Refining Boolean models with the partial most permissive scheme.

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Boolean modeling 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.\nRESULTS: 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.\nAVAILABILITY AND IMPLEMENTATION: The MRBM method and the BMs used in this article are available on GitHub at: https://github.com/NdnBnBn/MRBM, and archived in Zenodo (doi: 10.5281/ZENODO.14979798).", "claims": [{"id": "claim-data-access", "statement": "Supplementary data are available at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40119940", "locator": "sections[20] \"Supplementary data\" paragraph 2", "quote": "Supplementary data are available at Bioinformatics online."}], "state": "complete"}, {"id": "claim-target-result", "statement": "MRBM efficiently identifies the components of a Boolean model that should be multivalued to capture specified fixed-point reachabilities in asynchronous dynamics.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40119940", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "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."}, {"asset": "source:pmid:40119940", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "MRBM is supported by mathematical demonstrations and illustrated on a toy model and on two models of stem cell differentiation."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "MRBM efficiently identifies the components of a Boolean model that should be multivalued to capture specified fixed-point reachabilities in asynchronous dynamics.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40119940"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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