AR-News: (U.S.) alternative biomedical research methods

Mary Finelli hello_itz_me at hotmail.com
Wed Nov 12 15:06:01 EST 2003


DIGITAL BIOLOGY: CHALLENGES REMAIN
NIH symposium tackles difficult networking and reliability issues in 
computational research
The Scientist, Eugene Russo, Nov. 10, 2003
http://www.biomedcentral.com/news/20031111/02


If computational biology is to be truly integrated into biomedical research 
practice, the current computer networks that link labs across the United 
States are inadequate, panelists at a National Institutes of Health (NIH) 
symposium concluded last week. They urged an infusion of money and 
technology.

The meeting, organized by the Biomedical Information Science and Technology 
Initiative (BISTI), an interagency NIH body, brought together leaders in 
imaging, cellular, and molecular modeling and simulation, genome analysis, 
proteomics and microarrays. Participants discussed current examples of how 
computer science has facilitated major biomedical research projects such as 
applying bioinformatics to complex multigene diseases, the development of 
computational models of the heart, and the construction of digital brain 
atlases.

Participants also struggled with how to expand networking capabilities. "The 
real paradigm shift is that some time over the last decade or so, computing 
has become so integral in biomedical research that you just can't do modern 
research [without it]," Eric Jakobsson, director of the Center for 
Bioinformatics and Computational Biology at the National Institute of 
General Medial Sciences, told The Scientist. "Now we're at the point where 
we're realizing that we're really limited by the fact that the computing 
isn't better." He noted that because software and computing technologies 
have been born largely of a diverse cottage industry, there's no real 
coherent plan to put all these pieces together and build an efficient 
computing environment. The fact that software is hard to use, fragile, and 
that the different software programs don't interoperate with each other 
become rate-limiting steps to progress, Jakobsson said.

BISTI's first major project—an attempt to update networking and integration 
capabilities—will be to award $3 to $4 million per year for 5 years to three 
or four nonprofit "computational centers of excellence."

At one session, NIH Director Elias Zerhouni, who recently outlined specific 
computing initiatives in the NIH "roadmap," suggested that "brute force" 
computation is not the right approach for biomedical research and that there 
must be a strong emphasis on mathematical models. One critical component of 
future computing infrastructure, he said, will be improved access to the 
proper algorithms and an investment in tools that deliver better data 
points.

Stephen Katz, director of the National Institute of Arthritis and 
Musculoskeletal and Skin Diseases, said that computational methodology 
should be used to construct better predictors of bone fracture based on bone 
quality and density. Lawrence Tabak, director of the National Institute of 
Dental and Craniofacial Research, suggested that computational methods might 
help make saliva—which holds clues to everything from antibody and hormonal 
levels to signs of elicit drug use—a more convenient diagnostic tool. Noting 
that more than half of the US population visits the dentist at least once 
per year, Tabak said he envisioned a massive health surveillance network 
based on quick oral diagnostics.

In a keynote address, Nathan Myhrvold, former chief technology office at 
Microsoft and now managing director of a private entrepreneurial firm called 
Intellectual Ventures, said that Moore's Law—which states that the number of 
transistors on a microprocessor would double approximately every 18 
months—was applicable to a plethora of increasingly cost-efficient, 
sequenced "omes," including the entire "biome." GenBank itself, said 
Myhrvold, is doubling roughly every 18 months, a 60% growth rate.

But in order to efficiently address the multitude of computational 
projects—to, as Jakobsson put it, integrate all computational tools so that 
"they'll all work together like the office tools on your desktop"—better 
connected labs with better integrated data will be necessary.

At concurrent sessions on "Networked Science" and "Scientific Data 
Integration," participants expressed some worry about how the NIH will 
accomplish the mammoth data networking and integration challenges ahead. 
"The community needs to represent what they see in a rigorous way that's 
relevant and useable," meeting Cochair Richard Morris, of the National 
Institute of Allergy and Infectious Diseases, told The Scientist. "And when 
they collect data, the network must be much more reliable than it currently 
is." The ideas discussed in several sessions will be distributed for E-mail 
comment and be the subject of future workshops that will culminate in a 
report.

Nobel Laureate Sydney Brenner, a professor of biology at the Salk Institute, 
told participants that he envisioned a time when—just as the National 
Academy of Sciences no longer has a section for molecular biology because 
every biologist is essentially a molecular biologist—everyone is a 
computational biologist. But cultural issues must be addressed before such 
can happen, suggested Myhrvold, who said he is often asked, "Can computer 
people will be 'real biologists?'" Myhrvold said he usually answers, "You 
tell me. When are you gonna treat them as real colleagues?"

Links for this article
Biomedical Information Science and Technology Initiative Symposium 2003, 
Bethesda, Md., November 6–7, 2003
http://www.bisti.nih.gov/2003meeting/

Biomedical Informatics Research Network
http://www.loni.ucla.edu/BIRN/index.html

Center for Bioinformatics and Computational Biology
http://www.nigms.nih.gov/about_nigms/cbcb.html

E. Russo, "NIH presents new research 'roadmap,'" The Scientist, October 1, 
2003.
http://www.biomedcentral.com/news/20031001/04/

National Institute of Arthritis and Musculoskeletal and Skin Diseases
http://www.niams.nih.gov/

National Institute of Dental and Craniofacial Research
http://www.nidcr.nih.gov/

GenBank
http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html

National Institute of Allergy and Infectious Diseases
http://www.niaid.nih.gov/default.htm

Sydney Brenner
http://www.nobel.se/medicine/laureates/2002/

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