Journal of Chemical Information & Computer Sciences
Graphical rule-based representation of signal-transduction networks
Proceedings of the 2005 ACM symposium on Applied computing
Scalable simulation of cellular signaling networks
APLAS'07 Proceedings of the 5th Asian conference on Programming languages and systems
A language for biochemical systems: design and formal specification
Transactions on Computational Systems Biology XII
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
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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.