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.
A Rule-based and Imperative Language for Biochemical Modeling and Simulation
NIKOLIC, Durica;
2012-01-01
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.
File in questo prodotto:
Non ci sono file associati a questo prodotto.
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
