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Executable Knowledge for Molecular Systems Biology

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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).

This talk is part of the Microsoft Research Cambridge, public talks series.

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