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Matthieu Bouguéon, Pierre Boutillier, Jérôme Feret, Octave Hazard, and Nathalie Theret.
The Rule-based model approach. A Kappa model for hepatic stellate cells activation by TGFB1.
In Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools. E. De Maria (Ed.). Wiley. ©, 2022.

Abstract: In this chapter, we introduce Kappa, a site graph rewriting language. As a realistic case study, we model a population of hepatic stellate cells under the effect of the TGFB1 protein. Kappa offers a rule-centric approach, inspired from chemistry, where interaction rules locally modify the state of a system that is defined as a graph of components, connected or not. In this case study, the components will be occurrences of hepatic stellate cells in different states, and occurrences of the protein TGFB1. The protein TGFB1 induces different behaviors of hepatic stellate cells thereby contribut- ing either to tissue repair or to fibrosis. Better understanding the overall behavior of the mechanisms that are involved in these processes is a key issue to identify markers and therapeutic targets likely to promote the resolution of fibrosis at the expense of its progression. 

@incollection{bougueon:hal-03388100,
  TITLE = {{The rule-based model approach. A Kappa model for hepatic stellate cells activation by TGFB1}},
  AUTHOR = {Bougu{\'e}on, Matthieu and Boutillier, Pierre and Feret, J{\'e}r{\^o}me and Hazard, Octave and Th{\'e}ret, Nathalie},
  URL = {https://inria.hal.science/hal-03388100},
  BOOKTITLE = {{Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools}},
  EDITOR = {Elisabetta De Maria},
  PUBLISHER = {{Wiley}},
  PAGES = {1-76},
  YEAR = {2022},
  MONTH = Nov,
  PDF = {https://inria.hal.science/hal-03388100v2/file/tgf%20%281%29.pdf},
  HAL_ID = {hal-03388100},
}