The following seem relevant to the Pi-Calculus Biology connection
as well as some of the discussion of Graph Transformations:

* Pathway Logic: [](
It is based on modelling biological pathways in Maude, an implementation of Reflective Rewriting Logic.
Maude & RRL were developed by Jose Meseguer & his group.

* Greg Meredith's paper "Knots as Processes": [](
and his Biosimilarity blog [](