In this paper, we introduce a unified approach for querying simulation traces of rule-based models about the statistical behavior of individual agents. In our approach, a query consists in a trace pattern along with an expression that depends on the variables captured by this pattern. On a given trace, it evaluates to the multiset of all values of the expression for every possible matching of the pattern. We illustrate our proposed query language on a simple example, and then discuss its semantics and implementation for the Kappa language. Finally, we provide a detailed use case where we analyze the dynamics of β-catenin degradation in Wnt signaling from an agent-centric perspective.
CITATION STYLE
Laurent, J., Medina-Abarca, H. F., Boutillier, P., Yang, J., & Fontana, W. (2018). A Trace Query Language for Rule-Based Models. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 11095 LNBI, pp. 220–237). Springer Verlag. https://doi.org/10.1007/978-3-319-99429-1_13
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