Exploring Williams--Beuren syndrome using myGrid

  • Authors:

  • R. D. Stevens;H. J. Tipney;C. J. Wroe;T. M. Oinn;M. Senger;P. W. Lord;C. A. Goble;A. Brass;M. Tassabehji

  • Affiliations:

  • Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK,;University of Manchester, Academic Unit of Medical Genetics, St. Mary's Hospital, Hathersage Road, M13 0JH, UK;Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK,;European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK;Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK,;Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK,;Department of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK,;University of Manchester, Academic Unit of Medical Genetics, St. Mary's Hospital, Hathersage Road, M13 0JH, UK

  • Venue:
  • Bioinformatics
  • Year:
  • 2004

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Abstract

Motivation:In silico experiments necessitate the virtual organization of people, data, tools and machines. The scientific process also necessitates an awareness of the experience base, both of personal data as well as the wider context of work. The management of all these data and the co-ordination of resources to manage such virtual organizations and the data surrounding them needs significant computational infra-structure support. Results: In this paper, we show that myGrid, middleware for the Semantic Grid, enables biologists to perform and manage in silico experiments, then explore and exploit the results of their experiments. We demonstrate myGrid in the context of a series of bioinformatics experiments focused on a 1.5 Mb region on chromosome 7 which is deleted in Williams--Beuren syndrome (WBS). Due to the highly repetitive nature of sequence flanking/in the WBS critical region (WBSCR), sequencing of the region is incomplete leaving documented gaps in the released sequence. myGrid was used in a series of experiments to find newly sequenced human genomic DNA clones that extended into these 'gap' regions in order to produce a complete and accurate map of the WBSCR. Once placed in this region, these DNA sequences were analysed with a battery of prediction tools in order to locate putative genes and regulatory elements possibly implicated in the disorder. Finally, any genes discovered were submitted to a range of standard bioinformatics tools for their characterization. We report how myGrid has been used to create workflows for these in silico experiments, run those workflows regularly and notify the biologist when new DNA and genes are discovered. The myGrid services collect and co-ordinate data inputs and outputs for the experiment, as well as much provenance information about the performance of experiments on WBS. Availability: The myGrid software is available via http://www.mygrid.org.uk