Human genome on Compaq

Houston 26 June 2000When researchers at Celera Genomics, the Sanger Centre in the United Kingdom, the Whitehead Institute, and the National Institutes of Health announced that they had collaborated in completing the map of the human genome, they were highlighting a monumental scientific achievement made possible by high-performance computing technology from Compaq.

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The supercomputers used by Celera Genomics, the Sanger Centre, and the Whitehead Institute are Compaq systems running Tru64 UNIX and TruCluster software.

"This is the first time in history that the human genetic code has been assembled in a linear fashion", according to J. Craig Venter, Celera's Chief Executive Officer. Celera had to assemble the 3.2 billion base pairs in their correct order, a computational challenge among the largest ever attempted. During the assembly process, Celera deployed more than 600 Alpha processors from Compaq capable of nearly a trillion operations per second. The final assembly computations were run on Compaq's new GS160 because the algorithms and data required 64 gigabytes of shared memory to run successfully.

Since the start of the human genome project in the early 1990s, Compaq has been providing tools to handle the staggering amount of data and computing power necessary to decipher the 3.2 billion "base pairs" which make up the genome, all the genes and related DNA. Established by Wellcome Trust and the British Medical Research Council, the Sanger Centre in the United Kingdom needed a computing infrastructure that could meet the challenge of mapping and sequencing the human genome. According to Phil Butcher, Sanger's head of Information Technology, they based their choice on three steadfast design principles: scalability, adaptability and resiliency.

Sanger's initial configuration consisted of 160 Compaq Alpha workstations, four Compaq 1200 systems, and a small PC cluster running BLAST (basic local alignment search tool) to support public search access of their genomic databases over the Internet.

The Centre has continued to supplement their computing infrastructure, eventually acquiring approximately 250 Compaq systems and workstations running Tru64 UNIX. The Centre also employs a Compaq StorageWorks RAID system with four terabytes of disk space, a 300 GB Network Appliances RAID subsystem, and 48 Compaq Deskpro PCs.

Since 1990, Compaq has been at the forefront of developing and providing high-performance computer architectures that meet the needs of pharmaceutical, biotechnology and medical companies. "Today, it is increasingly difficult to separate the advances in biotechnology from advances in high-performance computing", explained Ben Rosen, Chairman of the Board of Compaq, during his keynote address at BIO '99. "In fact, some leading scientists believe that high-end computing is the future of biology and medicine . . . it will take increasingly powerful computers and software to gather, store, analyse, model and distribute information."

In 1998, Compaq was selected by Celera Genomics as their IT partner. Compaq designed and equipped Celera's data centre, eventually installing and interconnecting nearly 700 CPUs and 70 terabytes of storage.

In 1999, Compaq created a Bioinformatics Expertise Center in Marlboro, Massachusetts to better support customers and business partners in the industry. Compaq's Cambridge, Massachusetts Research Laboratory also began a focus on bioinformatics, contributing to the optimisation of applications performance and the development of data mining algorithms for genetic data.

In 1999, Compaq was selected by MIT's Whitehead Institute for Genomics Research to supply the IT infrastructure for their human genome efforts. Whitehead operates the largest public sequencing centre in the United States, and is one of four key centres funded by the National Institute of Health to complete the draft of the human genome, recently announced. The Institute also relies on Compaq ES40 systems and Compaq StorageWorks to manage and analyse their genomic data.

Compaq's most recent contribution to the Human Genome Project is a cluster of ES40 systems with 100 CPUs and a terabyte of storage, located at Compaq's Enterprise System Lab in Littleton, Massachusetts, that is being made available to the research institutions to complete the annotation of the human genome. More details on Compaq architecture for human genome research are available in the VMW January 2000 article Sanger Centre's scientists speed the search for the secret of life with decoding of human chromosome.


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