Refining Boolean models with the partial most permissive scheme

Abstract

Motivation

In systems biology, modelling strategies aim to decode how molecular components interact to generate dynamical behaviour. Boolean modelling is more and more used, but the description of the dynamics generated by discrete variables with only two values may be too limited to capture certain dynamical properties. Multivalued logical models can overcome this limitation by allowing more than two levels for each component. However, multivaluing a Boolean model is challenging.

Results

We present MRBM, a method for efficiently identifying the components of a Boolean model to be multivalued in order to capture specific fixed-point reachabilities in the asynchronous dynamics. To this goal, we defined a new updating scheme locating reachability properties in the most permissive dynamics. MRBM is supported by mathematical demonstrations and illustrated on a toy model and on two models of stem cell differentiation.

Availability and Implementation

The MRBM method and the BMs used in this manuscript are available on GitHub at: https://github.com/NdnBnBn/MRBM, and archived in Zenodo (doi: 10.5281/ZENODO.14979798).

Supplementary information

Supplementary data are available at Bioinformatics online.

Accepted manuscripts

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