A Logical Framework for Systems Biology

Felty, Amy P. ; Elisabetta De Maria ; et al.

In: [Research Report] 2014, pp.34 Springer LNCS 8738 FMMB 2014-First International Conference on Formal Methods in Macro-Biology FMMB 2014-First International Conference on Formal Methods in Macro-Biology, Sep 2014, Noumea, France. ⟨10.1007/978-3-319-10398-3_10⟩ Formal Methods in Macro-Biology ISBN: 9783319103976 FMMB; (2014)

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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.

Comment: (2014)

Titel:	A Logical Framework for Systems Biology
Autor/in / Beteiligte Person:	Felty, Amy P. ; Elisabetta De Maria ; Despeyroux, Joëlle ; Laboratoire d'Informatique, Signaux, et Systèmes de Sophia-Antipolis (I3S) / Equipe BIOINFO ; Modèles Discrets pour les Systèmes Complexes (Laboratoire I3S - MDSC) ; Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S) ; Université Nice Sophia Antipolis (... - 2019) (UNS) ; COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (... - 2019) (UNS) ; COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Laboratoire d'Informatique, Signaux, et Systèmes de Sophia Antipolis (I3S) ; COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA) ; Inria Sophia Antipolis - Méditerranée (CRISAM) ; Institut National de Recherche en Informatique et en Automatique (Inria) ; School of Electrical Engineering and Computer Science, Univ. of Ottawa (EECS, Ottawa) ; University of Ottawa [Ottawa] ; Université Nice Sophia Antipolis (1965 - 2019) (UNS) ; COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS) ; Mathematical, Reasoning and Software (MARELLE) ; Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria) ; Fages, François ; Piazza, Carla
Link:	View record in OpenAIRE (Volltext)
Quelle:	[Research Report] 2014, pp.34 Springer LNCS 8738 FMMB 2014-First International Conference on Formal Methods in Macro-Biology FMMB 2014-First International Conference on Formal Methods in Macro-Biology, Sep 2014, Noumea, France. ⟨10.1007/978-3-319-10398-3_10⟩ Formal Methods in Macro-Biology ISBN: 9783319103976 FMMB; (2014)
Veröffentlichung:	arXiv, 2014
Medientyp:	unknown
ISBN:	978-3-319-10397-6 (print)
DOI:	10.48550/arxiv.1404.5439
Schlagwort:	FOS: Computer and information sciences Computer Science - Logic in Computer Science Horn clause Theoretical computer science Computer science [SDV]Life Sciences [q-bio] logical frameworks computer.software_genre Prolog Description logic Linear temporal logic Computer Science::Logic in Computer Science computer.programming_language temporal properties Programming language Computational logic Multimodal logic Sequent calculus Modal logic [INFO.INFO-LO]Computer Science [cs]/Logic in Computer Science [cs.LO] systems biology Non-classical logic Other Quantitative Biology (q-bio.OT) [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] Signature (logic) Linear logic Quantitative Biology - Other Quantitative Biology First-order logic Logical framework biological networks ACM: F.: Theory of Computation/F.4: MATHEMATICAL LOGIC AND FORMAL LANGUAGES Computation tree logic Interval temporal logic ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES Mathematical proof theorem proving linear logic Temporal logic Bunched logic formal verification Formal verification modal logic Proof assistant [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology ACM: F.: Theory of Computation/F.4: MATHEMATICAL LOGIC AND FORMAL LANGUAGES/F.4.1: Mathematical Logic Logic in Computer Science (cs.LO) Automated theorem proving TheoryofComputation_MATHEMATICALLOGICANDFORMALLANGUAGES FOS: Biological sciences Dynamic logic (modal logic) Temporal logic of actions computer ACM: I.: Computing Methodologies/I.1: SYMBOLIC AND ALGEBRAIC MANIPULATION
Sonstiges:	Nachgewiesen in: OpenAIRE Rights: OPEN

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