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BAM: BioAmbient Machine

Vinod Muganthan, Andrew Phillips, Maria Vigliotti

Conference or Workshop Paper
8th International Conference on Application of Concurrency to System (ACDS'08)
8th International Conference on Application of Concurrency to System (ACDS'08)
IEEE Computer Society Press

In recent years it has become clear that techniques developed for concurrent programming are in fact very useful for the analysis of complex systems in biology. To some level of abstraction, it is possible to regard biological phenomena such as gene transcriptions, proteins interaction, communication among cells, as concurrent entities that compute according to the rules of chemical reactions. In this paper we present a tool to represent and stochastically simulate complex biological systems with mobile compartments. BAM, our tool, implements the stochastic version of Bioambients, which helps in understanding and reasoning about the multiple interconnections between components in bioregulatory networks.

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