A Syntactic Abstraction for Rule-Based Languages with Binding

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.