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Profile: Dr Brian Marsden

Profile: Dr Brian Marsden

June 7, 2016

DR BRIAN MARSDEN

Research and Infomatics Group

It is virtually impossible to perform any biomedical research these days without digital data or computers being involved in one way or another.

At the Kennedy Institute, the use of IT and Informatics underpins everything that we do. Whether it is using the Institute’s ‘BookIt’ web-based system to book time on a piece of equipment or order services from the Histology team, or simply storing images from our diverse microscopy platforms on our filestore, it’s important that our scientists find that IT and Informatics enable their work rather than hinder it.

We are fortunate to have a dedicated Research Informatics team at the Institute whose role is to make that aspiration a reality. Working in close collaboration with the Structural Genomics Consortium Research Informatics team in the Old Road Campus Research Building and Target Discovery Institute nearby, our broad range of experience and skills provides support for all Institute members, from basic desktop support all the way to developing new informatics methods for data capture, mining and dissemination.

Whilst the majority of data generated on a day to day basis by our scientists is manageable on desktop computers, there is a clear trend towards larger datasets. In particular ‘Big Data’, often characterised by being varied in content and generated in significant volumes and at high rates, is becoming increasingly prevalent. A clear example of the Institute’s move towards such datasets is the use of genomics data. The recent implosion in costs associated with sequencing has meant that this highly information-rich technique is now becoming a standard tool in contemporary research, and this is certainly true at the Kennedy Institute. For example, being able to assess at the level of a single cell which signalling and regulatory pathways and their proteins are underpinning the behaviour of diseased tissue can provide remarkably detailed insights, for the first time, into how these phenotypes might be modulated in a beneficial manner. On a larger scale, the analysis of the microbiota of the gut and its changes over time and during disease progression is a critical research question associated with the understanding of inflammatory bowel diseases. The sequencing and analysis, known as metagenomics, of this complex mixture of thousands of different strains of bacteria results in extremely large data sets which pose particular IT and informatics challenges if the data are to be analysed in a timely and informative fashion.

To meet these challenges, the Institute is fortunate to have been able to procure an in-house high performance compute (HPC) platform, generously funded by the Kennedy Trust, tailor-made to rapidly process genomics data. Currently made up of 25 specialist computers containing 664 processors connected via a very fast network to each other and very fast and high-capacity storage, our scientists are able to run pipelines of genomics analysis within each computer rapidly thanks to their large number of processors (up to 72) and very large amounts of memory (up to one terabyte). The unusually large vital statistics of these computers are particularly critical for metagenomics analysis where the sequencing data must be compared against many different bacterial genomes, in memory, in parallel to obtain optimal processing speed.

We expect that the diversity and scale of information andits analysis will continue to expand at increasing rates over the coming years, with continued focus on the aggregation and interpretation of data from pre-clinical and clinical sources.

The Kennedy Institute, withits wealth of expertise and collaborative network, underpinned by an effective IT and Informatics platform, is well-placed to take advantage of the opportunities presented.