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Bioinformatics Advance Access published online on September 17, 2008
Bioinformatics, 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

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

*To whom correspondence should be addressed. Dr. Khalid Belhajjame, E-mail: Khalid.Belhajjame{at}manchester.ac.uk


  Abstract

Motivation: The Functional Genomics Experiment Object Model (FuGE) supports modelling of experimental processes either directly or through extensions that specialise 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 standardised 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: Prof. Alfonso Valencia

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

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