BRE:IN - A Backend for Reasoning About Interaction Networks with Temporal Logic

Judah Goldfeder, Hillel Kugler

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

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.

Original languageEnglish
Title of host publicationComputational Methods in Systems Biology - 17th International Conference, CMSB 2019, Proceedings
EditorsLuca Bortolussi, Guido Sanguinetti
PublisherSpringer
Pages289-295
Number of pages7
ISBN (Print)9783030313036
DOIs
StatePublished - 2019
Event17th International Conference on Computational Methods in Systems Biology, CMSB 2019 - Trieste, Italy
Duration: 18 Sep 201920 Sep 2019

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume11773 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference17th International Conference on Computational Methods in Systems Biology, CMSB 2019
Country/TerritoryItaly
CityTrieste
Period18/09/1920/09/19

Bibliographical note

Publisher Copyright:
© 2019, Springer Nature Switzerland AG.

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