Computing maximal and minimal trap spaces of Boolean networks

DOI10.1007/s11047-015-9520-7zbMath1416.92072arXiv1509.07731OpenAlexW3102568738MaRDI QIDQ2003486

Hannes Klarner, Alexander Bockmayr, Heike Siebert

Publication date: 8 July 2019

Published in: Natural Computing (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1509.07731

zbMATH Keywords

attractorsinteger linear programmingBoolean networkssignal transductionanswer set programminggene regulation

Mathematics Subject Classification ID

Integer programming (90C10) Systems biology, networks (92C42)

Related Items (8)

Computing bottom SCCs symbolically using transition guided reduction ⋮ Correspondence of Trap Spaces in Different Models of Bioregulatory Networks ⋮ Attractor separation and signed cycles in asynchronous Boolean networks ⋮ CONTROLLING THE CELL CYCLE RESTRICTION SWITCH ACROSS THE INFORMATION GRADIENT ⋮ Trap spaces of Boolean networks are conflict-free siphons of their Petri net encoding ⋮ Modeling multi-valued biological interaction networks using fuzzy answer set programming ⋮ Variable stabilisation in Boolean monotonic model pools ⋮ Minimal trap spaces of logical models are maximal siphons of their Petri net encoding

Uses Software

• Gurobi
• JBool
• Potassco
• BoolNet

Cites Work

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• Analysis of discrete bioregulatory networks using symbolic steady states
• Parallel and sequential computation on Boolean networks
• An effective network reduction approach to find the dynamical repertoire of discrete dynamic networks
• Enumerating Prime Implicants of Propositional Formulae in Conjunctive Normal Form

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