A logical framework for systems biology

DOI10.1007/978-3-319-10398-3_10MaRDI QIDQ5500406zbMATH OpenOpenAlexFDO

Authors Elisabetta De Maria, J. Despeyroux, Amy P. Felty

Publication date 6 August 2015

Published in Formal Methods in Macro-Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1404.5439

zbMATH Keywords

modal linear logicproofsystems biology

Mathematics Subject Classification ID

Modal logic (including the logic of norms) (03B45) Proof-theoretic aspects of linear logic and other substructural logics (03F52) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Abstract: We propose a novel approach for the formal verification of biological systems based on the use of a modal linear logic. We show how such a logic can be used, with worlds as instants of time, as an unified framework to encode both biological systems and temporal properties of their dynamic behaviour. To illustrate our methodology, we consider a model of the P53/Mdm2 DNA-damage repair mechanism. We prove several properties that are important for such a model to satisfy and serve to illustrate the promise of our approach. We formalize the proofs of these properties in the Coq Proof Assistant, with the help of a Lambda Prolog prover for partial automation of the proofs.

Recommendations

• (Mathematical) logic for systems biology (invited paper)
• Modular verification of interactive systems with an application to biology
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Cited in

(14)

• (Mathematical) logic for systems biology (invited paper)
• Hybrid and subexponential linear logics
• On concurrent behaviors and focusing in linear logic
• Verification of spatial and temporal modalities in biochemical systems
• A proof theoretic view of spatial and temporal dependencies in biochemical systems
• Symbolic logic model of cellular adaptation
• Proof search in a context-sensitive logic for molecular biology
• Modular verification of interactive systems with an application to biology
• scientific article; zbMATH DE number 7453108 (Why is no real title available?)
• A Formal Framework for Composing Qualitative Models of Biological Systems
• Hybrid linear logic, revisited
• scientific article; zbMATH DE number 7065571 (Why is no real title available?)
• Logics in Artificial Intelligence
• Modular verification of interactive systems with an application to biology

Describes a project that uses

Uses Software

• PRISM
• Coq
• NuSMV

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