JSPIM
JSPIM is an interpreter of a language based on the stochastic pi-calculus. The formalism can be used to model biological processes and allows expression of simple spatial features (static compartments of fixed volume). JSPIM can execute simulations of a model (the arising continuous time Markov chains) and also derive and numerically solve a system of ordinary differential equations that deterministically approximates the model.
JSPIM was implemented by Anton Stefanek at Imperial College under the supervision of Dr. Maria Vigliotti.
Installation
- Ensure you have Java (version 1.5 or higher) installed
- Download JSPIM 1.0 (JAR archive, 3.9 megabytes)
- Run JSPIM (double-clicking will work on some systems, otherwise run
java -jar jspim-1.0.jarfrom the terminal)
Documentation
- JSPIM is described in my Master's thesis
- The source code with required libraries and build instructions is here
- A collection of examples (mostly adapted from SPIM, see bellow) can be downloaded here
Papers
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