Reaction systems models for the heatshock response

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.