Section: Mathematical & Computational Biology
Topic: Biophysics and computational biology, Genetics/Genomics

Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis

Paulevé, Loïc1  
1 Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France

Corresponding author(s): Paulevé, Loïc (loic.pauleve@labri.fr)

10.24072/pcjournal.255 - Peer Community Journal, Volume 3 (2023), article no. e30.

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Boolean networks (BNs) are discrete dynamical systems with applications to the modeling of cellular behaviors. In this paper, we demonstrate how the software BoNesis can be employed to exhaustively identify combinations of perturbations which enforce properties on their fixed points and attractors. We consider marker properties, which specify that some components are fixed to a specific value. We study 4 variants of the marker reprogramming problem: the reprogramming of fixed points, of minimal trap spaces, and of fixed points and minimal trap spaces reachable from a given initial configuration with the most permissive update mode. The perturbations consist of fixing a set of components to a fixed value. They can destroy and create new attractors. In each case, we give an upper bound on their theoretical computational complexity, and give an implementation of the resolution using the BoNesis Python framework. Finally, we lift the reprogramming problems to ensembles of BNs, as supported by BoNesis, bringing insight on possible and universal reprogramming strategies. This paper can be executed and modified interactively.

Published online:
DOI: 10.24072/pcjournal.255
Type: Research article
Keywords: Discrete dynamical systems, Control, Minimal trap spaces, Attractors, Reachability, Gene Regulatory Networks
Keywords: Systems and Control (eess.SY), Artificial Intelligence (cs.AI), Molecular Networks (q-bio.MN), FOS: Electrical engineering, electronic engineering, information engineering, FOS: Electrical engineering, electronic engineering, information engineering, FOS: Computer and information sciences, FOS: Computer and information sciences, FOS: Biological sciences, FOS: Biological sciences

Paulevé, Loïc 1

1 Univ. Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800, F-33400 Talence, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Paulevé, Loïc. Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis. Peer Community Journal, Volume 3 (2023), article  no. e30. doi : 10.24072/pcjournal.255. https://peercommunityjournal.org/articles/10.24072/pcjournal.255/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.mcb.100183

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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