development to find new technologies and
solutions to meet challenges related to very large databases (VLDB), which includes data distribution
problems when network speed is a bottleneck, and the solutions required to manage and
query VLDBs efficiently.
The size of bioinformatics databases has been increasing exponentially over the last ten years.
Some core resources are approaching, or have already reached, multi-terabytes in size. This trend
of growth has accelerated in recent years by the introduction of new data types and high-throughput
data producing technologies. Today, we are facing all the challenges a VLDB brings, such as
those in data operational management, data access performance, and data mirroring and distribution. Our current infrastructure in these areas
thus require upgrading in order to realise the full potential of data-rich resources, and optimise the usage of our human and hardware resources.
This year, our main focus has been to analyse the uniqueness of bioinformatics datasets, and conduct research into possible solutions to large
dataset distribution problems, especially over slow networks.
Future projects and goals
The development of a new delta compression algorithm will be continued. The goal is to develop prototype software, along with a data model
and repository to store the pre-computed metadata for the algorithm, to test the key features of this new distribution system. The later stage
of this work will be undertaken in collaboration with the Systems and Networking team and database projects requiring the distribution of
large data files, as well as with external partners in countries with slow network connections to the EBI. This will allow us to benchmark the
network saving for distributing large datasets using delta compression.
The data distribution problem is not unique to the bioinformatics community. It is also a problem for other domains, such as particle physics
and earth science. A workshop is planned for 2009 to share knowledge among scientists across specialisations. Another focus of this workshop
is to bring together Chinese bioinformaticians and network backbone administrators to explore the network optimisation possibilities
between China and the EBI.
We will continue to seek external funding for the project’s long term goal – to have a stable and well-maintained distribution system for the
EBI’s large databases.
Selected references
Cochrane, G. et al. (2008). Priorities for nucleotide trace, sequence
and annotation data capture at the Ensembl Trace Archive and the
EMBL Nucleotide Sequence Database. Nucleic Acids Res., 36, D5-
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