Temporal logic modeling of biological systems

DOI10.1007/978-3-319-40418-9_11MaRDI QIDQ5213786zbMATH OpenOpenAlexFDO

Authors Jean-Marc Alliot, Robert Demolombe, Martín Diéguez, Luis Fariñas del Cerro, Gilles Favre, Jean-Charles Faye, Naji Obeid, Olivier Sordet

Publication date 4 February 2020

Published in Towards Paraconsistent Engineering (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-319-40418-9_11

zbMATH Keywords

metabolic networkstemporal reasoningmolecular interaction logic (MIL)

Mathematics Subject Classification ID

Systems biology, networks (92C42) Temporal logic (03B44) Other applications of logic (03B80)

Recommendations

• Metabolic pathways as temporal logic programs
• A framework for modelling molecular interaction maps
• Abductive reasoning on molecular interaction maps
• Modeling and querying biomolecular interaction networks
• Bio-logics: logical analysis of bioregulatory networks

Cites work

• scientific article; zbMATH DE number 1348482 (Why is no real title available?)
• A generalization of the Lin-Zhao theorem
• An incremental method for generating prime implicants/implicates
• Enumerating prime implicants of propositional formulae in conjunctive normal form
• Loop formulas for splitable temporal logic programs
• Temporal Equilibrium Logic: A First Approach
• Temporal equilibrium logic: a survey
• Theory and Applications of Satisfiability Testing
• Translation of first order formulas into ground formulas via a completion theory

Cited in

(7)

• Abductive reasoning on molecular interaction maps
• Abstract interpretation based verification of temporal properties for BioAmbients
• A proof theoretic view of spatial and temporal dependencies in biochemical systems
• Modeling and querying biomolecular interaction networks
• A framework for modelling molecular interaction maps
• Metabolic pathways as temporal logic programs
• Temporal abductive reasoning about biochemical reactions

Describes a project that uses

Uses Software

• ASSAT
• MiniSat

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