Abstract

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).