Exploring Williams-Beuren syndrome using myGrid

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

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Abstract

    Motivation: In silica 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 infrastructure support. Results: In this paper, we show that myGrid, middleware for the Semantic Grid, enables biologists to perform and manage in silica 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 silica 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. © Oxford University Press 2003; all rights reserved.

    Conference

    ConferenceProceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, Glasgow, UK, July 31-August 4, 2004
    Period1/01/24 → …
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