I put together a list of formal systems being used in biology: https://github.com/prathyvsh/formal-systems-in-biology The list is largely incomplete, but it was great to find that graphical notation by von Neuman used to explain automata, in the search. Also, look at the stuff by Vandrella. He’s doing some lit modelling stuff in his website.

Nice compilation, thanks! I wonder if you consider "pragmatic" stuff like SBML (http://sbml.org/Main_Page) or Kappa (https://kappalanguage.org/, which grew out of Fontana's work you list) worth including.

Oh yeah, definitely could include these. Thanks!

HN https://news.ycombinator.com/item?id=23464471