An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence

Georgios Argyris; Alberto Lluch Lafuente; Mirco Tribastone; Max Tschaikowski; Andrea Vandin

doi:10.1007/978-3-031-15034-0_16

An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence

Georgios Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski, Andrea Vandin^*

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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Abstract

Boolean Networks (BN) are established tools for modelling biological systems. However, their analysis is hindered by the state space explosion: the exponentially many states on the variables of a BN. We present an extension of the tool for model reduction ERODE with support for BNs and their reduction with a recent method called Backward Boolean Equivalence (BBE). BBE identifies maximal sets of variables that retain the same value whenever initialized equally. ERODE has been also extended to support importing and exporting between different formats and model repositories, enhancing interoperability with other tools.

Original language	English
Title of host publication	Proceedings of 20^th International Conference Computational Methods in Systems Biology
Editors	Ion Petre, Andrei Păun
Publisher	Springer
Publication date	2022
Pages	294-301
ISBN (Print)	9783031150333
DOIs	https://doi.org/10.1007/978-3-031-15034-0_16
Publication status	Published - 2022
Event	20^th International Conference on Computational Methods in Systems Biology - University of Bucharest, Bucharest, Romania Duration: 14 Sept 2022 → 16 Sept 2022

Conference

Conference	20^th International Conference on Computational Methods in Systems Biology
Location	University of Bucharest
Country/Territory	Romania
City	Bucharest
Period	14/09/2022 → 16/09/2022

Series	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	13447 LNBI
ISSN	0302-9743

Keywords

Backward Equivalence
Boolean Network
Reduction

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10.1007/978-3-031-15034-0_16

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Argyris, Georgios ; Lafuente, Alberto Lluch ; Tribastone, Mirco et al. / An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence. Proceedings of 20^th International Conference Computational Methods in Systems Biology. editor / Ion Petre ; Andrei Păun. Springer, 2022. pp. 294-301 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI).

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Argyris, G, Lafuente, AL, Tribastone, M, Tschaikowski, M & Vandin, A 2022, An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence. in I Petre & A Păun (eds), Proceedings of 20^th International Conference Computational Methods in Systems Biology. Springer, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 13447 LNBI, pp. 294-301, 20^th International Conference on Computational Methods in Systems Biology, Bucharest, Romania, 14/09/2022. https://doi.org/10.1007/978-3-031-15034-0_16

An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence. / Argyris, Georgios; Lafuente, Alberto Lluch; Tribastone, Mirco et al.
Proceedings of 20^th International Conference Computational Methods in Systems Biology. ed. / Ion Petre; Andrei Păun. Springer, 2022. p. 294-301 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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Argyris G, Lafuente AL, Tribastone M, Tschaikowski M, Vandin A. An Extension of ERODE to Reduce Boolean Networks By Backward Boolean Equivalence. In Petre I, Păun A, editors, Proceedings of 20^th International Conference Computational Methods in Systems Biology. Springer. 2022. p. 294-301. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13447 LNBI). doi: 10.1007/978-3-031-15034-0_16