Abstract
We present the BRE:IN tool, a Backend for Reasoning about Interaction Networks. Our tool supports the framework and methodology originally introduced by the RE:IN tool, where an Abstract Boolean Network (ABN) specifies partial information about the network topology, and experimental observations are used to constrain the ABN, allowing to synthesize consistent models, or prove that no consistent model exists. RE:IN has been used successfully to derive mechanistic models of biological systems allowing to gain new insights into cellular decision-making and to make predictions that were validated experimentally. BRE:IN implements translations of experimental observations to temporal logic and captures the semantics of ABNs as transition systems, enabling to use off-the-shelf model checking algorithms. We make our tool and benchmarks publicly available and demonstrate the utility of the tool, providing speed-up gains for some benchmarks, while also enabling extensions of the experimental observations specification language currently supported in RE:IN by using the rich expressive power of temporal logic.
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Acknowledgment
The research was partially supported by the Horizon 2020 research and innovation programme for the Bio4Comp project under grant agreement number 732482. This research was also supported by the ISRAEL SCIENCE FOUNDATION (grant No. 190/19).
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Goldfeder, J., Kugler, H. (2019). BRE:IN - A Backend for Reasoning About Interaction Networks with Temporal Logic. In: Bortolussi, L., Sanguinetti, G. (eds) Computational Methods in Systems Biology. CMSB 2019. Lecture Notes in Computer Science(), vol 11773. Springer, Cham. https://doi.org/10.1007/978-3-030-31304-3_15
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DOI: https://doi.org/10.1007/978-3-030-31304-3_15
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