文章基本信息

标题：BlenX-based compositional modeling of complex reaction mechanisms
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作者：Judit Zámborszky ; Corrado Priami
期刊名称：Electronic Proceedings in Theoretical Computer Science
电子版ISSN：2075-2180
出版年度：2009
卷号：19
页码：85-102
DOI：10.4204/EPTCS.19.6
出版社：Open Publishing Association
摘要：Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological networks calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. The Gillespie's stochastic framework of BlenX requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown in this study. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of BlenX compositionality.