We present COSBI LAB Language ( $\mathcal{L}$ for short), a simple modeling language for biochemical systems. $\mathcal{L}$ features stochastic multiset rewriting, defined in part through rewriting rules, and in part through imperative code. We provide a continuous-time Markov chain semantics for $\mathcal{L}$ at three different abstraction levels, linked by Galois connections. We then describe a simulation algorithm for the most concrete semantics, which is then adapted to work at higher abstract levels while improving space and time performance. Doing so results in the well-known Gillespie’s Direct Method, as well as in a further optimized algorithm.

A rule-based and imperative language for biochemical modeling and simulation

Priami, Corrado;Zunino, Roberto
2012-01-01

Abstract

We present COSBI LAB Language ( $\mathcal{L}$ for short), a simple modeling language for biochemical systems. $\mathcal{L}$ features stochastic multiset rewriting, defined in part through rewriting rules, and in part through imperative code. We provide a continuous-time Markov chain semantics for $\mathcal{L}$ at three different abstraction levels, linked by Galois connections. We then describe a simulation algorithm for the most concrete semantics, which is then adapted to work at higher abstract levels while improving space and time performance. Doing so results in the well-known Gillespie’s Direct Method, as well as in a further optimized algorithm.
2012
Software engineering and formal methods : 10th international conference, SEFM 2012, Thessaloniki, Greece, October 1-5, 2012 : proceedings
Berlin
Springer
9783642338250
9783642338267
Đ., Nikolić; Priami, Corrado; Zunino, Roberto
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/96330
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