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Nucleic Acids Research Advance Access published online on May 30, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn335
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© 2008 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.

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bioNMF: a web-based tool for nonnegative matrix factorization in biology

E. Mejía-Roa1, P. Carmona-Saez2, R. Nogales1, C. Vicente1, M. Vázquez3, X. Y. Yang1, C. García1, F. Tirado1 and A. Pascual-Montano1,*

1Computer Architecture Department, Complutense University, 28040, 2Integromics, S.L. Calle Darwin 3. 28049 and 3Software Engineering Department, Complutense University, 28040 Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 913944420; Fax: +34 913944687; Email: pascual{at}fis.ucm.es

Received January 30, 2008. Revised April 18, 2008. Accepted May 10, 2008.

In the last few years, advances in high-throughput technologies are generating large amounts of biological data that require analysis and interpretation. Nonnegative matrix factorization (NMF) has been established as a very effective method to reveal information about the complex latent relationships in experimental data sets. Using this method as part of the exploratory data analysis, workflow would certainly help in the process of interpreting and understanding the complex biology mechanisms that are underlying experimental data. We have developed bioNMF, a web-based tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications in biology. This online tool provides a user-friendly interface, combined with a computational efficient parallel implementation of the NMF methods to explore the data in different analysis scenarios. In addition to the online access, bioNMF also provides the same functionality included in the website as a public web services interface, enabling users with more computer expertise to launch jobs into bioNMF server from their own scripts and workflows. bioNMF application is freely available at http://bionmf.dacya.ucm.es.


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