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Jérôme Feret & Kim Quyên Lý.
Local traces: an over-approximation of the behaviour of the proteins in rule-based models.
In IEEE/ACM Transactions on Computational Biology and Bioinformatics. Vol 15(4), Jul-Aug 2018, E. Bartocci, P. Lio', & N. Paoletti (Eds.),

Abstract: Thanks to rule-based modelling languages, we can assemble large sets of mechanistic protein-protein interactions within integrated models. Our goal would be to understand how the behaviour of these systems emerges from these low-level interactions. Yet this is a quite long term challenge and it is desirable to offer intermediary levels of abstraction, so as to get a better understanding of the models and to increase our confidence within our mechanistic assumptions. To this extend, static analysis can be used to derive various abstractions of the semantics, each of them offering new perspectives on the models. 

@ARTICLE{8306662,
  author = {J. Feret and K. Q. Ly},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  title = {Local Traces: An Over-Approximation of the Behavior of the Proteins in Rule-Based Models},
  year = {2018},
  volume = {15},
  number = {4},
  pages = {1124-1137},
  keywords={Proteins;Receptor (biochemistry);Biological system modeling;Computational modeling;Static analysis;Semantics;Analytical models},
  doi = {10.1109/TCBB.2018.2812195},
  url = {doi.ieeecomputersociety.org/10.1109/TCBB.2018.2812195},
  ISSN = {1545-5963},
  month={July-Aug.}
}