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.
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Titolo: | A rule-based and imperative language for biochemical modeling and simulation | |
Autori: | Đ., Nikolić; Priami, Corrado; Zunino, Roberto | |
Autori Unitn: | ||
Titolo del volume contenente il saggio: | Software engineering and formal methods : 10th international conference, SEFM 2012, Thessaloniki, Greece, October 1-5, 2012 : proceedings | |
Luogo di edizione: | Berlin | |
Casa editrice: | Springer | |
Anno di pubblicazione: | 2012 | |
Codice identificativo Scopus: | 2-s2.0-84868236077 | |
ISBN: | 9783642338250 9783642338267 | |
Handle: | http://hdl.handle.net/11572/96330 | |
Appare nelle tipologie: | 04.1 Saggio in atti di convegno (Paper in Proceedings) |