Executable Knowledge for Molecular Systems Biology
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Episode description
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).
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