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.
Highlights
A basic conviction in computational biology is that it should be possible to create computational tools allowing us to considerably increase our understanding of the functional properties of living organisms
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
Our purpose is to review several tools that use model checking in the analysis of biochemical networks, so as to assess the potential of model checking in computational biology
Summary
A basic conviction in computational biology is that it should be possible to create computational tools allowing us to considerably increase our understanding of the functional properties of living organisms. GRAPH SEARCH AND BRANCHING TIME The verification process in a model checker often uses a graphsearch algorithm accumulating, in a set, system states having a desired property. A reason is that because the behavior of the environment is not determined, and the state of the system being analyzed partially depends on the environment, the state of such a system is not completely determined either Other phenomena, such as asynchrony and incomplete knowledge of a network can be modeled with branching time as well (Thomas and D’Ari, 1990). We will see that many computer tools for biochemical network analysis employ model checking for verifying that a model has a desired property (as is usually done in other domains, like digital circuits).
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