proceeding Papers l: An Imperative DSL to Stochastically Simulate Biological Systems


Language-based modelling of biological systems is a growing field of research. Many proofs of concept have been published in the last decade. We propose a domain specific language, imperative in style, to step ahead of proof of concepts. Our DSL is compiled into C# and exploits the benefits of C# optimising compilers to gain in time performance of simulations. Additionally, we introduce a new simulation algorithm that is exact as the original Gillespie's algorithm and faster than each variant previously published. We report benchmarks of the algorithms relying on a mass-action model of the MAPK cascade and a Michaelis-Menten model of the one-carbon metabolism.

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R. Zunino,  D. Nikolic,  C. Priami,  O. Kahramanogullari,  T. Schiavinotto