Welcome to BAM, the BioAmbient Machine.

BAM is a simulator of stochastic BioAmbients (see also the original paper on BioAmbients). BAM is written in Java 1.5.

BAM can be used to simulate bioregulatory pathways as well as membrane interaction.

BAM was implemented by Vinod A. Muganthan at Imperial College under the supervision of Dr. Maria Vigliotti.

BAM project was supported by the EPSRC project SPARTACOS.

Installation

1. Ensure you have Java 1.5 (a.k.a Java 5) installed on your machine
2. Download BAM 0.0.5 (JAR archive, 2.5 megabytes)
3. Run BAM (double-clicking will most likely work, otherwise run java -jar bam-0.0.5.jar from the command line)

Documentation

• Download Source code BAM 0.0.5 (GZipped Tarball, 100K)
• Examples (ZIP file, 360K)
• The manual will follow shortly.

Papers

• John k. Heath, Ikra Khan, Steffen van Bakel and Maria G. Vigliotti Modelling intracellular fate of FGF receptors with BioAmbients, Proceedings of QAPL'08, Budapest, ENTCS To appear. paper.pdf
• Vinod A. Muganthan Andrew Phillips and Maria G. Vigliotti. BAM: BioAmbient Machine. In Proceedings of ACSD 08 IEEE. Computer Society. paper.pdf
• Maria G. Vigliotti and Peter G. Harrison. Stochastic Mobile Ambients. in Proceedings of 4th Int. Workshop Quantitative Aspects of Programming Languages (QAPL 2006),ENTCS, volume 164 (issue 3),pages 169--186, 2007. paper.pdf

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• SPIM
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