Bioinformatics

To help master that complexity, companies with expertise in the expanding field of computational biology, also known as bioinformatics, are bolstering the genetics-related research and technology development under way in government labs and by the pharmaceutical industry.

By using the power of computer hardware and software to process and analyze biological information, these public-private collaborations could bring an array of new drugs, therapeutics and diagnostics into homes and medicine cabinets.
The money-making action today appears to be centered on federal funds, largely dispensed by the National Institutes of Health, or monies coming from the pharmaceutical industry to help speed drugs to market. Budgeted at roughly $29 billion for fiscal 2005, NIH is funneling tens of millions of dollars to scores of projects in bioinformatics research.

"The federal government is the biggest player," said Kevin Biersack, bioinformatics program manager for Northrop Grumman Corp.'s Information Technology sector. "There is a need to capture genetics, proteomic and research information ? and legacy data ? into a usable system that can be accessed electronically over the Internet."

Northrop Grumman last month won a six-year bioinformatics contract worth $29.4 million from the National Institute of Allergy and Infectious Diseases. For the Immunology and Data Analysis Portal (ImmPort) project, the company will help create an integrated database and analysis tools and will provide technical training and support.

"Bioinformatics as a market opportunity is definitely headed up, not down," Biersack said. "We see an opportunity for ourselves as a systems integrator."

A growing enterprise

Bioinformatics is still in the early-adopter stage, said Tim Howard, founder and former CEO of Galt Associates Inc., a bioinformatics firm in Sterling, Va.

Howard said there are roughly 200 small to midsize bioinformatics companies nationwide with annual revenue in the $10 million to $25 million range. About 20 large firms, such as Northrop Grumman, are either playing or beginning to play "in the big leagues" in bioinformatics, Howard said.

The pharmaceutical giants also are relentlessly active, but, Howard said, "There are really no big, dedicated bioinformatics companies [anymore]."

U.S. biotech companies ? the biotech field includes bioinformatics as a subset ? rebounded in 2003 and 2004 from a steep stock market decline that had left many facing severe cash shortages, according to "Resurgence: The American Perspective," an Ernst and Young study released in May. The major force driving the resurgence is the biotech sector's success in moving new, first-in-class medicines through clinical trials and onto the market.

Citing the Ernst and Young report, Tamara Zemlo, director of the science advisory board for Arlington, Va., life sciences market research firm Bioinformatics LLC, said the 2003 biotech market globally stood at $46.5 billion, with the U.S. market accounting for $35.9 billion of that figure. Of those totals, bioinformatics as a discrete discipline accounted for perhaps 10 percent ? $4.6 billion and $3.6 billion, respectively, Zemlo estimates.

Looking back from 1998 through 2003, even taking in to account the downturns, biotech overall exhibited 115 percent aggregate growth in revenue.
"If that trend holds true, those numbers could essentially double," Zemlo said. "Bioinformatics [alone] could become a $10 billion industry by the end of the decade."

Counting on that growth is one of the nation's biggest IT firms, IBM Corp. of Armonk, N.Y., which is just now entering the bioinformatics arena with a life sciences emerging business opportunity unit.

On its own initiative, the company developed what it's calling the IBM Healthcare and Life Sciences Clinical Genomics Solution to identify the molecular mechanisms of disease and ultimately develop more personalized medicine. IBM's combination of computer hardware and software is designed to work with hospital and research systems to capture individual patient information.

The system also will pull and archive medical data from multiple health care institutions and diagnostic laboratories, and centralize data for integrated clinical research.

The Cleveland Clinic will use the IBM system to develop prototypes of individualized health care in which patients receive treatments targeting their conditions and genetic makeup. Project organizers initially are focusing on patients with abdominal aortic aneurysms; their hope is to identify disease triggers and spur development of more effective treatments.

Cleveland Clinic physicians could ultimately use information from electronic medical records to support basic and genetic research, and deliver more effective personalized patient care, incorporating research discoveries directly at the sickbed: what the collaborators are calling "clinical genomics."

"I'd call it medical informatics," said Michael Svinte, IBM's vice president of information-based medicine. "It's a way of thinking about a new treasure trove of information made possible by the decoding of the human genome."
The ultimate market value of such efforts, Svinte said, could amount to "hundreds of billions of dollars of opportunity" as IT and applied biology are refined and made routinely available.

"We are very bullish on the intersection of molecular medicine and informational technology," Svinte said.

Another emerging bioinformatics player is IT services firm SRA International Inc. of Fairfax, Va., which makes most of its money from contracts with the federal government.

According to Chairman Ernst Volgenau, bioinformatics is a "small, albeit interesting" pursuit that SRA at one time considered as a potential spinoff profit center. The company abandoned those plans because "the market went down, and it wasn't possible to find sufficient capital," Volgenau said.

Now SRA is supporting a bioinformatics-related project for one of the constituent facilities that comprise the National Institutes of Health.

Like Northrop Grumman, SRA will be working with the National Institute of Allergy and Infectious Diseases. In a project valued at $13.6 million over six years, SRA will develop a Web-based database to collect, store and analyze information that biomedical researchers use to facilitate the study of biology as it relates to biodefense and public health.

NIAID wants to improve the quality and increase the reuse of its genomic research data, particularly in the consolidation of known information about enterobacteria, a group of pathogens that can cause diseases such as dysentery, plague, food poisoning and typhoid fever.

SRA's services and solutions will include database design and development, data and text mining, systems integration and information security. The company will create an integrated system, accessible via a Web portal, that biodefense and infectious disease researchers will use to annotate and update multi-organism data, compare genomes, analyze related biological information, and share research progress and results.

Volgenau said eventually money will be made in what remains a young, up-and-coming field ? if purveyors know where and how to look.
"There are short-term growing pains," he said. "Clearly, the genome work is ongoing. Proteomics is going to be a huge area."

As computing speeds move into the tens and hundreds of trillions of mathematical operations per second, bioinformatics will profit. Already, distinctions are blurring as IT-aided biological computation accelerates and is refined.
But no matter what the ultimate technological success, the economic reality for would-be players is daunting. To stay in business, bio-IT companies must furnish unique and necessary applications.

"The bioinformatics industry needs a structured methodology," said Northrop Grumman's Biersack. "Bioinformatics provides the opportunity to take proven IT processes and export them to science and biology. We see it as a growing enterprise." n

James Schultz is a freelance writer living in Norfolk, Va. He can be reached at jschultz76@cox.net.
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The science behind the terms

Bioinformatics

A scientific term used widely by the mid-1980s, it originally referred to the analysis of sequential genetic data. As computer-aided biological analysis grows increasingly sophisticated, many people use the term bioinformatics to define the direct application of computer power to the
biological sciences. For many specialists, bioinformatics is synonymous with computational molecular biology, which is using computers to characterize the molecular components of living things.

Computational Biology

Coined to describe research into evolutionary, population and theoretical biology, rather than cell and molecular biomedicine, today the term is used more often to describe any use of computers to handle biological information. Sometimes it's used as a synonym for bioinformatics.

Medical informatics.

An emerging discipline defined as the study, invention and implementation of structures and algorithms to improve communication, understanding and
management of medical information. Some specialists assert that medical informatics is more concerned with
structures and algorithms for the
manipulation of medical data,
than with the data itself.

Pharmacogenomics

The application of genomic approaches and technologies to the identification of drug targets. Examples include: the bioinformatics trawling of entire genomes for potential drug receptors; investigating patterns of gene expression in both pathogens and hosts during infection; and the study of the characteristic genetic expression patterns found in tumors or patient samples obtained for diagnostic purposes, or in pursuit of potential cancer therapy targets.

Proteomics

The study and analysis of the role and function of proteins in any given cell, as well as their modifications, interactions and structures. The term also refers to the characterization of the tens of thousands of proteins expressed in a given cell type at a given time, and their complex of ongoing activities.

Source: The Bioinformatics Organization Inc. of
Worcester, Mass. http://bioinformatics.org/faq