[PRL] POPL Trip Report (part 2 of 2)

[Karl Lieberherr]

Ahmed and I interacted with Vincent Danos during my sabbatical at Novartis.
Ahmed experimented with the Kappa calculus and he
showed  that standard graph grammar tools answer some of the same questions
as Kappa. Vincent came to Northeastern twice and he
shared his OCaml source code with us after signing an NDA.

Ahmed negotiated with Vincent regarding an internship but GMO, Ahmed's
current sponsor, was the winner.

I have not built on this connection after Novartis closed their Systems
Biology department.

It would be great to have Walter Fontana as distinguished speaker.

Back then, Matthias got me in touch with Danos.

-- Karl

On Jan 10, 2008 8:44 PM, Mitchell Wand <wand at ccs.neu.edu> wrote:

> Alas, I have to leave tonite, so this will be the last installment.
> Enjoy. --Mitch
> ================================================================
>
> Invited Talk: Walter Fontana, Systems Biology, Harvard Medical School
> Systems Biology & Programming Languages
>
> This guy is a molecular biologist with a more-than-passing interest in
> CS and PL in particular. (He's found the shortest term for predecessor
> on Church numerals, using a genetic algorithm!).
>
> He's been working with Vincent Danos and several other heavyweights.
> Danos has a language called Kappa for describing molecular
> interactions.  The speaker claims that this language is good for
> describing models and suggesting the questions that wetlab biologists
> should ask.  (NOT in themselves as answering biological
> questions). "Models as a communication medium".
>
> eg if you do analysis of a Kappa program (AKA a model of a biological
> system), you can find possible pathways, etc.
>
> He also has a startup in Cambridge, called Plectix BioSystems,
> producing "Kappa Factory: a model-based reasoning environment useful
> to every molecular biologist".  (They do NOT have a website, but write
> to andrea at plectix.com for employment opportunities.  They are looking
> for a senior technologist + others).
>
> In any case we should invite him to give a talk (Distinguished
> Lecture?)
>
> ================================================================
>
>
>
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