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Exploring Williams-Beuren syndrome using myGrid.

R D Stevens1, H J Tipney, C J Wroe

  • 1Department of Computer Science, University of Manchester, Manchester, UK. robert.stevens@cs.man.ac.uk

Bioinformatics (Oxford, England)
|July 21, 2004
PubMed
Summary
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The (my)Grid system facilitates in silico experiments for biologists, enabling the management and exploration of bioinformatics data. This Semantic Grid middleware aids in analyzing genomic regions and discovering genes associated with Williams-Beuren syndrome.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • In silico experiments require robust computational infrastructure for organizing people, data, tools, and machines.
  • Managing complex data and coordinating resources for virtual organizations is a significant computational challenge.
  • Awareness of personal data and the broader scientific context is crucial for effective research.

Purpose of the Study:

  • To demonstrate how (my)Grid, a Semantic Grid middleware, enables biologists to conduct and manage in silico experiments.
  • To showcase the application of (my)Grid in bioinformatics experiments for mapping a specific genomic region associated with Williams-Beuren syndrome.
  • To illustrate the use of (my)Grid for exploring experimental results and discovering new biological insights.

Main Methods:

Related Experiment Videos

  • Utilized (my)Grid to manage virtual organizations and computational infrastructure for in silico experiments.
  • Applied (my)Grid to address sequencing gaps in the Williams-Beuren syndrome critical region (WBSCR) by identifying new human genomic DNA clones.
  • Employed a battery of prediction and bioinformatics tools within (my)Grid workflows to analyze DNA sequences, locate genes, and characterize their functions.

Main Results:

  • Successfully used (my)Grid to create, run, and monitor workflows for in silico experiments.
  • Identified newly sequenced DNA clones that filled gaps in the WBSCR, enabling the creation of a complete and accurate map.
  • Discovered putative genes and regulatory elements implicated in Williams-Beuren syndrome through systematic analysis.
  • Collected and coordinated experimental data, inputs, outputs, and provenance information using (my)Grid services.

Conclusions:

  • The (my)Grid system effectively supports biologists in performing and managing complex in silico experiments.
  • (my)Grid facilitates the exploration and exploitation of bioinformatics data, leading to the discovery of biologically relevant information.
  • The middleware provides essential computational infrastructure for virtual organizations and data management in scientific research.