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Bioinformatics Advance Access published online on July 16, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn363
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Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The Protein Information and Property Explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

H Ramos 1, P Shannon 1,* and R Aebersold 2,3,1

1Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA, 2Institute of Molecular Systems Biology, and Competence Center for Systems Physiology and Metabolic Disease, ETH Zurich, Zurich, Switzerland, 3Faculty of Science, University of Zurich, Zurich, Switzerland.

*To whom correspondence should be addressed. Paul Shannon, E-mail: pshannon{at}systemsbiology.org


  Abstract

Motivation: Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the Protein Information and Property Explorer (PIPE) the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server side data storage using Hibernate.

Availability: http://pipe.systemsbiology.net

Contact: pshannon{at}systemsbiology.org

Associate Editor: Dr. Trey Ideker

Received on April 8, 2008; revised on June 13, 2008; accepted on July 14, 2008

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