Graphs , rewriting and causality in rule-based models

@inproceedings{Danos2012GraphsR,
  title={Graphs , rewriting and causality in rule-based models},
  author={Vincent Danos and J{\'e}r{\^o}me Feret and Walter Fontana and Russell Harmer and Jonathan Hayman and Jean Krivine and Chris Thompson-Walsh and Glynn Winskel},
  year={2012}
}
The Kappa calculus defines how a graph, representing a system of linked agents, can be modified by rules that specify which changes may occur at places that match specific local patterns. Though the calculus has a wide degree of applicability, it has emerged as a natural description of proteinprotein interaction systems and pathways in molecular biology [1]. In this paper, we develop an intuitive graph-based semantics for Kappa that correctly handles subtle side-effects upon agent creation or… CONTINUE READING

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