How Computing Power is Driving the Advances in Biotechnology

He sees the genomic industry in three waves, the early pioneers with Genetech, Amgen, Biogen, the industrialization with human genome science, Incyte and Celera, and the industrialization of functional genomics with new technologies and new companies. The revenue growth for bioinformatics IT market is expected from more than 500 million US$ in 2000 to more than 1 billion in 2001 and more than 2.2 billion in 2002. This has the reasons:

• computational biology develops rapidly
• sequence data doubling every 12 months (2 x computing, 4 x storage)
• complex analysis routines produce more data
• improvement in algorithms and hardware efficiencies

IT Vendor Selection in Bioinformatics

Three different elements beneath availability (24x7), scalability and upgradability influence the selection of the vendors. The computation needs fast processors, large memory, 64 bits and lots of processors for the assembly, sequence searching and annotation codes. The data storage needs very large disk space and storage area networks. There reliable fast back-up and retrieval capabilities are necessary and Oracle is standard. The last issue is the data distribution and integration. Here good response time for accessing and sending the data within a web based technology is a must.

Compaq's offerings

Bill Blake listed the advanteges of a Compaq solution, best delivered bio application performance with 64-bit solutions, optimised applications, sometimes dramatically reduced run time and a top proce/performance. Compaq delivers pre-staged and tested complex systems, offers StorageWorks for reliability and flexibility, has planning, deployment and management services.

Then he mentioned a large computational bioinformatics benchmark example - the reasons why a major U.S. Commercial genomics company choose Compaq. The other Unix vendor needed 11 days (264 hours) to run the job and 3 days and 15 hours (87 hours) in the optimised version. Compaq needed 7 hours in the first stage and 5 minutes in the optimised program.

Following Bill Blake, Compaq Alpha is the leading platform in bioinformatics, as for example Sanger Centre, Washington University, St. Louis, MIT Whitehead Institute and Centre National de Sequencage use Alphas as research institutes, Celera Genomics, Geneva Proteomics, Incyte Pharmaceuticals and much more in industry have installed this platform.

Compaq's Alpha processors and their roadmap

Additionally Blake described the actual and coming Alpha processors. His reason number 1 for choosing Compaq and Alpha is the processor. The current Alpha, EV67, has 667 MHz clock rate, leading to1.3 GFlop/s, the memory bandwidth is 2.4 GByte/s peak and 1.3 GByte/s measured. This is an 8-fold increase compared to EV5. Additionally the highly optimizing compilers deliver the performance to the user.

The EV6 (21264) is scheduled to .5 to 1+ GHz, 1 to 2 GFlop/s, EV67 is the actual one, next is EV68 eith 833 MHz, 1.67 GFlop/s. The EV7 (21364) has a faster clock, 1 to 1.5 GHz, 2 to 3 GFlop/s, large L2 cache on-chip. RAMBUS increases the bandwidth to 12.6 GByte/s, 4- to 5-fold improvement. By the on-chip router this processor is ready for glueless SMPs. The EV8 (21464) has a faster clock, 1.5 to 2 Ghz and is 8-wide superscaler, has a doubled instruction rate and delivers 6+ GFlop/s. It builds on EV7 structure. The simultaneous multithreading boosts the sustained performance.

Compaq invests 300 mio US$ per year for the Alpha and the operating system development.

He mentioned an other aspect, the very fast and very scalable interconnect. The user has the choice between Myrinet and Quadrics interconnect. Last but not least the system software is a differentiator. Some highlights are the parallel file system spanning multiple physical file systems, coherent file access resource job management, LSF and parallel tools.