proceeding Papers A Rule-based and Imperative Language for Biochemical Modeling and Simulation


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 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.



Paper Details

Authors

D. Nikolic,  C. Priami,  R. Zunino

Publication

The 10th International Conference on Software Engineering and Formal Methods (SEFM 2012), 7504, , 16 - 32

Download

http://dx.doi.org/10.1007/978-3-642-33826-7_2

Language

English
.