An overview of existing modeling tools making use of model checking in the analysis of biochemical networks

Frontiers in Plant Science
Miguel CarrilloDavid A Rosenblueth

Abstract

Model checking is a well-established technique for automatically verifying complex systems. Recently, model checkers have appeared in computer tools for the analysis of biochemical (and gene regulatory) networks. We survey several such tools to assess the potential of model checking in computational biology. Next, our overview focuses on direct applications of existing model checkers, as well as on algorithms for biochemical network analysis influenced by model checking, such as those using binary decision diagrams (BDDs) or Boolean-satisfiability solvers. We conclude with advantages and drawbacks of model checking for the analysis of biochemical networks.

Citations

Oct 7, 2015·Frontiers in Bioengineering and Biotechnology·Hannes Klarner, Heike Siebert
Mar 25, 2014·Seminars in Cancer Biology·Ali Masoudi-NejadEdwin Wang
Jun 28, 2016·Journal of Theoretical Biology·Ronan M T FlemingMichael A Saunders
Mar 12, 2020·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Enrico BorrielloManfred D Laubichler
Mar 22, 2018·Frontiers in Genetics·Stalin MuñozDavid A Rosenblueth

Related Concepts

Analysis
Computational Molecular Biology
Boolean

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