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Reaction Systems Models for the Heat Shock Response

Sepinoud Azimi, Bogdan Iancu, Ion Petre, Reaction Systems Models for the Heat Shock Response. TUCS Technical Reports 1075, TUCS, 2013.


Reaction systems are a formal framework for modeling processes driven by bio-
chemical reactions. They are based on the mechanisms of facilitation and inhi-
bition. A main assumption is that if a resource is available, then it is present in
sufficient amounts and as such, several reactions using the same resource will not
compete concurrently against each other; this makes reaction systems very differ-
ent as a modeling framework than traditional frameworks such as ODEs or con-
tinuous time Markov chains. We construct in this paper a reaction systems model
for the heat shock response in such a way that its (qualitative) behavior correlates
well with the quantitative behavior of the corresponding ODE model. We discuss
two different approaches for building the model. We conclude with a discussion
on the expressivity of reaction systems as compared to that of ODE-based models.


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BibTeX entry:

  title = {Reaction Systems Models for the Heat Shock Response},
  author = {Azimi, Sepinoud and Iancu, Bogdan and Petre, Ion},
  number = {1075},
  series = {TUCS Technical Reports},
  publisher = {TUCS},
  year = {2013},

Belongs to TUCS Research Unit(s): Computational Biomodeling Laboratory (Combio Lab)

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