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By Michael Goldman

Nov. 12, 2002 | "It's partly a problem of education," says David R. Brown, professor of pharmacology, neurosciences, and toxicology at the University of Minnesota. "Are we training pharmacologists who are well aware of advances in genomics and proteomics? Are we training molecular biologists to participate in the drug discovery process?"

Not only must molecular biologists and pharmacologists become information scientists, but the information of genomics, proteomics, physiology, medicine, and biochemistry will have to be interchangeable. The common language for them will likely be an offshoot of the hypertext markup language, or HTML. The extensible markup language — XML — is beginning to gain ground as a standard that can be readily adapted for specialized needs, such as annotating metabolic pathways.

Michael Hucka and his fellow researchers at the California Institute of Technology may play a role, too. The team is developing SBML, or systems biology markup language, a derivative of XML, along with a systems biology workbench that will be a common set of programs for data analysis.

Gene Network Sciences Inc. (GNS) is convinced that many languages are just too inflexible to encode the complex information in physiological networks and too cumbersome for the average biologist who wants to encode relevant findings. Enter the company's proprietary diagrammatic cell language (DCL), which is meant to close that gap. DCL was invented by GNS scientist Ron Maimon, who says the language is "precise enough for computer simulation, [yet] rich enough for a biologist to say what the function of a molecule is with the convenience of spoken English." Although commercial users must pay a fee for DCL, several academic institutions have already signed no-cost license agreements.

In this early stage of development, it is not surprising that the trend is toward more diverse languages, rather than a settlement on one. Advocates for each language believe they have the best available. It may mean the biological equivalent of the browser wars.

But it also may be nothing more than preliminaries, argues Nat Goodman of the Institute for Systems Biology in Seattle, "because there's plenty of fundamental work still to be done."

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