Abstracting the Differential Semantics of Rule-Based Models: Exact and Automated Model Reduction

ing the differential semantics of rule-based models: exact and automated model reduction (Invited Lecture) Vincent Danos∗§, J´erˆome Feret†, Walter Fontana‡, Russell Harmer‡§ and Jean Krivine§ ∗University of Edinburgh †LIENS, INRIA-ENS-CNRS ‡Harvard Medical School §CNRS, Universit´e Paris-Diderot —Rule-based approaches (as in our own Kappa [1], [2], or the BNG language [3], or many other propositions allowing the consideration of “reaction classes”) offer new and more powerful ways to capture the combinatorial interactions that are typical of molecular biological systems. They afford relatively compact and faithful descriptions of cellular interaction networks despite the combination of two broad types of interaction: the formation of complexes (a biological term for the ubiquitous noncovalent binding of bio-molecules), and the chemical modifications of macromolecules (aka post-translational modifications). However, all is not perfect. This same combinatori...

• Type: Journal
• Year: 2010
• Where: LICS
• Authors: Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine
• Keywords: Automated Reasoning, Biological Systems, LICS 2010, Molecular Biological Systems, Ubiquitous Noncovalent Binding