The Stochastic Pi Machine (SPiM) is a
simulator
for the stochastic pi-calculus that can be used to execute models of
biological systems. The machine has been formally specified, and the
specification has been proved correct with respect to the calculus. The
following documents are available:
- Coupled chemical reactions in SPiM [pdf]
- The SPiM language definition [pdf] [html]
- A collection of SPiM examples and simulation results [pdf]
- A SPiM overview and tutorial [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 on SPiM are also available:
- Ralf Blossey, Luca Cardelli and Andrew Phillips. Compositionality, Stochasticity and
Cooperativity in Dynamic Models of Gene Regulation. HFSP Journal, 2(1):17–28 February
2008. ©HFSP. [pdf]. Supplement [pdf]
- Andrew Phillips and Luca Cardelli. Efficient, Correct Simulation of
Biological
Processes in the Stochastic
Pi-calculus. In Proceedings of Computational Methods
in Systems Biology (CMSB'07), 4695:184–199, September
2007.©Springer. [pdf].
Extended
Version [pdf]
- Andrew Phillips, Luca Cardelli and Giuseppe Castagna. A Graphical Representation for Biological
Processes in the Stochastic Pi-calculus. Transactions
in Computational Systems
Biology (TCSB), 4230:123–152, November 2006. ©Springer.
[pdf]
- Ralf Blossey, Luca Cardelli and Andrew Phillips. A
Compositional Approach to the Stochastic
Dynamics of Gene Networks, Transactions
in Computational Systems
Biology (TCSB), 3939:99–122, January 2006. ©Springer.
[pdf]
Supplement [pdf]
Simulator
The
SPiM
Player 1.13 is a graphical
interface to
SPiM, developed by
James
Margetson, Luca Cardelli and Andrew Phillips. (Requires the
.Net
2.0 Runtime)
A command-line version of SPiM is available in three distribution
formats:
