Modelling the lambda switch in the pi calculus

Working group at ACI Vicanne meeting, Nice, Jan 20/21, 2005
coordinated by Celine Kuttler

[ck]

Recommended readings:


  • Pi calculus:
    • for a formal overview of pi-calculus syntax & semantics I recommend the first sections of CHAPTER 2 of Martin Berger's thesis (2004). Note that previous background in logics or lambda calculi helps.
    • for completeness, a reference to Robin Milner's book "Communicating and Mobile Systems: the Pi-Calculus" (1999). Great investment!

Pi calculus tools:

Two tools for the execution of stochastic pi calculus models have been proposed so far:


  • BioSpi - the biochemical stochastic pi system (since 2001/2)

Slides: new!

Two sets of slides, for a lecture on the topic (audience: Bioinformatics Master's course in Lille):

Excercises: new!

Excercise sheet to work with during the workhop: [discussion material PDF]
Pre-workshop excercises for the workshop, and prior to it if there is time and interest. Try to plug into BioSpi and run!
Simple examples from the lecture:
Brief how-to:
  • install BioSpi
  • start it where you've put the code files
  • compile a file by saying 'c FILE.cp'
  • execute it with: record(FILE#"System"(N,M), log.txt, time)
    • where N and M are suitable values for the number of molecules to start with (check examples for arity). Try values in the order of tens up to hundreds.
    • log.txt will be used for output
    • time: how many simulated seconds you want to run. Be modest, try small values. :-)
  • use the "spi2t" script from the directory yourBioSpi/Aspic-release/bin/ to convert the log file into a table with the system state recorded once per second (1 line per second)
  • you may visualize the result using your favorite statistics tool for plotting (gnuplot, Gnumeric, R, Excel).
More examples: to come.

any comments are welcome!


last update: Jan 10, 2005