University of Dundee

Wellcome Resource Grant For Computational Biology

24 Nov 2013

Professor Geoff Barton of the College of Life Sciences has been awarded a highly-prized Biomedical Resource Grant from the Wellcome Trust. Geoff Barton, Professor of Bioinformatics at the University of Dundee, is Head of the new CLS Division of Computational Biology, an interdisciplinary group, which is the focal point for the convergence of computing, mathematics and the physical sciences with experimental biology.

The funded project, Jalview tackles the problem of ‘Big Data’ in biology - the huge amount of information currently being produced through biological research and genome sequencing - by integrating large collections of biological sequences, such as DNA, RNA and protein with information about their function and role in disease.

Professor Barton said, “The Wellcome Grant will allow us to maintain and enhance Jalview, a user-friendly application currently used by tens of thousands of scientists world-wide to help them understand the function of genes and the effect mutations in DNA have on gene function and disease. This award will help us to further develop the platform making bug-fixing and dissemination more resilient and responsive so that it can meet the demands of our substantial user community in the face of new sequence analysis challenges.” 

Jalview works on computers that run Windows, Apple and Linux operating systems and provides tools to align sequences to see which regions are similar and so help work out what their function is. It connects to over 1000 different international databases that store information about sequences and can show that information graphically on the alignment to help the user understand their wider scientific context.

It has features to allow calculations, too time-consuming for a laptop, to be routed to remote servers that perform these tasks efficiently. Jalview also has built in functions to calculate and display evolutionary trees and the three-dimensional structures of proteins and other molecules. The application is used extensively in teaching and the Wellcome Grant will allow the team to make it easier for scientists and students to get the best out of Jalview, by developing manuals and online videos that show how to use it, and allow them to run courses throughout each year.

Dr Jim Procter is the co-ordinator of Jalview, to maintain the software, develop new features and training material and will take a leading role in managing the new Wellcome Trust funded personnel.

The grant of £842,437 will support two full-time Scientist-Programmers and create the opportunity to employ one Outreach and Training Officer for a period of five years.  It will enable scientists working on genetic disease to make sense of their data and so improve the prediction of the effect of mutations in the human genome on disease. Under the supervision of Dr. Proctor, the newly appointed staff will also help the team to improve their training and outreach programmes.

 

More on Jalview for the technologically discerning reader:

Jalview (www.jalview.org) is a GPL-licenced multiple sequence alignment editor and functional analysis workbench that is widely regarded as the standard desktop tool and web applet for these tasks.  The current version of Jalview (2.8) is installed on over 55,000 computers world-wide, and is mentioned on over 100,000 web pages.  The two papers describing Jalview have attracted over 1,400 citations and the most recent paper (2009) was flagged by ISI as a “hot paper”.  Jalview is exploited by major databases such as Pfam/Rfam and the EBI services.  In addition to sophisticated multiple alignment editing functions for DNA, RNA and protein sequences, Jalview provides linked views of phylogenetic trees, DNA and protein sequences, and protein three-dimensional structures.  It communicates with remote servers via SOAP and REST protocols for CPU intensive analyses. Jalview also reads and displays annotations from more than 70 DAS (Distributed Annotation Service) servers available world-wide.

Jalview (www.jalview.org) is a free software system for the analysis, editing and visualisation of biological sequence data. It has been developed continuously since 1996. As an applet it is central to hundreds of web resources including those from the EBI and the Sanger Institute. The Jalview Desktop Application is started over 22,000 times per month by users in more than 100 countries. With the massive expansion in sequencing brought about by Next Generation technologies, the need for a tool like Jalview to help interpret the data and put it into functional context has never been higher. In addition to sophisticated, multiple-sequence alignment editing functions, Jalview provides linked views of phylogenetic trees, DNA and protein sequences, and protein three-dimensional structures.

 

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