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This article is part of the supplement: IEEE 7th International Conference on Bioinformatics and Bioengineering at Harvard Medical School

Open Access Open Badges Research

ILOOP – a web application for two-channel microarray interwoven loop design

Mehdi Pirooznia1, Ping Gong2, Jack Y Yang3, Mary Qu Yang4, Edward J Perkins5 and Youping Deng1*

Author Affiliations

1 Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, 39406, USA

2 SpecPro Inc., Vicksburg, MS, 39180, USA

3 Harvard University, Harvard Medical School, Cambridge, MA 02140-0888, USA

4 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20852, USA

5 Environmental Laboratory, U.S. Army Engineer Research and Development Center, Vicksburg, MS, 39180, USA

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BMC Genomics 2008, 9(Suppl 2):S11  doi:10.1186/1471-2164-9-S2-S11

Published: 16 September 2008


Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available from webcite.