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Home > iSGTW 07 May 2008 > iSGTW Feature - Cell biologists dig new DiGS

 

Feature - Cell biologists dig new DiGS


Cell biologists at the University of Edinburgh and University of Oxford are using grid technology called DiGS to support their investigation into the transport and anchoring of mRNA in Drosophila flies.
Image courtesy of Wikipedia

As cell biology moves from labs to computer desktops, researchers must deal with increasingly vast volumes of data. Traditional ways of sharing this data—such as physically shipping hard drives—just cannot keep up.

UK Quantum Chromodynamics has been working to solve these data management challenges using grid technology since 2002, developing QCDGrid to share, publish and preserve their large datasets. And although UKQCD are a physics outfit, they’ve made their software—renamed DiGS or Distributed Grid Storage—available to the wider scientific community.

First off the block: biology

“The EPCC team focused initially on the needs of particle physicists,” explains George Beckett of the Edinburgh Parallel Computing Centre, “but it is clear that the success of this work can bring significant benefits to other scientific groups as well.”

Cell biologists have been the first to get started. The EPCC and UKQC are now working to tailor DiGS technology to biological applications. The new project, called “A Data Grid For Cell Biology,” aims to create a simple and secure method for sharing biological data.

Images such as this, created using data from a specialized microscope at the University of Oxford, can be transported quickly and easily to team members at the University of Edinburgh. This image shows RNA movement in a living Drosophila embryo.
Image courtesy of Ilan Davis

A fly-ing start for Drosophila project

The prototype system will provide data generated by a microscope in Oxford University for use by collaborators at Edinburgh University, who are working on an RNA-tracking project using Drosophila flies.

Researcher Russell Hamilton of the University of Oxford says the approach can only be good for the science. “Biologists can spend their time performing experiments and analysing results rather than transferring files between labs,” he says.

Alan Irving from the group at Liverpool has found working with the system a lot easier than previous methods. “In the past I’ve had to battle with different computer systems and search through endless directories to get my hands on the data files I need. Now I can access all these files using one, easy-to-use system.”

DiGS has proven so successful that DEISA—the Distributed European Infrastructure for Supercomputing Applications—have shortlisted it as one of three data management technologies to be evaluated for future deployment across the DEISA infrastructure.

- Neason O-Neil, GridPP

This project is funded by Science and Technology Facilities Council through its Industrial Programme Support Scheme after a successful feasibility study run with money from edikt2 (e-Science Data, Information and Knowledge Transformation), based in Edinburgh University, UK.

 

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