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

* Pathway Logic: [http://pl.csl.sri.com/](http://pl.csl.sri.com/).
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": [http://arxiv.org/abs/1009.2107](http://arxiv.org/abs/1009.2107
)
and his Biosimilarity blog [http://biosimilarity.blogspot.com/](http://biosimilarity.blogspot.com/)