Scottish profs get IT bio-funding

Sunday 18th November 2012
From research to prediction, slides 1 and 6. Courtesy;

While three players at the EMBL European Bioinformatics Institute receive funds from the Biotechnology and Biological Sciences Research Council (BBSRC) which is allocating an investment of £5.5m for 10 research projects, a trio of University Professors based at Dundee and Edinburgh respectively, have won research funds for their work

The Dundee led project, receiving around £700,000 from BBSRC, is headed by Professor Geoffrey Barton from Dundee College of Life Sciences, Resource for Protein Structure Prediction and Sequence Analysis will provide scientists with the software tools to take raw genetic sequence data and make prediction about the structure and function of the proteins that they encode, helping to make use of the enormous volumes of DNA sequence data that are generated in modern bioscience.

“We have developed tools at Dundee that are now  used by researchers around the world thousands of times a month and across the scientific spectrum, from research into diseases like cancer to areas such as  plant sciences,” said Professor  Barton,

“Research now generates massive amounts of data which has to be handled, stored and analysed. The work we have done and which we continue to develop provides fundamental capabilities for researchers to use this data efficiently.”

Edinburgh for visualisation  and parallel networking

At University of Edinburgh,  Professor Thomas Freeman (left),  with Dr Anton Enright, (right) EMBL European Bioinformatics Institute are awarded funding for the Development of a Rapid Processing Pipeline and Graph-based Visualization for the Analysis of Next Generation Sequencing Data .  

Here the development of BioLayout Express3D has been specifically designed for visualisation, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological data is a powerful tool for the visualisation and analysis of network graphs, primarily, but not exclusively, from biological data.

SPRINT for HPC micro analysis
Professor Peter Ghazal (RIGHT) at University of Edinburgh is also awarded for the SPRINT (Simple Parallel R INTerface) approach to network biology. This is an easy-to-use parallel version of R, a statistical language that processes the data gleaned from microarray analysis, a technique which allows the simultaneous measurement of thousands to millions of genes or sequences across tens to thousands of different samples.

Processing the data that is produced by microarray analysis tests the limits of existing bioinformatics computing infrastructure. An approach  is to use HPC systems, which offer more processors and memory than desktop computer systems. However, R must be able to utilise multiple processors if it is to fully exploit the power of HPC systems to analyse genomic data.

There are existing modules that enable R to do this, but they are either difficult for HPC novices or cannot be used to solve certain classes of problem. SPRINT allows parallelised functions to be added to R without the need to master parallel programming methods, enabling the easy exploitation of HPC systems. SPRINT will greatly increase the computing power available to many researchers and is therefore a unique opportunity to accelerate the discovery of the genes linked to diseases.

The other awards were to:

  •  Professor Bonnie Ann Wallace,  Birkbeck College with Dr Robert Janes, Queen Mary, University of London – The Protein Circular Dichroism Data Bank, the DichroWeb Server, and ValiDichro: Data Sharing, Analysis and Standards Resources for CD Spectroscopy.
  • Dr Alex Bateman and Dr Paul Kersey, EMBL European Bioinformatics Institute – The RNA central database of non-coding RNAs Dr Nicolas Le Novere, EMBL European Bioinformatics Institute – BioModels Database, the comprehensive resource for   computational models in biology and  Mr Henning Hermjakob, EMBL European Bioinformatics Institute – DAS in the age of data-driven research
  • Professor Michael J Sternberg, Imperial College London – Maintaining and extending PHYRE2 to deliver an internationally-recognised resource for protein model
  •  Professor Pedro Mendes, University of Manchester – COPASI - Open source software for advanced biochemical network modelling
  •  Professor Andy Greenland, National Institute of Agricultural Botany (NIAB) –
    A community resource in wheat transformation
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