A Trace Query Language for Rule-Based Models
| Autor: | Pierre Boutillier, Hector F. Medina-Abarca, Jonathan Laurent, Walter Fontana, Jean Yang |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Multiset Theoretical computer science Rule-based modeling BETA (programming language) Semantics (computer science) Computer science Rule-based system Expression (computer science) Query language 03 medical and health sciences 030104 developmental biology computer computer.programming_language TRACE (psycholinguistics) |
| Zdroj: | Computational Methods in Systems Biology ISBN: 9783319994284 CMSB |
| DOI: | 10.1007/978-3-319-99429-1_13 |
| Popis: | 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 \(\beta \)-catenin degradation in Wnt signaling from an agent-centric perspective. |
| Databáze: | OpenAIRE |
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