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Documents authored by Fages, François

Document
Invited Talk
DOI: 10.4230/LIPIcs.ICLP.2010.2
A Logical Paradigm for Systems Biology (Invited Talk)

Authors: François Fages

Published in: LIPIcs, Volume 7, Technical Communications of the 26th International Conference on Logic Programming (2010)

Abstract
Biologists use diagrams to represent complex systems of interaction between molecular species. These graphical notations encompass two types of information: interactions (e.g. protein complexation, modification, binding to a gene, etc.) and regulations (of an interaction or a transcription). Based on these structures, mathematical models can be developed by equipping such molecular interaction networks with kinetic expressions leading to quantitative models of mainly two kinds: ordinary differential equations for a continuous interpretation of the kinetics and continuous-time Markov chains for a stochastic interpretation of the kinetics. Since 2002, we investigate the transposition of programming concepts and tools to the analysis of living processes at the cellular level.
Cite as

François Fages. A Logical Paradigm for Systems Biology (Invited Talk). In Technical Communications of the 26th International Conference on Logic Programming. Leibniz International Proceedings in Informatics (LIPIcs), Volume 7, pp. 2-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{fages:LIPIcs.ICLP.2010.2,
  author =	{Fages, Fran\c{c}ois},
  title =	{{A Logical Paradigm for Systems Biology}},
  booktitle =	{Technical Communications of the 26th International Conference on Logic Programming},
  pages =	{2--3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-17-0},
  ISSN =	{1868-8969},
  year =	{2010},
  volume =	{7},
  editor =	{Hermenegildo, Manuel and Schaub, Torsten},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICLP.2010.2},
  URN =		{urn:nbn:de:0030-drops-25776},
  doi =		{10.4230/LIPIcs.ICLP.2010.2},
  annote =	{Keywords: temporal logic, model-checking, systems biology, hybrid systems}
}
Document
DOI: 10.4230/DagSemProc.06161.3
06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification

Authors: Gregory Batt, Jeremy T. Bradley, Roland Ewald, François Fages, Holger Hermans, Jane Hillston, Peter Kemper, Alke Martens, Pieter Mosterman, Flemming Nielson, Oleg Sokolsky, and Adelinde M. Uhrmacher

Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)

Abstract
Simulation has found widespread use for experimentation and exploration of the possible impacts of a variety of conditions on a system. In contrast, formal verification is concerned with proving or disproving the correctness of a system with respect to a certain property, using mathematical and logical methods.
Cite as

Gregory Batt, Jeremy T. Bradley, Roland Ewald, François Fages, Holger Hermans, Jane Hillston, Peter Kemper, Alke Martens, Pieter Mosterman, Flemming Nielson, Oleg Sokolsky, and Adelinde M. Uhrmacher. 06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{batt_et_al:DagSemProc.06161.3,
  author =	{Batt, Gregory and Bradley, Jeremy T. and Ewald, Roland and Fages, Fran\c{c}ois and Hermans, Holger and Hillston, Jane and Kemper, Peter and Martens, Alke and Mosterman, Pieter and Nielson, Flemming and Sokolsky, Oleg and Uhrmacher, Adelinde M.},
  title =	{{06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification}},
  booktitle =	{Simulation and Verification of Dynamic Systems},
  pages =	{1--21},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6161},
  editor =	{David M. Nicol and Corrado Priami and Hanne Riis Nielson and Adelinde M. Uhrmacher},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.06161.3},
  URN =		{urn:nbn:de:0030-drops-7249},
  doi =		{10.4230/DagSemProc.06161.3},
  annote =	{Keywords: Modelling, Simulation, Verification, Systemsbiology}
}
Document
DOI: 10.4230/DagSemProc.05371.1
05371 Abstracts Collection – Principles and Practices of Semantic Web Reasoning

Authors: François Bry, François Fages, Massimo Marchiori, and Hans-Jürgen Ohlbach

Published in: Dagstuhl Seminar Proceedings, Volume 5371, Principles and Practices of Semantic Web Reasoning (2006)

Abstract
From 11.09.05 to 16.09.05, the Dagstuhl Seminar 05371 ``Principles and Practices of Semantic Web Reasoning'' % generate automaticall was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
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François Bry, François Fages, Massimo Marchiori, and Hans-Jürgen Ohlbach. 05371 Abstracts Collection – Principles and Practices of Semantic Web Reasoning. In Principles and Practices of Semantic Web Reasoning. Dagstuhl Seminar Proceedings, Volume 5371, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{bry_et_al:DagSemProc.05371.1,
  author =	{Bry, Fran\c{c}ois and Fages, Fran\c{c}ois and Marchiori, Massimo and Ohlbach, Hans-J\"{u}rgen},
  title =	{{05371 Abstracts Collection –  Principles and Practices of Semantic Web Reasoning}},
  booktitle =	{Principles and Practices of Semantic Web Reasoning},
  pages =	{1--14},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5371},
  editor =	{Fran\c{c}ois Bry and Fran\c{c}ois Fages and Massimo Marchiori and Hans-J\"{u}rgen Ohlbach},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.05371.1},
  URN =		{urn:nbn:de:0030-drops-4813},
  doi =		{10.4230/DagSemProc.05371.1},
  annote =	{Keywords: Semantic Web, reasoning, rules, ontologies, Advanced Web Applications, rule-based reasoning}
}
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