Sunday, July 27, 2008

Harvard Researchers Create Computer Language That can Penetrate the "Mind" of a Cell

Humancellstained_2 "This language is stepping into an unknown universe, when your computer starts building things for you."

Jeremy Gunawardena, director of the Virtual Cell Program in Harvard Medical School's department of systems biology

Enter into the world of Little b, a computational language developed by a team of Harvard Medical School researchers.

"Through incorporating principles of engineering, we've developed a language that can describe biology in the same way a biologist would," says Gunawardena. "The potential here is enormous. This opens the door to actually performing discovery science, to look at things like drug interactions, right on the computer."

The analogy is of writing a document with pen and paper. You need the pen, the paper, and the paper is blank, you’ve got nothing to work with; you have to create everything from the bottom up. You probably have that information available to you, but you have to put it down on the pen and paper.

Little b, a program written in a programming language called LISP, a language used widely in the field of artificial intelligence research, is not like our analogy. It has the ability to bypass the limitations of most programs and languages, and create its own code that, in turn, can write its own code. "LISP isn't like typical programs, it's more like a conversation," says Gunawardena. "When we input data into Little b, Little b responds to it and reasons over the data."

Gunawardena’s impetus for the creation of Little b is not for something as mediocre as looking in to the human genome, but the human protein. The protein does much more of the work, and is home to a massive wealth of genomic information far and away past the simple DNA. In particular, Gunawardena’s lab works on kinases, otherwise known as a phosphotransferase, an enzyme that transfers phosphate groups from molecules to molecules.

The researchers are now able to use Little b as a scientific collaborator, rather than as a simple passive tool. "This language is stepping into an unknown universe, when your computer starts building things for you," says Gunawardena. "Your whole relationship with the computer becomes a different one. You've ceded some control to the machine. The machine is drawing inferences on your behalf and constructing things for you."

At the moment, Little b acts very much like those unnamed programs I mentioned at the top. They are for the early adopters who know the code back to front. But the researchers realize that in order for the program to get out of that early adopter community, it has to be made more accessible. "The next step is to create an interface that's easy to use," says Gunarwardena. "Think of web page development. Lots of people are creating web pages with little or no knowledge of HTML. They use simple interfaces like Dreamweaver. Once we've developed the equivalent, scientists will be able to use our system without having to learn Little b."

Posted by Josh Hill.

Original here

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