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Documents authored by Breitling, Rainer

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.
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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.09091.4
BioModel Engineering: Its role in Systems Biology and Synthetic Biology

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

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

Abstract
BioModel Engineering takes place at the interface of computing science, mathematics, engineering and biology, and provides a systematic approach for designing, constructing and analyzing computational models of biological systems. Some of its central concepts are inspired by efficient software engineering strategies. BioModel Engineering does not aim at engineering biological systems per se, but rather aims at describing their structure and behavior, in particular at the level of intracellular molecular processes, using computational tools and techniques in a principled way. The two major application areas of BioModel Engineering are systems biology and synthetic biology. In the former, the aim is the design and construction of models of existing biological systems, which explain observed properties and predict the response to experimental interventions; in the latter, BioModel Engineering is used as part of a general strategy for designing and constructing synthetic biological systems with novel functionalities. The overall steps in building computational models in a BioModel Engineering framework are: Problem Identification, Model Construction, Static and Dynamic Analysis, Simulation, and Model management and development. A major theme in BioModel Engineering is that of constructing a (qualitative) model means (1) finding the structure, (2) obtaining an initial state and (3) parameter fitting. In an approach that we have taken, the structure is obtained by piecewise construction of models from modular parts, the initial state which describes concentrations of species or numbers of molecules is obtained by analysis of the structure, and parameter fitting comprises determining the rate parameters of the kinetic equations by reference to trusted data. Model checking can play a key role in BioModel Engineering – for example in recent work we have shown how parameter estimation can be achieved by characterising the desired behaviour of a model with a temporal logic property and altering the model to make it conform to the property as determined through model checking.
Cite as

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)

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@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-dev.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.}
}
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