(Mathematical) logic for systems biology (invited paper)

DOI10.1007/978-3-319-45177-0_1MaRDI QIDQ1706576zbMATH OpenOpenAlexFDO

Authors J. Despeyroux

Publication date 22 March 2018

Full work available at URL https://arxiv.org/abs/1701.05063

zbMATH Keywords

systems biologysequent calculus

Mathematics Subject Classification ID

Systems biology, networks (92C42) Modal logic (including the logic of norms) (03B45)

Abstract: We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The potential candidate logics should have a traditional proof theoretic pedigree (including a sequent calculus presentation enjoying cut-elimination and focusing), and should come with (certified) proof tools. Beyond providing a reliable framework, this allows the adequate encodings of our biological systems. We present two candidate logics (two modal extensions of linear logic, called HyLL and SELL), along with biological examples. The examples we have considered so far are very simple ones-coming with completely formal (interactive) proofs in Coq. Future works includes using automatic provers, which would extend existing automatic provers for linear logic. This should enable us to specify and study more realistic examples in systems biology, biomedicine (diagnosis and prognosis), and eventually neuroscience.

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Cited in

(10)

• Modelling and Analysing Qualitative Biological Models using Rewriting Logic
• Proof search in a context-sensitive logic for molecular biology
• scientific article; zbMATH DE number 7453108 (Why is no real title available?)
• Mathematical Logic for Life Science Ontologies
• scientific article; zbMATH DE number 7065571 (Why is no real title available?)
• A logical framework for systems biology
• \(\epsilon\)-semantics computations on biological systems
• A proof theoretic view of spatial and temporal dependencies in biochemical systems
• The role of theorem proving in systems biology
• Adding logic to the toolbox of molecular biology

Describes a project that uses

Uses Software

• Coq

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