University of Dundee

Over £1.5 million to Jason Swedlow and OME to tackle bioscience 'big data' challenges

13 Feb 2015

Jason Swedlow and the OME team are to lead a major project to help tackle one of four key biosciences `big data’ challenges identified by the UK’s Biotechnology and Biological Sciences Research Council.

The BBSRC has announced an investment of £7.5 million in new infrastructure to tackle bioscience big data challenges. The new funding will improve the storage and curation of enormous datasets that will unlock untold discoveries in important areas like health, agriculture and sustainable fuels.

£1.79 million of the funding has been awarded to a project led by Professor Jason Swedlow at the College of Life Sciences, University of Dundee to build a next generation image repository, allowing access for scientists and the public around the world to genome-scale imaging datasets. 

What is the Open Microscopy Environment? Watch the film

Imaging in the life sciences has undergone a revolution in recent years. It is used to understand the behaviour of organisms, the formation of embryos, the structure and dynamics of cells, and the function and interactions of molecules that are the building blocks of life. However, imaging datasets are complex, diverse in character or content, and often extremely large. This means that they are rarely shared or published.

Professor Swedlow and his Open Microscopy Environment (OME) team in the College of Life Sciences at Dundee will work with the European Bioinformatics Institute (EMBL-EBI) and the University of Cambridge to create a next generation image data resource to host, serve, and make available original scientific image data that underpins life sciences research.

“We are seeing things that we have never been able to see before, thanks to a new generation of imaging technology and techniques,” said Professor Swedlow. “But with these advances also come challenges. The new imaging techniques generate enormous amounts of complex data and so special tools are required to mange, share and analyse that data.. At Dundee we have built several open software platforms that are used by scientists worldwide for accessing and managing these enormous datasets.  

“This new project will take that work up another level.”

The new resource will be built using OME’s open source technologies and will be housed at EMBL-EBI, which is the established home of molecular and structural life sciences data. The resource will interface with ELIXIR, Europe’s research infrastructure for life science informatics. It will build links with established molecular and structural resources and work towards a seamless integration of these data, so that any scientist can easily browse, query and compute on genomic, structural and phenotypic data across several scales.

Dundee has an international reputation for excellence in imaging and microscopy. The University recently announced the launch of the Dundee Imaging Facility, an £8million resource helping to drive the University’s objectives to develop transformational research in physical, life and medical sciences.

OME’s work is part of this internationally recognised activity.  Professor Swedlow founded OME with colleagues at MIT in 2000.  Since then, OME has grown into an international consortium, based in Dundee, that has revolutionised the ability of researchers and industrial partners to handle, analyse, share and interpret vast amounts of image data.

Biological Sciences research at Dundee was rated top among universities in the UK in the 2014 Research Excellence Framework. The REF is the main test of research quality carried out by higher education funding bodies.

BBSRC is strengthening investment in bioinformatics and biological resources, focusing on the needs of the research community, and facilitating the development of sustainable models of operation.

Professor Jackie Hunter, BBSRC Chief Executive, said, “This funding is one example of BBSRC strengthening investment in big data infrastructure so that scientists can access vast quantities of data to create the knowledge that will be needed to tackle the challenges of tomorrow.

“We experience problems coping with our own local data storage – videos, picture and other media take up huge amounts of space on our home computers. In life sciences, the data required for research is unimaginably larger and growing at unprecedented rates. The reference wheat genome takes up about 6 Gigabytes, for example, and a high resolution video of the human heart of just one patient can be around 50 Gigabytes, or the equivalent of 50 feature length films at standard definition.

“This data provides a mine of information that will help us now and in the future but it needs to be properly stored, curated and made easily accessible. These investments will help us achieve this in important areas, from discovering new drugs to breeding crops that are more resistant to climate change.”

NOTES TO EDITORS

The other projects being supported by the BBSRC investment are:
£2M for big data infrastructure for crop genomics
•    Stimulating new opportunities in crop development to help improve some of the world’s most important crops.
•    Dr Sarah Ayling, The Genome Analysis Centre (TGAC), with EMBL-EBI

£1.9M to establish infrastructure for functional annotation of farmed animal genomes
•    To help feed us in the future by providing an important framework for the discovery of genetic variation in domesticated animals and how that influences their characteristics
•    Lead: Professor Alan Archibald, The Roslin Institute at the University of Edinburgh, with EMBL-EBI and TGAC

£1.78M to create cyber infrastructure for the plant sciences.
•    The UK iPlant node that will help to spread expertise and best practice between the UK and US
•    Professor Jim Beynon, University of Warwick, with TGAC, University of Liverpool, University of Nottingham, University of Arizona and the Texas Advanced Computing Center

 

 

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