BAM: BioAmbient Machine

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 transcription, protein interaction and communication among cells, as concurrent entities that compute according to the rules of chemical reactions. In this paper we present a tool for representing and stochastically simulating complex biological systems with mobile compartments. BAM, our tool, implements a stochastic version of the BioAmbient calculus and helps in understanding and reasoning about the multiple interconnections between components in bioregulatory networks.

In  Application of Concurrency to System Design

Publisher  IEEE Computer Society
Copyright © 2007 IEEE. Reprinted from IEEE Computer Society. This material is posted here with permission of the IEEE. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to pubs-permissions@ieee.org. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.

Details

TypeArticle
URLhttp://dx.doi.org/10.1109/ACSD.2008.4574594
Pages45-49
> Publications > BAM: BioAmbient Machine