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Taming Living Logic Using Formal Methods

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Models, Algorithms, Logics and Tools

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10460))

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Abstract

One of the goals of synthetic biology is to build genetic circuits to control the behavior of a cell for different application domains, such as medical, environmental, and biotech. During the design process of genetic circuits, biologists are often interested in the probability of a system to work under different conditions. Since genetic circuits are noisy and stochastic in nature, the verification process becomes very complicated. The state space of stochastic genetic circuit models is usually too large to be handled by classical model checking techniques. Therefore, the verification of genetic circuit models is usually performed by the statistical approach of model checking. In this work, we present a workflow for checking genetic circuit models using a stochastic model checker (Uppaal) and a stochastic simulator (D-VASim). We demonstrate with experimentations that the proposed workflow is not only sufficient for the model checking of genetic circuits, but can also be used to design the genetic circuits with desired timings.

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Acknowledgment

We would like to thank Marius Mikucionis (Aalborg University) for providing us an extensive support and help on using Uppaal. We would further like to thank Prof. Chris Myers (University of Utah) for providing us the SBML models of the genetic circuits, and Associate Prof. Michael Reichhardt Hansen (Technical University of Denmark) for fruitful discussions on model checking and for giving constructive feedback.

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Correspondence to Jan Madsen .

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Baig, H., Madsen, J. (2017). Taming Living Logic Using Formal Methods. In: Aceto, L., Bacci, G., Bacci, G., Ingólfsdóttir, A., Legay, A., Mardare, R. (eds) Models, Algorithms, Logics and Tools. Lecture Notes in Computer Science(), vol 10460. Springer, Cham. https://doi.org/10.1007/978-3-319-63121-9_25

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