BoNesis: a Python-Based Declarative Environment for the Verification, Reprogramming, and Synthesis of Most Permissive Boolean Networks
摘要
BoNesis is a Python library which offers a declarative framework for the synthesis of Boolean networks from advanced dynamical properties, such as reachability, bifurcation, minimal trap spaces, stable states, and mutations. It combines recent theoretical advances on Boolean networks with the Most Permissive update mode and efficient resolution of logic programs expressed in Answer-Set Programming. Its main application domain is the inference of Boolean models from bulk and single-cell gene expression data of cell-fate, differentiation and reprogramming processes. BoNesis is distributed under the GPLv3-compatible free software license CeCILL and is available at https://bnediction.github.io/bonesis .