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UW s Cell Systems Initiative to Develop Shorthand for Biologists

PHILADELPHIA, May 14 - The Cell Systems Initiative, a technology incubator at the University of Washington, is working to develop a set of symbols to represent biological interactions that would be the equivalent of the chemical symbols used to represent chemical activity, Bob Franza, the director of CSI, said Monday.

Franza told GenomeWeb that his information technology group at CSI, which is headed by Joseph Duncan, a former executive at software giant Oracle, is currently building a prototype of the symbolic language. Eventually, the researchers also hope that the shorthand would be recognized by personal computing devices like the Palm Pilot.

"It's a way to symbolize the things that we're trying to understand, and it's got rules associated with it," said Franza, during a break at a proteomics conference.

"It's meant to be like a shorthand for biology the way 'C dash C' is a shorthand for the chemists," he said, adding that it would enable biologists to sit in the library and quickly take shorthand notes from scientific papers and draft experiments.

Franza said he is working with collaborators in the information technology industry to develop the language, but that the project is still in the development stage.

"It's not ready for prime time yet, but it will be soon," he said.

CSI is also working with collaborators to develop new methods for studying gene expression, such as protein transduction and antisense techniques, in addition to developing new microscopic and spectroscopic techniques for studying cells, Franza said.

The biological systems modeling team at CSI is also building a computer server that would allow biologists to view different ways of representing data, from animated models of interactions to graphs and equations, all using one "user interface," or computer screen, Franza said.

Franza said the ability to view disparate types of data in one interface would allow biologists to see new relationships between biological systems they would not have noticed before.

"That user interface is not about putting up pretty pictures--that user interface is about users not wanting to jump between half a dozen or more different applications in order to do something," Franza said. "There's no reason why they should have to do that."

Franza added that several large information technology companies, such as IBM, have also taken steps towards building a similar type of user interface, and that "it would be not unlikely" for CSI to look for a such a partner to develop its own user interface.

CSI currently has partnerships with several pharmaceutical companies, including Immunex, Isis Pharmaceuticals, Amnis, and Merck-Frosst Canada.

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