ArticleFrontiers in plant science2012
An overview of existing modeling tools making use of model checking in the analysis of biochemical networks.
Article in Frontiers in plant science, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Verifiable biology.Journal of the Royal Society, Interface · 2023Review
- Model-checking ecological state-transition graphs.PLoS computational biology · 2022Article
- Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Parameter estimation of qualitative biological regulatory networks on high performance computing hardware.BMC systems biology · 2018Article
- Griffin: A Tool for Symbolic Inference of Synchronous Boolean Molecular Networks.Frontiers in genetics · 2018Article
- Conditions for duality between fluxes and concentrations in biochemical networks.Journal of theoretical biology · 2016Article
- Formal modeling and analysis of ER-PeerJ · 2016Article
- Quantitative and logic modelling of molecular and gene networks.Nature reviews. Genetics · 2015Review
- Approximating Attractors of Boolean Networks by Iterative CTL Model Checking.Frontiers in bioengineering and biotechnology · 2015Article
- Genome scale modeling in systems biology: algorithms and resources.Current genomics · 2014Article
- An integrative modeling framework reveals plasticity of TGF-β signaling.BMC systems biology · 2014Article
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.BMC systems biology · 2013Article
- An interdisciplinary view on dynamic models for plant genetics and morphogenesis: scope, examples and emerging research avenues.Frontiers in plant science · 2013Article
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Authors and funding
3 authors.
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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.
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