Executable Knowledge for Molecular Systems Biology

March 30, 2011
Walter Fontana | Harvard Medical School

I will give an overview of an ongoing long-term project aimed at developing a formal yet pragmatic framework for representing and exploring the behavior of complex molecular systems of interaction, such as they occur in cellular signalling. The approach recognizes the convergence of a scientific challenge—the need for transparent models respectful of the combinatorial complexity of protein-protein interaction networks—and a knowledge representation challenge—the formalization, collation, and curation of mechanistic interaction data through which models can become open-source collaborative documents.

This is a “vision” talk, more than a technical talk, covering three facets:

A characterization of the problem and associated opportunities, especially the changing role of the notion of “model” in systems biology;
A survey of the approach: the definition of a (site-)graph rewriting language along with a suite of tools and web infrastructure;
An outline of the road ahead.

This is joint work with Russ Harmer (Harvard, CNRS), Vincent Danos (Edinburgh), Jerome Feret (ENS, Paris), and Jean Krivine (CNRS, Paris).

Speaker Details

Walter Fontana studied biochemistry and theoretical chemistry at the University of Vienna, Austria. He did postdoctoral work at Los Alamos National Laboratory and the Santa Fe Institute in the early nineties. In 1994, Walter returned to Vienna and became an associate professor at the Institute for Theoretical Chemistry and Molecular Structural Biology. In 1998 he could no longer resist the siren call of the Santa Fe Institute. He resigned tenure in Vienna and returned to the Land of Enchantment. From 1999 to 2000 he was a member in residence with the Program in Theoretical Biology at the Institute for Advanced Study in Princeton, New Jersey. He was about to join Microsoft in 2004 when he fell into the gravitational field of Systems Biology at Harvard Medical School, whose faculty he joined as a full professor in September 2004. His theoretical interests focus on understanding principles of information processing in molecular systems and developing new concepts of modeling in systems biology. In 2005 he added to his group an experimental research component on aging in C.elegans using (abusing?) consumer electronics flatbed scanners as scientific instruments. http://fontana.med.harvard.edu/