Fighting Malaria With The Grid

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Computing on The GridThe Internet allows users to share information across vast geographical distances. Using similar technology, computing grids provide a capability to share both computing power and storage.

Users interact with the Grid through middleware, which automatically directs jobs to the available computing power, and manages data storage tasks. Metadata supplements this by providing the ability to query vast databases for interesting phenomena.

EGEE1 (Enabling Grids for E-sciencE) is an EC-funded project which has developed an international computing Grid infrastructure. As a result, scientists from a diverse range of disciplines have access to 30,000 CPUs at over 200 sites across 39 countries.

GridPP2 manages the UK’s contribution to this world-wide Grid. As a member of the GridPP collaboration, Glasgow University provides a hardware capacity and metadata development team.

The UK Grid

WISDOM on The GridThe UK Particle Physics Grid played a leading role in EGEE’s latest biomedical data challenge; finding potential news drugs to combat malaria. Each year over one million people, most of them young children living in Africa, are killed by malaria.

The WISDOM3 (Wide In Silico Docking On Malaria) project analysed an average of 80,000 candidate drug compounds per hour, computing the probability that a potential drug will dock with a target protein.

In silico docking is one of the most promising techniques to accelerate and reduce the cost of drug development. Over the lifetime of the WISDOM project over 140 million compounds were tested, yielding many Gigabytes of data.

The next phase of the WISDOM project will exploit metadata techniques to trawl through this vast quantity of data, in order to identify potential anti-malarial compounds.

MiddlewaregLite is EGEE’s middleware for grid computing, providing a framework for building grid applications.

The gLite metadata catalogue is a generic solution which deals with the multi-faceted nature of grid dataset metadata. Its interface was designed to fulfil the requirements of high-energy physics but is generic enough to be used for biomedical applications and was exploited by the WISDOM project.

Metadata Development at GlasgowMetadata can be described as “data about data”. It provides a summary of the information contained within a dataset, helping researchers to identify and select interesting events for further analysis.

The Glasgow Metadata Group focuses on developing metadata-handling tools for the Particle Physics community, including:

An interface which allows physicists to search for interesting datasets amongst the many Terabytes of data produced by the ATLAS detector at CERN.

Integrating metadata search facilities with data analysis tools.Additional information

[1] http://www.eu-egee.org[2] http://www.gridpp.ac.uk[3] http://wisdom.eu-egee.fr

The FutureThe impact of WISDOM goes much beyond malaria. The method developed can be extended to all diseases and this opens interesting industrial perspectives. Until now, the search for new drugs in the academic sector was done at a relatively small scale whereas the WISDOM approach allows a systematic inquiry of all the potentially interesting molecules.