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EnglishWe present COSBI LAB Language (L for short), a simple modeling language for biochemical systems. 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 L at three dierent 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.
| Titolo: | A Rule-based and Imperative Language for Biochemical Modeling and Simulation | |
| Autori: | ||
| Data di pubblicazione: | 2012 | |
| Abstract: | We present COSBI LAB Language (L for short), a simple modeling language for biochemical systems. 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 L at three dierent 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. | |
| Handle: | http://hdl.handle.net/11562/426939 | |
| ISBN: | 9783642338250 | |
| Appare nelle tipologie: | 04.01 Contributo in atti di convegno |
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