Working group: "Computational Biology"
2010, the 20th of April
Espen Højsgaard
Title: Simulating Biology with Bigraphs
Abstract:
The theory of bigraphs has been proposed as a formalism for modelling
molecular biological systems with dynamic compartmentalization. For
example, Damgaard et al. have used bigraphs to model the formation of
clathrin-coated cytoplasmic vesicles, through budding from the plasma
membrane (the cell-wall) [1].
Bigraphical Reactive Systems (BRSs) is a rule based model of
concurrency developed by Milner [2], that in essence generalizes and
unifies the connectivity of CCS with the spatiality of the ambient
calculus in one framework. Many process calculi can be expressed as
BRSs, such as CCS, pi calculus, ambient calculus, CSP, and
kappa. Recently, Krivine et al. have equipped the theory with a
stochastic semantics [3].
In this talk, I will give an introduction to bigraphs and BRSs and
present ongoing work on implementing an efficient simulator for
stochastic bigraphs.
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[1] Troels C. Damgaard, Vincent Danos, and Jean Krivine. "A Language
for the Cell", IT University Technical Report Series, TR-2008-116,
2008.
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[2] Robin Milner. "The Space and Motion of Communicating Agents",
Cambridge University Press, 2009.
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[3] Jean Krivine, Robin Milner, and Angelo Troina. "Stochastic
Bigraphs", 24th Conference on the Mathematical Foundations of
Programming Semantics (MFPS'08), invited paper, ENTCS 218,
pp. 73-96, 2008.