Computational Methods in Systems Biology

Volume 2602 of the series Lecture Notes in Computer Science pp 34-46


Graphs for Core Molecular Biology

  • Vincent DanosAffiliated withÉquipe PPS, CNRS and University of Paris 7
  • , Cosimo LaneveAffiliated withDepartment of Computer Science, University of Bologna

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A graphic language—the graphic κ calculus—modeling protein interactions at the domain level is introduced. Complexation, activation and mixed forms of interaction are expressed as graph rewriting rules. A compilation in a low-level graph rewriting calculus, called mobile κ, is given and shown to be correct up to some suitable notion of observational equivalence. This intermediate language is of independent interest and can be easily implemented in π-like calculi.