Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Thanks to rule-based modelling languages,  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. #R##N#,  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,  use simplicial complexes to abstract away the interleaving order of the transformations beten conformations that commute. As a result,  get a compact summary of the potential behaviour of each protein of the model.
['Jérôme Feret', 'Kim Quyên Lý']
I am writing a research paper on a idea Local traces: an over-approximation of the behaviour of the proteins in rule-based models
[{"from": "human", "value": "I am writing a research paper on a idea Local traces: an over-approximation of the behaviour of the proteins in rule-based models"}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Thanks to rule-based modelling languages,  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. #R##N#,  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,  use simplicial complexes to abstract away the interleaving order of the transformations beten conformations that commute. As a result,  get a compact summary of the potential behaviour of each protein of the model."}]