Book Review Department Editor Warren Keuffel

Applying Grid Computing to Bioinformatics

Art Sedighi

Grid Computing in Life Science: First International Workshop on Life Science Grid by Akihiko Konagaya and Kenji Satou, eds., Springer, 2005, ISBN 3-540-25208-8, 188 pp., US$58.00.

Grid Computing in Life Science collects 14 papers from the First International Life Science Grid Workshop, held in Kanazawa, Japan in 2004. The papers discuss life science applications of Grid systems, especially for bionetwork research and systems biology. They cover a broad range of popular bioinformatics methodologies and techniques, such as data integration from genome to phenome, mathematical modeling, simulation techniques, and high-performance computing.

Several papers discuss current Grid infrastructure setups. “The Architectural Design of High-Throughput Blast Services on OBIGrid,” by Fumikazu Konishi and Akihiko Konagaya, discusses an Open Bioinformatics Grid architecture focused on parallelizing Blast searches, analyzing and demonstrating the architecture. A second OBIGrid paper is “Genome-Wide Functional Annotation Environment for Thermus thermophilus in OBIGrid,” by Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, and Akihiko Konagaya. They discuss bioinformatics genomic search algorithms that used the OBIGrid environment.

“Developing a Grid Infrastructure for Functional Genomics,” by Richard Sinnott, Micha Bayer, Derek Houghton, David Berry, and Magnus Ferrier, discusses a distributed environment for determining the properties of genes. The architecture is particularly interesting because it uses Web services to integrate several heterogeneous databases. The authors explore such complex topics as security and access rights. 

In “Mega Process Genetic Algorithm Using Grid MP,” Yoshiko Hanada, Tomoyuki Hiroyasu, Mitsunori Miki, and Yuko Okamoto introduce a genetic algorithm that uses the Tabu local search mechanism. They use United Devices’ Grid MP to test and run their application. The authors demonstrate the use of commercial software applications for research, arguing that bioinformatics research isn’t far behind industry.  

Above all, the papers in this compact text are indicative of the broad, complex bioinformatics field. OBIGrid receives a lot of attention throughout the proceedings—a good sign that openness has already made it to the industry. I highly recommend this book for researchers and practitioners interested in bioinformatics.

is a senior consulting engineer at DataSynapse and a freelance writer. Contact him at

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