Russ Harmer (Paris/Harvard):
Rule-based Modeling: Theory and Practice

We will discuss the theory and practice of rule-based modeling. We will first present the fundamental conceptual motivations for rules and their formalization in the general mathematical setting of site-graphs, before turning to the specific application of these methods to describing bio-chemical reaction networks.

In particular, we will discuss some of the intrinsic difficulties involved in collating empirical biological knowledge into this formal framework---but also the benefits that doing this brings.