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Bioinformatics Advance Access published online on November 17, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm559
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

KUTE-BASE: Storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours

Sorin Draghici 1,*, Adi L. Tarca 1,2,3, Longfei Yu 1, Stephen Ethier 3 and Roberto Romero 2

1Dept. of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202
2Perinatology Research Branch-NIH/NICHD, 4 Brush, 3990 John R, Detroit, MI 48201
3Barbara Ann Karmanos Cancer Institute,, 110 Warren Ave., Detroit, MI 48201

*To whom correspondence should be addressed. Dr. Sorin Draghici, E-mail: sorin{at}wayne.edu


  Abstract

Motivation: The BioArray Software Environment (BASE) is a very popular MIAME-compliant, web-based microarray data repository. However in BASE, like in most other microarray data repositories, the experiment annotation and raw data uploading can be very time consuming, especially for large microarray experiments.

Results: We developed KUTE (Karmanos Universal daTabase for microarray Experiments), as a plug-in for BASE 2.0 that addresses these issues. KUTE provides an automatic experiment annotation feature and a completely redesigned data work-flow that dramatically reduce the human-computer interaction time. For instance, in BASE 2.0 a typical Affymetrix experiment involving 100 arrays required 4h 30 mins of user interaction time for experiment annotation, and 45 mins for data upload/download. In contrast, for the same experiment, KUTE required only 28 mins of user interaction time for experiment annotation, and 3.3 mins for data upload/download.

Availability: http://vortex.cs.wayne.edu/kute/index.html.

Contact: sorin{at}wayne.edu

Associate Editor: Prof. John Quackenbush

Received on October 14, 2007; revised on October 14, 2007; accepted on November 2, 2007

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