CABEAN: a software for the control of asynchronous Boolean networks | Zendy

Cui Su | Zendy; Jun Pang | Zendy

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CABEAN: a software for the control of asynchronous Boolean networks

Author(s) -

Cui Su,

Jun Pang

Publication year - 2020

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btaa752

Subject(s) - computer science , executable , software , boolean network , asynchronous communication , theoretical computer science , set (abstract data type) , attractor , distributed computing , boolean circuit , boolean expression , and inverter graph , gene regulatory network , reprogramming , software engineering , boolean function , programming language , algorithm , computer network , mathematics , cell , biology , mathematical analysis , gene expression , biochemistry , genetics , gene

Direct cell reprogramming, also called transdifferentiation, has great potential for tissue engineering and regenerative medicine. Boolean networks, a popular modelling framework for gene regulatory networks, make it possible to identify intervention targets for direct cell reprogramming with computational methods. In this work, we present our software, CABEAN, for the control of asynchronous Boolean networks. CABEAN identifies efficacious nodes, whose perturbations can drive the dynamics of a network from a source attractor (the initial cell type) to a target attractor (the desired cell type). CABEAN provides several control methods integrating practical constraints. Thus, it has the ability to provide a rich set of control sets, such that biologists can select suitable ones for validation based on specific experimental settings.

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