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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 Proceedings of the 14th Conference on Computational Methods in Systems Biology (CMSB 2016), Cambridge, UK, September 21--23, 2016. E. Bartocci, P. Lio', & N. Paoletti (Eds.). In Lecture Notes in Computer Sciences / Lecture Notes in BioInformatics, volume 9859. © 2016, Springer.

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.
In this paper, we propose an abstract interpretation of the behaviour of each protein, in isolation. Given a model written in Kappa, this abstraction computes for each kind of protein a transition system that describes which conformations this protein can take and how a protein can pass from one conformation to another one. Then, we use simplicial complexes to abstract away the interleaving order of the transformations between conformations that commute. As a result, we get a compact summary of the potential behaviour of each protein of the model.

title = "Local traces: an over-approximation of the behaviour of the proteins in rule-based models",
booktitle = "Fourteenth Conference on Computational Method in Systems Biology (CMSB'16)",
series = "LNCS/LNBI",
volume = "9859"
publisher = "Springer",
year = "2016",
editor = "E. Bartocci and P. Lio', and N Paoletti",
author = "J{\'e}r{\^o}me Feret and Kim Quy{\^e}n L{\'y}"}