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International Conference on Computational Methods in Systems Biology

CMSB 2022: Computational Methods in Systems Biology pp 158–176Cite as

Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13447))

Abstract

Boolean modelling of gene regulation but also of post-transcriptomic systems has proven over the years that it can bring powerful analyses and corresponding insight to the many cases where precise biological data is not sufficiently available to build a detailed quantitative model. This is even more true for very large models where such data is frequently missing and led to a constant increase in size of logical models à la Thomas. Besides simulation, the analysis of such models is mostly based on attractor computation, since those correspond roughly to observable biological phenotypes. The recent use of trap spaces made a real breakthrough in that field allowing to consider medium-sized models that used to be out of reach. However, with the continuing increase in model-size, the state-of-the-art computation of minimal trap spaces based on prime-implicants shows its limits as there can be a huge number of implicants.

In this article we present an alternative method to compute minimal trap spaces, and hence complex attractors, of a Boolean model. It replaces the need for prime-implicants by a completely different technique, namely the enumeration of maximal siphons in the Petri net encoding of the original model. After some technical preliminaries, we expose the concrete need for such a method and detail its implementation using Answer Set Programming. We then demonstrate its efficiency and compare it to implicant-based methods on some large Boolean models from the literature.

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Notes

  1. 1.

    https://github.com/bnediction/mpbn.

  2. 2.

    https://www.pnml.org/.

  3. 3.

    http://www.colomoto.org/biolqm/.

  4. 4.

    http://colomoto.org/.

  5. 5.

    https://github.com/hklarner/pyboolnet/tree/master/pyboolnet/repository.

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Authors and Affiliations

  1. LIS, Aix-Marseille Université, Marseille, France

    Van-Giang Trinh & Belaid Benhamou

  2. School of Information Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan

    Kunihiko Hiraishi

  3. Lifeware Team, Inria Saclay Center, Palaiseau, France

    Sylvain Soliman

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  1. Van-Giang Trinh
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  2. Belaid Benhamou
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  3. Kunihiko Hiraishi
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  4. Sylvain Soliman
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Correspondence to Sylvain Soliman .

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  1. University of Turku, Turku, Finland

    Ion Petre

  2. University of Bucharest, Bucharest, Romania

    Andrei Păun

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Trinh, VG., Benhamou, B., Hiraishi, K., Soliman, S. (2022). Minimal Trap Spaces of Logical Models are Maximal Siphons of Their Petri Net Encoding. In: Petre, I., Păun, A. (eds) Computational Methods in Systems Biology. CMSB 2022. Lecture Notes in Computer Science(), vol 13447. Springer, Cham. https://doi.org/10.1007/978-3-031-15034-0_8

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