The structures of Red Storm and Blue Gene are quite different. Red Storm, says Marshall Peterson, Celera's chief of infrastructure technology, is taking "reasonably standard components and putting them together in somewhat creative ways." The architecture for Blue Gene, on the other hand, will be built largely from scratch by replicating many identical chips, which altogether will contain 1 million processors.
Compaq and IBM aren't necessarily counting on their machines being widely used. Rather, the supercomputers are intended to further computer technology as much as biology, and they'll act as prototypes for future bio-supercomputers. "We look at Blue Gene and say it's a research experiment," says Peter Ungaro, head of IBM's high-performance-computing division. "This is not a machine that will have broad-base commercial use." Peterson says he wouldn't be surprised if Celera never used the Compaq machine at all, instead applying knowledge gained from the project to design its own.
Is it good business to devote four years and $100 million to a computer that may never attract many paying customers? This was not, for the most part, the spirit that drove companies like IBM, Compaq, Hitachi (HIT) and others to construct supercomputers for national labs like Lawrence Livermore and Los Alamos. Still, owning the world's most powerful supercomputer isn't bad for business. Its novelty alone could attract life-science clients that don't require supercomputing at all. And as microbiologists and genetic scientists increasingly rely on information science, such business is growing - IBM predicts a $40 billion market for life-science technology by 2004.
Blue Gene already has piqued the interest of at least one company, MDS (MDZ) Proteomics. The Toronto-based biotech firm chose IBM to help it analyze protein data and establish Blueprint, a nonprofit company that will create a protein database. "They've committed $100 million to build the world's fastest computer," says MDS Chief Executive Frank Gleeson. "That caught our interest."
Morningstar (dossier) analyst Joseph Beaulieu says that while bio-supercomputer projects may not be immediately profitable, they raise their sponsors' profiles for high-end biological computing. "They're priming the pump," he notes of Compaq and IBM. These two tech giants are not alone in aggressively courting the biology market. Though not currently involved in a big bio-supercomputer project, Sun Microsystems has been working with biotech and pharmaceutical firms to develop hardware and software for genomic research. Sia Zadeh, head of Sun's life-sciences group, says the bio-supercomputer being built by his company's rivals are more attention-grabbing ploys than sound business strategy. "We do not believe in the creation of special-purpose machines," adds Zadeh, referring to Blue Gene.
Indeed, IBM's bet on Blue Gene, though admired, has raised questions about how specialized bio-supercomputers should be. Because hardware tends to become quickly outdated, some scientists question the logic of designing an extraordinarily powerful machine to tackle just one type of problem. Even Compaq's Red Storm - designed to "switch-hit between different kinds of operations," as one company executive puts it - can't necessarily meet the needs of a broad swath of genetic researchers.
Still, bio-supercomputers are an attractive option to scientists like Jill Mesirov, director of bioinformatics and computational biology at the Massachusetts Institute of Technology (dossier)'s Whitehead Center for Genome Research. The Whitehead Center was one of the participants in the Human Genome Project, the government-supported effort that competed with Celera to sequence the human genome. When Mesirov arrived at Whitehead four years ago from IBM, genetic research was chugging rather than flying. The Whitehead Center's computers sat on a wire rack in a room without air conditioning, the servers crashing in the summer heat. As the need for ever-more computing power escalates with the pace of genomic research, Mesirov says she's given up trying to squeeze even one more computer into rooms already crammed with a hundred of them. But whether MIT would buy time on a bio-supercomputer like Blue Gene or Red Storm depends on the computer's capabilities and its compatibility with MIT's software.
Even as Red Storm and Blue Gene take supercomputing to a new level of complexity, Celera's Peterson is impatient for something even more mind-boggling: systems that can analyze biological data even more intelligently than the bio-supercomputers that are still years from completion. "What we really need is something a lot more dramatic," he says, pointing to current research to create DNA-based computers as one possibility.
Just as biology is pressing the limits of computing, so too is computing pressing the limits of biology.
