A Syntactic Abstraction for Rule-Based Languages with Binding

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• 作者：Michael  ; Pedersen¹ ;   ; ^{mdp40@cam.ac.uk}
• 关键词：Rule-based languages ; Kappa ; BioNetGen ; syntax ; protein complexes ; binding
• 刊名：Electronic Notes in Theoretical Computer Science
• 出版年：2011
• 出版时间：27 October 2011
• 年：2011
• 卷：277
• 期：Complete
• 页码：53-64
• 全文大小：624 K

文摘

Rule-based languages such as Kappa and BioNetGen excel in their support for handling combinatorial explosion of the number of protein complexes encoded by a signal transduction model. They do so by representing the transformation of complexes at the level of protein binding sites. However, this detailed level of representation can make models cumbersome to write and difficult to read. This paper introduces a syntactic abstraction of binding, away from specific sites, which in many cases results in shorter and more concise rules.