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Documents authored by Priami, Corrado

Document
DOI: 10.4230/DagRep.1.4.41
Formal Methods in Molecular Biology (Dagstuhl Seminar 11151)

Authors: Rainer Breitling, Adelinde M. Uhrmacher, Frank J. Bruggeman, and Corrado Priami

Published in: Dagstuhl Reports, Volume 1, Issue 4 (2011)

Abstract
This report documents the program and the outcomes of the Seminar 11151 `Formal Methods in Molecular Biology' that took place in Dagstuhl, Germany, on 10--15 Apr 2011. The most recent advances in Systems Biology were discussed, as well as and the contribution of computational formalisms to the modeling of biological systems, with the focus on stochasticity. About 30 talks were given. The participants formed 5 teams that worked on selected case studies. Two teams were awarded prizes, for their efforts in analyzing and further elucidating published biological models.
Cite as

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)

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@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-dev.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}
}
Document
DOI: 10.4230/DagSemProc.09091.1
09091 Abstracts Collection – Formal Methods in Molecular Biology

Authors: Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
From 23. February to 27. February 2009, the Dagstuhl Seminar 09091 ``Formal Methods in Molecular Biology '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. 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.
Cite as

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)

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@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-dev.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}
}
Document
DOI: 10.4230/DagSemProc.09091.2
09091 Executive Summary – Formal Methods in Molecular Biology

Authors: Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
Formal logical models play an increasing role in the newly emerging field of Systems Biology. Compared to the classical, well-established approach of modeling biological processes using continuous and stochastic differential equations, formal logical models offer a number of important advantages. Many different formal modeling paradigms have been applied to molecular biology, each with its own community, formalisms and tools. In this seminar we brought together modelers from various backgrounds to stimulate closer interaction within the field and to create a common platform for discussion. A central feature of the seminar was a modeling competition (with a highly collaborative flavor) of various modeling paradigms.
Cite as

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)

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@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-dev.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.}
}
Document
DOI: 10.4230/DagSemProc.06161.1
06161 Abstracts Collection – Simulation and Verification of Dynamic Systems

Authors: David M. Nicol, Corrado Priami, Hanne Riis-Nielson, and Adelinde M. Uhrmacher

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

Abstract
From 17.04.06 to 22.04.06, the Dagstuhl Seminar 06161 ``Simulation and Verification of Dynamic Systems'' 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.
Cite as

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)

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@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-dev.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}
}
Document
DOI: 10.4230/DagSemProc.06161.2
06161 Executive Summary – Simulation and Verification of Dynamic Systems

Authors: Hanne Riis-Nielson, David M. Nicol, Corrado Priami, and Adelinde M. Uhrmacher

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

Abstract
Simulation is widely used for modeling engineering artifacts and natural phenomena to gain insight into the operation of those systems. Formal verification is concerned with proving or disproving the correctness of a system with respect to a certain property. Despite of these different objectives, the fields of simulation and verification address similar research challenges. Particularly, in the application area systems biology simulation and verification are moving together. The Dagstuhl Seminar was dedicated to intensifying this dialogue, and stimulating the exchange of ideas. Three working groups discussed questions: Why are biological systems difficult to model?, What role does refinement and abstraction play in combining simulation and verification?, What is the role of communication and composition in simulating and analysing dynamic systems? The results of the working groups can be found in the working groups' report.
Cite as

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)

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@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-dev.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}
}
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