ACM TechNews

Biology Enters 'The Matrix' Through New Computer Language

Harvard Medicine (07/22/08)

A team of Harvard Medical School researchers have developed Little b, a new computer language that can describe biology the same way a biologist would. Little b can "think" like cells and molecular mechanisms, and simulate the dynamics of biological phenomenon. Little b allows biologists to create programs that can reason about biological knowledge, helping them overcome the barrier of complexity. Cell biologist and computer scientist Aneil Mallavarapu says that overcoming the limitations of previous techniques required assimilating fundamental concepts of engineering, such as modularity and abstraction, into the biological realm. Mallavarapu wrote Little b in the LISP programming language. The researchers have demonstrated how Little b can be used to build complex models of kinase activity, using Little b as a kind of scientific collaborator and not just as a passive tool. The researchers have also used the program to examine the development of fruit fly embryos. "Through incorporating principles of engineering, we've developed a language that can describe biology in the same way a biologist would," says Jeremy Gunawardena, director of the Virtual Cell Program in Harvard Medical School's department of systems biology. "This opens the door to actually performing discovery science, to look at things like drug interactions, right on the computer."

http://web.med.harvard.edu/sites/RELEASES/html/072208Gunawardena.html

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