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Temporal logic modeling of biological systems. (English) Zbl 1429.92071
Akama, Seiki (ed.), Towards paraconsistent engineering. Cham: Springer. Intell. Syst. Ref. Libr. 110, 205-226 (2016).
Summary: Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of these reactions. Cancer, for example, can sometimes appear in a cell as a result of some pathology in a metabolic pathway. Most of these pathways are formed by an intricate and complex network of chain reactions, and can be represented in a human readable form using graphs which describe the cell signaling pathways. In this paper, we define a logic, called Molecular Interaction Logic (MIL), able to represent these graphs, and we present a method to automatically translate graphs into MIL formulas. Then, we show how MIL formulas can be translated into linear time temporal logic, and then grounded into propositional classical logic. This enables us to solve complex queries on graphs using only propositional classical reasoning tools such as SAT solvers.
For the entire collection see [Zbl 1366.03010].
92C42 Systems biology, networks
03B44 Temporal logic
03B80 Other applications of logic
ASSAT; MiniSat
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