Variable Stabilisation in Boolean Monotonic Model Pools

Pastva, Samuel

doi:10.1007/978-3-031-15034-0_6

Cited by 1 publication

(1 citation statement)

References 25 publications

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“…There are currently two editions of the BBM dataset, both available as Zenodo archives: edition 2021 23 at the address https://doi.org/10.5281/zenodo.8020272, and edition 2022 24 at https://doi.org/10.5281/zenodo.8020309. Any future updates to the dataset will be announced using the git repository at https://github.com/sybila/biodivine-boolean-models.…”

Section: Data Recordsmentioning

confidence: 99%

Repository of logically consistent real-world Boolean network models

Pastva

Šafránek

Beneš

et al. 2023

Preprint

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Recent developments in both computational analysis and data-driven synthesis enable a new era of automated reasoning with logical models (Boolean networks in particular) in systems biology. However, these advancements also motivate an increased focus on quality control and performance comparisons between tools. At the moment, to illustrate real-world applicability, authors typically test their approaches on small sets of manually curated models that are inherently limited in scope. This further complicates reuse and comparisons, because benchmark models often contain ad hoc modifications or are outright not available. In this paper, we describe a new, comprehensive, open source dataset of 210+ Boolean network models compiled from available databases and a literature survey. The models are available in a wide range of formats. Furthermore, the dataset is accompanied by a validation pipeline that ensures the integrity and logical consistency of each model. Using this pipeline, we identified and repaired 400+ potential problems in a number of widely used models.

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Section: Data Recordsmentioning

confidence: 99%