Skip Navigation


Bioinformatics Advance Access originally published online on November 17, 2007
Bioinformatics 2008 24(5):738-740; doi:10.1093/bioinformatics/btm559
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrowOA All Versions of this Article:
24/5/738    most recent
btm559v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Draghici, S.
Right arrow Articles by Romero, R.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Draghici, S.
Right arrow Articles by Romero, R.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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

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

*To whom correspondence should be addressed.


  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 timeconsuming, 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 4 h 30 min of user interaction time forexperiment annotation, and 45 min for data upload/download. In contrast, for the same experiment, KUTE required only 28 min of user interaction time for experiment annotation, and 3.3 min for data upload/download.

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

Contact: sod{at}cs.wayne.edu

Associate Editor: John Quackenbush

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.