Stochastic Pi Machine
Established: November 21, 2008
The Stochastic Pi Machine (SPiM) is a programming language for designing and simulating computer models of biological processes. The language is based on a mathematical formalism known as the pi-calculus, and the simulation algorithm is based on standard kinetic theory of physical chemistry. The language features a simple graphical notation for modelling a range of biological systems, and can be used to model large systems incrementally, by directly composing simpler models of subsystems
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- Prototype Web Simulator (requires Silverlight 4.0 for Windows or Mac).
- Introductory Tutorial.
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- 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, under the SPiM License:
- Windows Executable.
- OCaml Bytecode (Linux, MacOS X). (Requires Objective Caml 3.08)
- Source Code. (Requires Objective Caml 3.08)
- Release notes are also available
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- A tool for translating text narrative to SPiM, developed by Ozan Kahramanogullari.
- A tool for translating SBML to SPiM, developed by Claudio Eccher.
- Further information on process calculi for biology at Luca Cardelli’s Biocomputing Page, including an advanced tutorial.
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- Luca Cardelli worked on the formal specification of SPiM, the design of the SPiM language, and on extensive testing and debugging.
- Rich Williams developed the Network 3D software for visualising simulations in 3D.
- Stefan Leye assisted with debugging the SPiM scheduling algorithm.
- James Margetson and Luca Cardelli developed the SPiM GUI.
- Pascal Zimmer assisted with debugging the OCaml bytecode distribution.
- The BioSpi project was the main inspiration for SPiM, and many of the SPiM chemical examples are adaptations of earlier BioSpi models.
- The core SPiM language was developed in F#.
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- CMSB 2010 (Updated 2010-05-17)