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Hardware Vendors Draw First Blood in Battle for Biological Modeling Market


Soon, according to Jeremy Levin, CEO of Physiome Sciences, “there will be no other biology except computational biology.” Hardware vendors, at least, seem to believe this prediction. Within a matter of days last week, Princeton, NJ-based Physiome announced it had entered into a partnership with IBM, while its chief competitor in the biological simulation field, Entelos of Menlo Park, Calif., signed a deal with Compaq Computer.

The agreements highlight several strategic differences between the hardware giants as they continue to court new high-performance computing customers in the life sciences sector. As part of its deal with Physiome to provide early access to its next-generation Power4 supercomputing technology, IBM also agreed to license Physiome’s new PathwayPrism biological modeling technology for its internal research use. In addition, IBM will co-market Physiome’s simulation technology platforms while becoming the company’s preferred IT supplier for high-performance computing, professional services, and data integration.

Levin cited “the totality of the deal structure and the complete picture that they brought to us” as the primary reason Physiome chose IBM as its hardware partner.

By contrast, Entelos entered into a straightforward vendor agreement to double its compute capacity with Compaq, which suits CTO Alex Bangs just fine. “They’ve got the fastest machines out there,” said Bangs.

The Alpha Question

The deal couldn’t come at a better time for Compaq. Since announcing its plans to migrate its Alpha chip technology to the Intel Pentium platform in June, the company has struggled to ensure prospective customers that its commitment to high-performance computing remains strong.

Entelos — the first life science client Compaq has announced since its decision to phase out the Alpha — is confident that the vendor will continue to support the technology. “I’m not concerned,” said Bangs. “Long-term it’s a great thing because you’re going to get the processor architecture in more of an industry standard, high-volume, and hopefully lower-cost package, but then you’ll get Compaq’s system architecture along with that, so I see that as the best of both worlds.” Entelos and Compaq intend to work together to ensure a smooth transition to the Itanium processor.

Physiome’s Levin, however, admitted that Compaq’s decision to move away from the Alpha technology was one of several factors that influenced the company’s decision to go with IBM. Noting that the announcement came midway through a performance benchmark that Physiome was conducting with several leading hardware vendors, Levin said, “We were a little surprised that Compaq decided to walk away from supercomputing.”

Adding that the Alpha phase-out “certainly caused us some concern,” Levin emphasized that “the primary analysis was whether the benchmark fit or did not fit. What [Compaq was] able to do for us, IBM could do a lot better.”

Sources close to the deal said that Compaq’s impending agreement with Entelos further influenced Physiome’s decision to partner with IBM rather than share a vendor with its chief competitor. While not confirming this, Levin said that IBM’s “strategic thinking about the companies they want to work with” was a selling point.

More than a Vendor

Peter Brooks, vice president of products and operations at Physiome, said the company had dropped its previous hardware vendor, who he declined to specify. However, he described the company’s decision not as a change of vendor but as a move from a vendor to a partner. “The other company was someone we just bought hardware from, but the IBM relationship has about five different aspects to it.”

In addition to the Power4 purchase and IBM’s licensing of the PathwayPrism technology, the companies are involved in joint marketing and Physiome will make use of IBM’s Global Services unit to aid the deployment of its technology in pharmaceutical companies. The companies also plan future research collaborations and IBM has pledged to support Physiome Sciences’ XML-based CellML open source modeling language ( Finally, Physiome Sciences will write wrappers for its products to run on IBM offerings.

As the first PathwayPrism licensee, the computational biology group at IBM Research will use the technology in internal biochemical pathway modeling projects it is conducting in order to gain a better understanding of the computational requirements of the field. “The commitment of IBM to invest the kind of money in the research team to understand biological systems was very important to us,” said Levin. “That research commitment is significant, it is way beyond product development, and represents for us the ability to take this to a totally different level, which none of the other companies can do.”

For Entelos, on the other hand, the key issue was its scalability needs, which Bangs said were better met by Compaq. “We’re setting ourselves up to be scalable so that when we bring in new collaborations and work on new models, we can just plug in more computational power,” said Bangs. “And the way Compaq has their systems set up makes it really easy for us to do that.”

Despite appearances that they’ve taken tactical positions in a turf war between opposing hardware vendors, both Physiome and Entelos maintained that competition between the two biological modeling companies remains friendly. Said Levin, “It’s our belief that biological simulations will be the way that all drug discovery is performed. And having ourselves and others in the field making commitments like this is tremendously important to getting the field advanced.”

— BT

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