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Bioinformatics Advance Access originally published online on September 17, 2008
Bioinformatics 2008 24(22):2647-2649; doi:10.1093/bioinformatics/btn496
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A toolkit for capturing and sharing FuGE experiments

Khalid Belhajjame 1,*, Andrew R. Jones 2 and Norman W. Paton 1

1School of Computer Science, University of Manchester, Oxford Road, Manchester and 2Department of Pre-clinical Veterinary Science, Faculty of Veterinary Science, University of Liverpool, Liverpool, L69 7ZJ, UK

*To whom correspondence should be addressed.


  Abstract

Motivation: The Functional Genomics Experiment Object Model (FuGE) supports modelling of experimental processes either directly or through extensions that specialize FuGE for use in specific contexts. FuGE applications commonly include components that capture, store and search experiment descriptions, where the requirements of different applications have much in common.

Results: We describe a toolkit that supports data capture, storage and web-based search of FuGE experiment models; the toolkit can be used directly on FuGE compliant models or configured for use with FuGE extensions. The toolkit is illustrated using a FuGE extension standardized by the proteomics standards initiative, namely GelML.

Availability: The toolkit and a demonstration are available at http://code.google.com/p/fugetoolkit

Contact: khalid.belhajjame{at}manchester.ac.uk

Associate Editor: Alfonso Valencia

Received on July 7, 2008; revised on August 26, 2008; accepted on September 16, 2008

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