The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models

In this paper we introduce the Atomizer, an expert system for extracting implicit information from reaction network models, like those encoded by the Systems Modeling Markup Language (SBML), to create a structured translation using the rule-based modeling paradigm. Atomized models can be visualized in a compact form through contact maps, which show the underlying molecules, components, and interactions used to construct a model. Analysis of the atomized reactions reveals simplifying assumptions made in the construction of a model that limit the combinatorial complexity. These benefits are elucidated through a case study. We anticipate that the library of translated rule-based models we can generate using the Atomizer will be useful to the biological modeling community by providing a more accessible view of the available models and by facilitating their extension and merging. 9939