From Biochemistry to Stochastic Processes

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• 作者：Cosimo Laneve ; Sylvain Pradalier ; Gianluigi Zavattaro
• 关键词：Stochastic process calculi ; systems biology ; encoding from reactive to process-oriented formalisms
• 刊名：Electronic Notes in Theoretical Computer Science
• 出版年：2009
• 出版时间：1 November 2009
• 年：2009
• 卷：253
• 期：3
• 页码：167-185
• 全文大小：367 K

文摘

The nanoκ calculus is a formalism that models biochemical systems by defining its set of reactions. We study the implementation of nanoκ into the Stochastic Pi Machine where biochemical systems are defined by regarding molecules as processes, and deriving the overall behaviour by means of communication rules. Our implementation complies with the stochastic behaviors of systems, thus allowing one to use nanoκ as an intelligible front-end for a process-oriented simulator. This study also permits to reuse, in nanoκ, the theories and tools already developed for process calculi.