San Diego’s life sciences expertise made it a world leader in biotechnology. Now, biotech’s frontier has changed from a science of lab mice and centrifuges to one of supercomputers and software — and San Diego is leading the way.

San Diego has some of the world’s top computer experts, such as Larry Smarr, whose lab at the University of Illinois invented Mosaic, the first graphical Web browser. San Diego also is home to the San Diego Supercomputer Center, one of three such centers in the nation, funded by the National Science Foundation. The state’s Institute for Telecommunications and Information Technology (Cal(IT)2), headed by Smarr, is located at University of California, San Diego and University of California, Irvine.

Combine this trove of computer talent with San Diego’s massive biotechnology base, and you arrive at biotechnology’s new frontier. It’s a perfect marriage: life’s most complicated problems need solving, and the world’s most advanced computer companies need new markets.

While much of corporate computing is well-trodden territory and increasingly dominated by a certain software company in Redmond, Wash., the science of applying computers to biological problems is in its infancy, and competition is robust. These problems, such as computing the permutations of protein folding, will require more powerful computers and software and new disciplines and subdisciples to describe what’s being done. (Yes, this means you’ll have to learn a new set of buzzwords.)

Even more ambitiously, researchers and companies are recreating biological reactions, cells and tissues in software, a process known as in silico modeling. Imagine testing drugs on virtual cells, virtual hearts, even virtual mice — pleasing both animal rights advocates and speeding the process of finding and testing new drugs. Insilicomed, a new San Diego company, is using this concept to develop medical devices, improve surgical procedures and personalize medicine according to an individual’s unique genetic makeup.

In short, biotechnology is becoming more abstract by the day, as its frontier moves away from direct observation to computer modeling.

Early biology was performed to a large degree by direct observation. Biology in the first half of the 20th century made great strides by refining instrumentation. In the second half of that century, biologists understood data at a higher level, marrying it to information technology.

In the 21st century, the frontier lies entirely within the computer and sequences of 1s and 0s, promising vastly greater speed and accuracy in developing new drugs. Failure of a virtual liver due to drug toxicity is far preferable to the real thing.

So even while investors, doctors and patients sour on the unfulfilled hype associated with the Human Genome Project, San Diego is springing ahead to create a new biotechnology.

Convergence Steam

The convergence of San Diego’s infotech and biotech has picked up steam in the last couple of years. Sun Microsystems recently moved its global life sciences division to San Diego. IBM has allied with San Diego companies such as GeneFormatics, Lion Biosciences and Structural Bioinformatics. And UC San Diego’s computer and biological science faculty are collaborating more closely than before in an increasing number of new programs.

“The convergence of information technology, biotechnology and nanotechnology, which finds all meeting in the field of bioengineering, is probably the most critical convergence of this century,” says Andrew McCulloch, a professor of bioengineering at UCSD, noting that the university dedicates a new bioengineering building on Aug. 12.

As co-founder and CEO of Insilicomed, McCulloch is part of that convergence. Shankar Subramaniam is another. Director of the bioinformatics graduate program, Subramaniam has become world famous among biotech researchers for his Biology Workbench, a set of software computational tools he describes as a “one-stop shop for people who want to go in and do a whole lot of analysis of genome sequences, structure and so forth.”

Subramaniam singled out San Diego and Cambridge, Mass., as the main hotspots of biotech’s transformation into a computer-driven science, even eclipsing the San Francisco region, the birthplace of biotechnology some 30 years ago. “The most important feature about San Diego is that we see the next generation of biotechnology — post genome-sequence biology, and it’s not happening anywhere else in the country except in Cambridge.”

Subramaniam says San Diego’s tight-knit scientific community encourages collaboration between biologists, engineers and medical researchers. This is critical because software databases and tools that describe biological functions only are as good as the biological information they contain. Modern science is very specialized, so communication is essential: the software engineer working on a biological product needs guidance to understand what the biologist regards as important. Besides academic products such as the Biology Workbench, this collaboration leads to new companies such as Insilicomed, sprouting from UCSD, the Salk Institute and The Scripps Research Institute. “UCSD biology faculty are the best in the world to work with in cell biology,” Subramaniam says. “Arguably, we have the best bioinformatics program in the country.”

‘Big Iron’ Calls

The tremendous challenge of high-performance computing and San Diego’s expertise has persuaded Sun Microsystems and IBM to expand their local presence. Sun, based in Santa Clara, already has a division here, which temporarily houses its Global Life Sciences Division. The head of that division is Howard Asher, a prominent member of San Diego’s biotech community and well connected outside of it.

Database maker Oracle Corp. has allied with Sun to supply life sciences software to complement Sun’s mainframe computing hardware. In April, Oracle announced an ambitious new product called Information Architecture for Life Sciences, software that brings together scientific and business applications for drug and biotech companies. The goal is staggering: to provide all the software needed “from drug research to sales and marketing,” as Oracle put it in the announcement.

Locally, the Supercomputing Center and now Cal(IT)2 have become major focuses of computer-driven biotech research. The Supercomputer Center’s home page — www.sdsc.edu — puts biology-related projects at the top, such as integrative biosciences, a center initiative to link biology research across all disciplines, along with research on biodiversity.

Peter Arzberger, director of life sciences initiatives at UCSD and Cal(IT)2’s deputy leader, said at a July 17 Biocom meeting that some people mistakenly believe all bioinformatics work is confined to Cal(IT)2’s sister institute in Northern California, the California Institute for Bioengineering, Biotechnology & Quantitative Biomedical Research.

“While we’re talking a lot about the technologies of telecommunication information, they’re driven explicitly by applications,” Arzberger said in his talk, which can be viewed on Cal(IT)2’s Web site — www.calit2.net.

In other words, while the institute is developing new telecommunications and information technologies, these technologies are meaningless unless they solve some problem. And considering San Diego’s prominence in biotechnology, many of these problems will be biological in nature. Arzberger’s talk, and those of other researchers speaking at Biocom, is linked to the headline “Cal-(IT)2 Researchers Brief San Diego Biotechnology Executives on Bioinformatics.”

Arzberger says wireless technologies are a major part of the institute’s work, and the applications include biomedical research. For example, the knowledge from genomics of a person’s unique genetic makeup can be combined with wireless sensors attached to patients. This process enables a continuous stream of data collection, instead of that from sporadic office visits, making diagnoses more reliable. Another example: a wirelessly connected “video pill” that when swallowed transmits images of what’s taking place in the digestive tract, enabling non-invasive observation.

The Institute calls this linkage of wireless networks and genetic information Digitally Enabled Genomic Medicine.

“Because of the type of commitment here in San Diego, and because of the research prowess at several institutions, we have an edge in La Jolla,” Arzberger says.

Biotech Opportunity

What’s missing from this sunny picture? More participation from smaller biotech companies who aren’t aware of their new potential partners, says Joe Panetta, president and CEO of Biocom San Diego.

“The fact that the Supercomputer Center has so much to offer is something the big companies are beginning to take advantage of,” Panetta says. “What we need to do here, in partnership with the Supercomputer Center and the whole Cal(IT)2 program here, is to increase the level of awareness among the smaller companies that there’s a great opportunity, in the bioinformatics area, in genomics and proteomics. Companies like Pfizer here in San Diego, and Merck and Elan already are well aware of that opportunity and have begun to form partnerships with UCSD. The pharmaceutical industry is interested in finding new cost-effective opportunities to research and develop new drugs, because their pipelines are beginning to run dry.”