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Experimental Biological Protocols with Formal Semantics by Abate, Alessandro; Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca; Yordanov, Boyan is a scholarly article available to read on EtoBox.

What is Experimental Biological Protocols with Formal Semantics about?

Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from data. However, integration between automated tasks in the process of biological discovery is still lacking, largely due to incompatible or missing formal representations. While theories are expressed formally as computational models, existing languages for encoding and automating experimental protocols often lack formal semantics. This makes it challenging to extract novel understanding by identifying when theory and experimental evidence disagree due to errors in the models or the protocols used to validate them. To address this, we formalize the syntax of a core protocol language, which provides a unified description for the models of biochemical systems being experimented on, together with the discrete events representing the liquid-handling steps of biological protocols. We present both a deterministic and a stochastic semantics to this language, both defined in terms of hybrid processes. In particular, the stochastic semantics captures uncert

Author

Abate, Alessandro; Cardelli, Luca; Kwiatkowska, Marta; Laurenti, Luca; Yordanov, Boyan

Published

2017

Language

EN