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Monday, July 16, 2012
3:00 PM - 4:00 PM
CNLS Conference Room (TA-3, Bldg 1690)


Executable Knowledge

Walter Fontana
Harvard Medical School

The notion of model must be reconceptualized to play a significant role in molecular systems biology. Models and knowledge representation must become twin sides of a single reasoning process: a model should be a transparent, formal and executable representation of the facts it rests upon. For a specific slice of systems biology, these facts describe the interaction capabilities of proteins, by reference to their biophysical features, and can be written as abstract rules in a formal language. A rule is a schema that implicitly represents myriads of potential reactions, which traditional models must - yet cannot - enumerate explicitly. I will review for a general audience the idea of rule-based modeling and extant tools for simulating and analyzing the dynamical behavior of rule collections, concluding with a few thoughts on the road ahead.

Host: Bill Hlavacek