## 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.jar`

from 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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