The Stochastic Pi Machine (SPiM) is a
simulator
for the stochastic pi-calculus that can be used to simulate models of
biological systems. The machine has been formally specified, and the
specification has been proved correct with respect to the calculus. The
following talks are available:
- A SPiM overview and tutorial [ppt] (Printer-friendly version [ppt] [pdf] )
- An abstract for a short course on SPiM [pdf]
- Some 3D videos of SPiM simulations: Repressilator [wmv] Mapk [wmv] MHCI [wmv]
The following papers are available:
Further information on process calculi for biology is available from
Luca Cardelli's
Biocomputing Page, including an advanced tutorial.
Simulator
The
SPiM
Player 1.12 is a graphical interface to
SPiM, developed by
James
Margetson, Luca Cardelli and Andrew Phillips. (Requires the
.Net
2.0 Runtime)
SPiM is available in three distribution formats:
