Affiliations: Computational Biomodeling Laboratory, Turku Centre for Computer Science, Åbo Akademi University, 20520 Turku, Finland. {Sepinoud.Azimi, Bogdan.Iancu, Ion.Petre}@abo.fi
Note: [] Address for correspondence: Department of Information Technologies, Åbo Akademi University, Joukahaisenkatu 3-5, 20520 Turku, Finland
Abstract: Reaction systems are a formal framework for modeling processes driven by biochemical reactions. They are based on the mechanisms of facilitation and inhibition. 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 different as a modeling framework than traditional frameworks such as ODEs or continuous time Markov chains. We demonstrate in this paper that reaction systems are rich enough to capture the essential characteristics of ODE-based models. We construct a reaction system 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 construct our reaction system model based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We conclude with a discussion on the expressivity of reaction systems as compared to that of ODE-based models.
