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Formal Methods for Computational Systems Biology

Author: Marco Bernardo

Publisher: Springer Science & Business Media

Published: 2008-05-20

Total Pages: 533

ISBN-13: 3540688927

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This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications.

Book Synopsis Formal Methods for Computational Systems Biology by : Marco Bernardo

Download or read book Formal Methods for Computational Systems Biology written by Marco Bernardo and published by Springer Science & Business Media. This book was released on 2008-05-20 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a set of 14 papers accompanying the lectures of leading researchers given at the 8th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2008, held in Bertinoro, Italy in June 2008. SFM 2008 was devoted to formal techniques for computational systems biology and covered several aspects of the field, including computational models, calculi and logics for biological systems, and verification and simulation methods. The first part of this volume comprises nine papers based on regular lectures, the second part of this volume comprises five papers based on talks given by people involved in the Italian BISCA research project on Bio-Inspired Systems and Calculi with Applications.

Formal Methods for Computational Systems Biology

Author: Marco Bernardo

Publisher: Springer

Published: 2008-05-31

Total Pages: 0

ISBN-13: 9783540688945

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Book Synopsis Formal Methods for Computational Systems Biology by : Marco Bernardo

Download or read book Formal Methods for Computational Systems Biology written by Marco Bernardo and published by Springer. This book was released on 2008-05-31 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Formal Methods for Computational Systems Biology

Author: Marco Bernardo

Publisher: Springer

Published: 2009-08-29

Total Pages: 527

ISBN-13: 9783540848219

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Book Synopsis Formal Methods for Computational Systems Biology by : Marco Bernardo

Download or read book Formal Methods for Computational Systems Biology written by Marco Bernardo and published by Springer. This book was released on 2009-08-29 with total page 527 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology

Author: David A. Rosenblueth,

Publisher: Frontiers Media SA

Published: 2016-11-21

Total Pages: 115

ISBN-13: 2889450422

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The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research.

Book Synopsis Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology by : David A. Rosenblueth,

Download or read book Computational Methods for Understanding Complexity: The Use of Formal Methods in Biology written by David A. Rosenblueth, and published by Frontiers Media SA. This book was released on 2016-11-21 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of living organisms surpasses our unaided habilities of analysis. Hence, computational and mathematical methods are necessary for increasing our understanding of biological systems. At the same time, there has been a phenomenal recent progress allowing the application of novel formal methods to new domains. This progress has spurred a conspicuous optimism in computational biology. This optimism, in turn, has promoted a rapid increase in collaboration between specialists of biology with specialists of computer science. Through sheer complexity, however, many important biological problems are at present intractable, and it is not clear whether we will ever be able to solve such problems. We are in the process of learning what kind of model and what kind of analysis and synthesis techniques to use for a particular problem. Some existing formalisms have been readily used in biological problems, others have been adapted to biological needs, and still others have been especially developed for biological systems. This Research Topic has examples of cases (1) employing existing methods, (2) adapting methods to biology, and (3) developing new methods. We can also see discrete and Boolean models, and the use of both simulators and model checkers. Synthesis is exemplified by manual and by machine-learning methods. We hope that the articles collected in this Research Topic will stimulate new research.

Formal Methods in Systems Biology

Author: Jasmin Fisher

Publisher: Springer Science & Business Media

Published: 2008-05-26

Total Pages: 146

ISBN-13: 3540684107

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Thisvolumecontainstheproceedingsofthe?rstinternationalmeetingonFormal Methods in Systems Biology, held at Microsoft Research, Cambridge, UK, June 4–5, 2008. While there are several venues that cover computational methods in systems biology,there is to date no single conference that brings together the application of the range of formal methods in biology. Therefore, convening such a meeting could prove extremely productive. The purpose of this meeting was to identify techniques for the speci?cation, development and veri?cation of biological m- els.Italsofocusedonthedesignoftoolstoexecuteandanalyzebiologicalmodels in ways that can signi?cantly advance our understanding of biological systems. As a forum for this discussion we invited key scientists in the area of formal methods to this unique meeting. Although this was a one-o? meeting, we are exploring the possibility of this forming the ?rst of what might become an annual conference. Presentations at the meeting were by invitation only; future meetings are expected to operate on a submission and review basis. The Steering Committee and additional referees reviewed the invited papers. Each submission was evaluated by at least two referees. The volume includes nine invited contributions. Formal Methods in Systems Biology 2008 was made possible by the cont- bution and dedication ofmany people. First of all,we wouldlike to thank allthe authors who submitted papers. Secondly, we would like to thank our additional invited speakers and participants. We would also like to thank the members of the Steering Committee for their valuable comments. Finally, we ackno- edge the help of the administrative and technical sta? at the MicrosoftResearch Cambridge lab.

Book Synopsis Formal Methods in Systems Biology by : Jasmin Fisher

Download or read book Formal Methods in Systems Biology written by Jasmin Fisher and published by Springer Science & Business Media. This book was released on 2008-05-26 with total page 146 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thisvolumecontainstheproceedingsofthe?rstinternationalmeetingonFormal Methods in Systems Biology, held at Microsoft Research, Cambridge, UK, June 4–5, 2008. While there are several venues that cover computational methods in systems biology,there is to date no single conference that brings together the application of the range of formal methods in biology. Therefore, convening such a meeting could prove extremely productive. The purpose of this meeting was to identify techniques for the speci?cation, development and veri?cation of biological m- els.Italsofocusedonthedesignoftoolstoexecuteandanalyzebiologicalmodels in ways that can signi?cantly advance our understanding of biological systems. As a forum for this discussion we invited key scientists in the area of formal methods to this unique meeting. Although this was a one-o? meeting, we are exploring the possibility of this forming the ?rst of what might become an annual conference. Presentations at the meeting were by invitation only; future meetings are expected to operate on a submission and review basis. The Steering Committee and additional referees reviewed the invited papers. Each submission was evaluated by at least two referees. The volume includes nine invited contributions. Formal Methods in Systems Biology 2008 was made possible by the cont- bution and dedication ofmany people. First of all,we wouldlike to thank allthe authors who submitted papers. Secondly, we would like to thank our additional invited speakers and participants. We would also like to thank the members of the Steering Committee for their valuable comments. Finally, we ackno- edge the help of the administrative and technical sta? at the MicrosoftResearch Cambridge lab.

Computational Methods in Systems Biology

Author: Corrado Priami

Publisher: Springer Science & Business Media

Published: 2006-10-11

Total Pages: 332

ISBN-13: 3540461663

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This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.

Book Synopsis Computational Methods in Systems Biology by : Corrado Priami

Download or read book Computational Methods in Systems Biology written by Corrado Priami and published by Springer Science & Business Media. This book was released on 2006-10-11 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the International Conference on Computational Methods in Systems Biology, CMSB 2006, held in Trento, Italy, in October 2006. The 22 fully revised papers presented together with 2 invited talks were carefully reviewed and selected from 68 submissions. The papers present a variety of techniques from computer sciences, such as language design, concurrency theory, software engineering, and formal methods.

Formal Cell Biology

Author: Francois Fages

Publisher: Chapman and Hall/CRC

Published: 2014-12-06

Total Pages: 306

ISBN-13: 9781466505841

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This book explores the use of concepts and tools from theoretical computer science to tackle the complexity of cell processes. In a unified framework, it presents the different modeling formalisms of systems biology, emphasizing their formal relationships by abstraction functions and putting them into practice for building predictive models of cell functions. With exercises and computational models, the book reflects the author’s many years of researching, developing, and applying computer science methods in systems biology.

Book Synopsis Formal Cell Biology by : Francois Fages

Download or read book Formal Cell Biology written by Francois Fages and published by Chapman and Hall/CRC. This book was released on 2014-12-06 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book explores the use of concepts and tools from theoretical computer science to tackle the complexity of cell processes. In a unified framework, it presents the different modeling formalisms of systems biology, emphasizing their formal relationships by abstraction functions and putting them into practice for building predictive models of cell functions. With exercises and computational models, the book reflects the author’s many years of researching, developing, and applying computer science methods in systems biology.

Formal Methods for Dynamical Systems

Author: Marco Bernardo

Publisher: Springer

Published: 2013-06-12

Total Pages: 181

ISBN-13: 3642388744

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This book presents 5 tutorial lectures given by leading researchers at the 13th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2013, held in Bertinoro, Italy, in June 2013. SFM 2013 was devoted to dynamical systems and covered several topics including chaotic dynamics; information theory; systems biology; hybrid systems; quantum computing; and automata-based models and model checking.

Book Synopsis Formal Methods for Dynamical Systems by : Marco Bernardo

Download or read book Formal Methods for Dynamical Systems written by Marco Bernardo and published by Springer. This book was released on 2013-06-12 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents 5 tutorial lectures given by leading researchers at the 13th edition of the International School on Formal Methods for the Design of Computer, Communication and Software Systems, SFM 2013, held in Bertinoro, Italy, in June 2013. SFM 2013 was devoted to dynamical systems and covered several topics including chaotic dynamics; information theory; systems biology; hybrid systems; quantum computing; and automata-based models and model checking.

Formal Methods in Macro-Biology

Author: François Fages

Publisher: Springer

Published: 2014-08-14

Total Pages: 204

ISBN-13: 3319103989

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This book constitutes the refereed proceedings of the First International Conference on Formal Methods in Macro-Biology, FMMB 2014, held in Nouméa, New Caledonia, in September 2014. The 7 revised full and 3 short papers presented together with 7 invited presentations were carefully reviewed and selected from 17 submissions. The scientific program consists of papers on a wide variety of topics, including ecological systems, medical applications, logical frameworks, and discrete continuous and hybrid models for the analysis of biological systems at macroscopic levels.

Book Synopsis Formal Methods in Macro-Biology by : François Fages

Download or read book Formal Methods in Macro-Biology written by François Fages and published by Springer. This book was released on 2014-08-14 with total page 204 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the First International Conference on Formal Methods in Macro-Biology, FMMB 2014, held in Nouméa, New Caledonia, in September 2014. The 7 revised full and 3 short papers presented together with 7 invited presentations were carefully reviewed and selected from 17 submissions. The scientific program consists of papers on a wide variety of topics, including ecological systems, medical applications, logical frameworks, and discrete continuous and hybrid models for the analysis of biological systems at macroscopic levels.

Computational Methods in Systems Biology

Author: Corrado Priami

Publisher: Springer

Published: 2003-07-01

Total Pages: 224

ISBN-13: 3540364811

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This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003. The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.

Book Synopsis Computational Methods in Systems Biology by : Corrado Priami

Download or read book Computational Methods in Systems Biology written by Corrado Priami and published by Springer. This book was released on 2003-07-01 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the International Workshop on Computational Methods in Systems Biology, CMSB 2003, held in Rovereto, Italy, in February 2003. The 11 revised full papers presented together with 2 invited papers, 7 position papers, and 11 abstracts were carefully reviewed and selected from 30 submissions. Among the topics addressed are modeling languages for systems biology, concurrency in biological systems, constraint programming, logical methods in systems biology, formal methods for the analysis of biomolecular systems, quantitative analysis of biomolecular systems, and simulation and modeling techniques for systems biology.