文章基本信息

标题：Graphs, Rewriting and Pathway Reconstruction for Rule-Based Models
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作者：Vincent Danos ; Jerome Feret ; Walter Fontana 等
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2012
卷号：18
页码：276-288
DOI：10.4230/LIPIcs.FSTTCS.2012.276
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：In this paper, we introduce a novel way of constructing concise causal histories (pathways) to represent how specified structures are formed during simulation of systems represented by rule-based models. This is founded on a new, clean, graph-based semantics introduced in the first part of this paper for Kappa, a rule-based modelling language that has emerged as a natural description of protein-protein interactions in molecular biology [Bachman 2011]. The semantics is capable of capturing the whole of Kappa, including subtle side-effects on deletion of structure, and its structured presentation provides the basis for the translation of techniques to other models. In particular, we give a notion of trajectory compression, which restricts a trace culminating in the production of a given structure to the actions necessary for the structure to occur. This is central to the reconstruction of biochemical pathways due to the failure of traditional techniques to provide adequately concise causal histories, and we expect it to be applicable in a range of other modelling situations.
关键词：concurrency; rule-based models; graph rewriting; pathways; causality