|
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.
|