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Nucleic Acids Research Advance Access originally published online on May 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W86-W90; doi:10.1093/nar/gkm302
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W86-W90
© 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.

Articles

MAGMA: analysis of two-channel microarrays made easy

Hubert Rehrauer*, Stefan Zoller and Ralph Schlapbach

Functional Genomics Center Zurich, UZH/ETH Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland

*To whom correspondence should be addressed. Tel: +41 44 635 3924; Fax: +41 44 635 3922; Email: Hubert.Rehrauer{at}fgcz.uzh.ch

Received January 30, 2007. Revised March 30, 2007. Accepted April 15, 2007.

The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch.


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