Published in: Dagstuhl Reports, Volume 1, Issue 4 (2011)
Rainer Breitling, Adelinde M. Uhrmacher, Frank J. Bruggeman, and Corrado Priami. Formal Methods in Molecular Biology (Dagstuhl Seminar 11151). In Dagstuhl Reports, Volume 1, Issue 4, pp. 41-64, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2011)
@Article{breitling_et_al:DagRep.1.4.41, author = {Breitling, Rainer and Uhrmacher, Adelinde M. and Bruggeman, Frank J. and Priami, Corrado}, title = {{Formal Methods in Molecular Biology (Dagstuhl Seminar 11151)}}, pages = {41--64}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2011}, volume = {1}, number = {4}, editor = {Breitling, Rainer and Uhrmacher, Adelinde M. and Bruggeman, Frank J. and Priami, Corrado}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagRep.1.4.41}, URN = {urn:nbn:de:0030-drops-31975}, doi = {10.4230/DagRep.1.4.41}, annote = {Keywords: Bioinformatics, systems biology, formal modeling, computational biology, stochastic, model, simulation, checking, verification, abstraction, petri nets, process algebra} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami. 09091 Abstracts Collection – Formal Methods in Molecular Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-24, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{breitling_et_al:DagSemProc.09091.1, author = {Breitling, Rainer and Gilbert, David Roger and Heiner, Monika and Priami, Corrado}, title = {{09091 Abstracts Collection – Formal Methods in Molecular Biology }}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--24}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.1}, URN = {urn:nbn:de:0030-drops-19972}, doi = {10.4230/DagSemProc.09091.1}, annote = {Keywords: Formal models, systems biology, biological processes} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami. 09091 Executive Summary – Formal Methods in Molecular Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{breitling_et_al:DagSemProc.09091.2, author = {Breitling, Rainer and Gilbert, David Roger and Heiner, Monika and Priami, Corrado}, title = {{09091 Executive Summary – Formal Methods in Molecular Biology}}, booktitle = {Formal Methods in Molecular Biology}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.2}, URN = {urn:nbn:de:0030-drops-19964}, doi = {10.4230/DagSemProc.09091.2}, annote = {Keywords: Formal models, systems biology, biological processes.} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini. Analyzing various models of Circadian Clock and Cell Cycle coupling. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{csikasznagy_et_al:DagSemProc.09091.3, author = {Csik\'{a}sz-Nagy, Attila and Faure, Adrien and Larcher, Roberto and Lecca, Paola and Mura, Ivan and Jordan, Ferenc and Palmisano, Alida and Romanel, Alessandro and Sedwards, Sean and Siebert, Heike and Soliman, Sylvain and Thieffry, Denis and Z\'{a}mborszky, Judit and Mazza, Tommaso and Ballarini, Paolo}, title = {{Analyzing various models of Circadian Clock and Cell Cycle coupling}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--6}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.3}, URN = {urn:nbn:de:0030-drops-19944}, doi = {10.4230/DagSemProc.09091.3}, annote = {Keywords: Cell cycle, circadian clock, computational modelling} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
David Roger Gilbert, Rainer Breitling, and Monika Heiner. BioModel Engineering: Its role in Systems Biology and Synthetic Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{gilbert_et_al:DagSemProc.09091.4, author = {Gilbert, David Roger and Breitling, Rainer and Heiner, Monika}, title = {{BioModel Engineering: Its role in Systems Biology and Synthetic Biology}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--2}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.4}, URN = {urn:nbn:de:0030-drops-19929}, doi = {10.4230/DagSemProc.09091.4}, annote = {Keywords: Biochemical systems, models, design, construction, systems biology, synthetic biology, model checking.} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Federica Ciocchetta, Andrea Degasperi, John Heath, and Jane Hillston. Modelling and analysis of the NF-$kappa$B pathway in Bio-PEPA. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{ciocchetta_et_al:DagSemProc.09091.5, author = {Ciocchetta, Federica and Degasperi, Andrea and Heath, John and Hillston, Jane}, title = {{Modelling and analysis of the NF-\$kappa\$B pathway in Bio-PEPA}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--18}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.5}, URN = {urn:nbn:de:0030-drops-19911}, doi = {10.4230/DagSemProc.09091.5}, annote = {Keywords: Process algebras, NF-\$kappa\$B pathway, modelling, analysis} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{kuttler_et_al:DagSemProc.09091.6, author = {Kuttler, C\'{e}line and Lhoussaine, C\'{e}dric and Nebut, Mirabelle}, title = {{Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--22}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.6}, URN = {urn:nbn:de:0030-drops-19938}, doi = {10.4230/DagSemProc.09091.6}, annote = {Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Cristian Versari. Stochastic modelling of cellular growth and division by means of the pi@ calculus. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{versari:DagSemProc.09091.7, author = {Versari, Cristian}, title = {{Stochastic modelling of cellular growth and division by means of the pi@ calculus}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--15}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.7}, URN = {urn:nbn:de:0030-drops-19907}, doi = {10.4230/DagSemProc.09091.7}, annote = {Keywords: Process algebra, pi-calculus, simulation, stochastic} }
Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)
Heike Siebert. Symbolic Steady States and Dynamically Essential Subnetworks of Discrete Regulatory Networks. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-3, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2009)
@InProceedings{siebert:DagSemProc.09091.8, author = {Siebert, Heike}, title = {{Symbolic Steady States and Dynamically Essential Subnetworks of Discrete Regulatory Networks}}, booktitle = {Formal Methods in Molecular Biology}, pages = {1--3}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2009}, volume = {9091}, editor = {Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.8}, URN = {urn:nbn:de:0030-drops-19957}, doi = {10.4230/DagSemProc.09091.8}, annote = {Keywords: Discrete networks, logical analysis, symbolic steady states} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
David M. Nicol, Corrado Priami, Hanne Riis-Nielson, and Adelinde M. Uhrmacher. 06161 Abstracts Collection – Simulation and Verification of Dynamic Systems. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
@InProceedings{nicol_et_al:DagSemProc.06161.1, author = {Nicol, David M. and Priami, Corrado and Riis-Nielson, Hanne and Uhrmacher, Adelinde M.}, title = {{06161 Abstracts Collection – Simulation and Verification of Dynamic Systems}}, booktitle = {Simulation and Verification of Dynamic Systems}, pages = {1--13}, 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.06161.1}, URN = {urn:nbn:de:0030-drops-7102}, doi = {10.4230/DagSemProc.06161.1}, annote = {Keywords: Modeling, Simulation, Verification, Dynamic Systems, Systemsbiology} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
Henrik Pilegaard, Hanne Riis-Nielson, and Flemming Nielson. Context Dependent Analysis of BioAmbients. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
@InProceedings{pilegaard_et_al:DagSemProc.06161.6, author = {Pilegaard, Henrik and Riis-Nielson, Hanne and Nielson, Flemming}, title = {{Context Dependent Analysis of BioAmbients}}, booktitle = {Simulation and Verification of Dynamic Systems}, pages = {1--18}, 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.06161.6}, URN = {urn:nbn:de:0030-drops-7093}, doi = {10.4230/DagSemProc.06161.6}, annote = {Keywords: Static analysis, abstract interpretation, BioAmbients} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
Hanne Riis-Nielson, David M. Nicol, Corrado Priami, and Adelinde M. Uhrmacher. 06161 Executive Summary – Simulation and Verification of Dynamic Systems. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
@InProceedings{riisnielson_et_al:DagSemProc.06161.2, author = {Riis-Nielson, Hanne and Nicol, David M. and Priami, Corrado and Uhrmacher, Adelinde M.}, title = {{06161 Executive Summary – Simulation and Verification of Dynamic Systems}}, booktitle = {Simulation and Verification of Dynamic Systems}, pages = {1--2}, 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.06161.2}, URN = {urn:nbn:de:0030-drops-7028}, doi = {10.4230/DagSemProc.06161.2}, annote = {Keywords: Modelling, Simulation, Verification, Systemsbiology} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
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)
@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} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
Peter Kemper and Carsten Tepper. A Petri Net Approach to Verify and Debug Simulation Models. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
@InProceedings{kemper_et_al:DagSemProc.06161.4, author = {Kemper, Peter and Tepper, Carsten}, title = {{A Petri Net Approach to Verify and Debug Simulation Models}}, booktitle = {Simulation and Verification of Dynamic Systems}, pages = {1--13}, 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.06161.4}, URN = {urn:nbn:de:0030-drops-7084}, doi = {10.4230/DagSemProc.06161.4}, annote = {Keywords: Discrete event simulation, verification, debugging, process interaction, Petri net analysis} }
Published in: Dagstuhl Seminar Proceedings, Volume 6161, Simulation and Verification of Dynamic Systems (2006)
Jörg Bauer and Reinhard Wilhelm. Abstract Interpretation of Graph Transformation. In Simulation and Verification of Dynamic Systems. Dagstuhl Seminar Proceedings, Volume 6161, pp. 1-4, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2006)
@InProceedings{bauer_et_al:DagSemProc.06161.5, author = {Bauer, J\"{o}rg and Wilhelm, Reinhard}, title = {{Abstract Interpretation of Graph Transformation}}, booktitle = {Simulation and Verification of Dynamic Systems}, pages = {1--4}, 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.06161.5}, URN = {urn:nbn:de:0030-drops-7039}, doi = {10.4230/DagSemProc.06161.5}, annote = {Keywords: Abstract Interpretation, Graph Transformation} }
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