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.
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Nikolić, Đ., Priami, C., Zunino, R. (2012). A Rule-Based and Imperative Language for Biochemical Modeling and Simulation. In: Eleftherakis, G., Hinchey, M., Holcombe, M. (eds) Software Engineering and Formal Methods. SEFM 2012. Lecture Notes in Computer Science, vol 7504. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33826-7_2
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DOI: https://doi.org/10.1007/978-3-642-33826-7_2
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