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I started a page

after noticing the Microsoft has a 'stochastic pi machine', and Luca Cardelli has been using the 'stochastic pi calculus' in biology.

I encourage all of you to create pages on the wiki and add information to them, instead of posting information here on the forum, where it gets lost in the long run. The forum is for talking, the wiki is for collecting information and references - and writing blog articles and other articles!

## Comments

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/. 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 and his Biosimilarity blog http://biosimilarity.blogspot.com/

`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/)`

Daniel - I edited your post so the links are clickable. Click 'edit' to see how; the main trick is to enable Markdown+ITeX.

`Daniel - I edited your post so the links are clickable. Click 'edit' to see how; the main trick is to enable Markdown+ITeX.`

The material on pathway logic looks interesting, but I haven't found the paper that explains the formalism!

`The material on pathway logic looks interesting, but I haven't found the paper that explains the formalism!`

The underlying formalism is the Maude language http://maude.cs.uiuc.edu/, which is based on Reflective Rewrite Logic. There is a lot of documentation & literature on it. The main people behind it are Jose Meseguer & Manuel Clavel.

`The underlying formalism is the Maude language [http://maude.cs.uiuc.edu/](http://maude.cs.uiuc.edu/), which is based on Reflective Rewrite Logic. There is a lot of documentation & literature on it. The main people behind it are Jose Meseguer & Manuel Clavel.`

David Mahler mentioned:

By the way, my student Mike Stay quit working for Google and is now working for Greg Meredith's company. He's going to use the pi calculus to help deal with big biological databases. (I don't know how, yet - he's been busy moving to a new town!)

I renamed our Pi calculus page: now it's

which is more general. The old page name still works, thanks to the automatic redirect system.

`David Mahler mentioned: > Greg Meredith’s paper "Knots as Processes": http://arxiv.org/abs/1009.2107 and his Biosimilarity blog http://biosimilarity.blogspot.com/ By the way, my student Mike Stay quit working for Google and is now working for Greg Meredith's company. He's going to use the pi calculus to help deal with big biological databases. (I don't know how, yet - he's been busy moving to a new town!) I renamed our Pi calculus page: now it's * [[Process calculus]] which is more general. The old page name still works, thanks to the automatic redirect system.`

And Jose Meseguer has been the co-author with Vladimiro Sassone of a host of papers on Petri nets since the early 1990s.

`And Jose Meseguer has been the co-author with Vladimiro Sassone of a host of [papers on Petri nets](http://www.ecs.soton.ac.uk/people/vs/publications) since the early 1990s.`