MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs
1 Computer Engineering Department, Middle East Technical University, Ankara, Turkey
2 Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
3 Department of Industrial and Systems Engineering, The Ohio State University, Columbus, OH, USA
BMC Bioinformatics 2009, 10:304 doi:10.1186/1471-2105-10-304Published: 22 September 2009
Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments that can help minimize the errors in the resulting inferences has recently received increasing attention. However, a general and scalable search tool and a corresponding database of optimal designs were still missing.
An efficient and scalable search method for finding near-optimal dual-channel microarray designs, based on a greedy hill-climbing optimization strategy, has been developed. It is empirically shown that this method can successfully and efficiently find near-optimal designs. Additionally, an improved interwoven loop design construction algorithm has been developed to provide an easily computable general class of near-optimal designs. Finally, in order to make the best results readily available to biologists, a continuously evolving catalog of near-optimal designs is provided.
A new search algorithm and database for near-optimal microarray designs have been developed. The search tool and the database are accessible via the World Wide Web at http://db.cse.ohio-state.edu/MicroarrayDesigner webcite. Source code and binary distributions are available for academic use upon request.