Singapore's Biopolis builds its biomedical grid

By Sophia Heng
Wednesday, 20 February, 2002

THE Singapore Bioinformatics Institute (BII) is exploring the potential of Itanium processor clustering based on Linux open source code as a platform for its Biomedical Grid.

"We are already in the process of deploying Itanium systems in our testbed," said BII's acting director Gunaretnam Rajagopal. "We hope to scale up as we gain experience and expertise in using these platforms."

The Itanium processor is the first in a family of 64-bit products by Intel.

Grid computing is central to Singapore's biomedical initiatives because it provides readily available and relatively cheap computing power that can be mustered in the form of clusters from basic PC technologies. It is suitable for bioinformatics because data storage systems are now affordable enough for large quantities of data to b e stored, processed and distributed or updated on a regular basis.

Singapore's Biomedical Grid, targeted to be completed by June 2003, will allow sharing, collaboration and cooperation among all research institutes and centres involved in biomedical activities funded by the Biomedical Research Council, A*Star (Agency for Science, Technology & Research), universities and polytechnics.

Louis Lim, executive director of A*Star's Biomedical Research Council, said that biomedical science relied heavily on information science, "therefore it is important to have an excellent IT infrastructure to support and sustain biomedical activity in Singapore."

BII intends to install 16 CPUs and will be using the Intel Itanium clusters sourced from Compaq and Hewlett-Packard as part of the test bed for the Biomedical Grid.

"We will be using them to learn how to use the capabilities of the processor in biomedical computing by porting and tuning open source code," Rajagopal said. "In addition, we will be exploring the hardware capabilities of connecting these processors via a Linux cluster using Myrnet switches to see how they perform as a cluster."

BII and Intel last week signed a memorandum of understanding to collaborate on the government's biomedical sciences initiative. Christian Morales, vice-president and general manager of Intel in Asia Pacific, said Intel would provide the BII with knowledge and expertise in the areas of -super computing training, peer-to peer technology, porting consulting, security initiatives and advanced training of selected staff from leading research institutes.

According to Rajagopal, BII will install genomic database applications related to comparison of gene functions and structures and molecular modelling of proteins on the Biomedical Grid platform.

Clusters in BII, National University of Singapore and Nanyang Technological University will be linked to test the grid middleware, study the network characteristics and where necessary make improvements on the relevant architecture, Rajagopal said.

The Biomedical Grid will also be linked to other R&D institutions worldwide. Rajagopal said the Biomedical Grid would be connected to the TeraGrid project in the United States involving San Diego Supercomputer Centre, Argonne National Lab, The National Centre for Supercomputing Applications and CalTech.

The BII is also discussing collaboration efforts with European and Japanese grid organisations in the development of middleware and application software.

"There are many technical, organisational and scientific/computational challenges that need to be overcome before a fully working grid computing infrastructure that links compute resources in Singapore and elsewhere becomes a reality," Rajagopal said.

Singapore's Biomedical Grid will be the heart of Biopolis, a dedicated science park for lab-based R&D activities tailored to biomedical sciences companies and research activities encompassing drug discovery research, clinical development and medical device research. The Biopolis, due for completion in June next year, will be located in Buona Vista.

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