Formal Methods in Systems Biology
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.

Formal Methods for Computational Systems Biology
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.

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

PROCEEDINGS OF THE 20TH CONFERENCE ON FORMAL METHODS IN COMPUTER-AIDED DESIGN – FMCAD 2020
PROCEEDINGS OF THE 20TH CONFERENCE ON FORMAL METHODS IN COMPUTER-AIDED DESIGN – FMCAD 2020

Author: Alexander Ivrii

Publisher: TU Wien Academic Press

Published: 2020-09-11

Total Pages: 284

ISBN-13: 3854480423

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Formal Methods in Computer-Aided Design (FMCAD) is a conference series on the theory and applications of formal methods in hardware and system verification. FMCAD provides a leading forum to researchers in academia and industry for presenting and discussing ground-breaking methods, technologies, theoretical results, and tools for reasoning formally about computing systems. FMCAD covers formal aspects of computer-aided system design including verification, specification, synthesis, and testing.

Systems Biology Modelling and Analysis
Systems Biology Modelling and Analysis

Author: Elisabetta De Maria

Publisher: John Wiley & Sons

Published: 2022-12-13

Total Pages: 468

ISBN-13: 1119716535

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Describes important modelling and computational methods for systems biology research to enable practitioners to select and use the most suitable technique Systems Biology Modelling and Analysis provides an overview of state-of-the-art techniques and introduces related tools and practices to formalize models and automate reasoning for systems biology. The authors present and compare the main formal methods used in systems biology for modelling biological networks, including discussion of their advantages, drawbacks, and main applications. Each chapter includes an intuitive presentation of the specific formalism, a brief history of the formalism and of its applications in systems biology, a formal description of the formalism and its variants, at least one realistic case study, some applications of formal techniques to validate and make deep analysis of models encoded with the formalism, and a discussion on the kind of biological systems for which the formalism is suited, along with concrete ideas on its possible evolution. Written by a highly qualified author with significant experience in the field, some of the methods and techniques covered in Systems Biology Modelling and Analysis include: ● Petri nets, an important tool for studying different aspects of biological systems, ranging from simple signaling pathways to metabolic networks and beyond ● Pathway Logic, a formal, rule-based system and interactive viewer for developing executable models of cellular processes ● Boolean networks, a mathematical model which has been widely used for decades in the context of biological regulation networks ● Answer Set Programming (ASP), which has proven to be a strong logic programming paradigm to deal with the inherent complexity of biological models For systems biologists, biochemists, bioinformaticians, molecular biologists, pharmacologists, and computer scientists, Systems Biology Modelling and Analysis is a comprehensive all-in-one resource to understand and harness the field’s current models and techniques while also preparing for their potential developments in coming years with the help of the author’s expert insight.

Formal Methods in Macro-Biology
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.

FM 2009: Formal Methods
FM 2009: Formal Methods

Author: Ana Cavalcanti

Publisher: Springer

Published: 2009-11-04

Total Pages: 836

ISBN-13: 3642050891

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th FM 2009, the 16 International Symposium on Formal Methods, marked the 10th an- versary of the First World Congress on Formal Methods that was held in 1999 in Toulouse, France. We wished to celebrate this by advertising and organizing FM 2009 as the Second World Congress in the FM series, aiming to once again bring together the formal methods communities from all over the world. The statistics displayed in the table on the next page include the number of countries represented by the Programme Committee members, as well as of the authors of submitted and accepted papers. Novel this year was a special track on tools and industrial applications. Subm- sions of papers on these topics were especially encouraged, but not given any special treatment. (It was just as hard to get a special track paper accepted as any other paper.) What we did promote, however, was a discussion of how originality, contri- tion, and soundness should be judged for these papers. The following questions were used by our Programme Committee.

Formal Modeling: Actors; Open Systems, Biological Systems
Formal Modeling: Actors; Open Systems, Biological Systems

Author: Gul Agha

Publisher: Springer

Published: 2011-10-30

Total Pages: 465

ISBN-13: 3642249337

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This Festschrift volume, published in honor of Carolyn Talcott on the occasion of her 70th birthday, contains a collection of papers presented at a symposium held in Menlo Park, California, USA, in November 2011. Carolyn Talcott is a leading researcher and mentor of international renown among computer scientists. She has made key contributions to a number of areas of computer science including: semantics and verification of progamming languages; foundations of actor-based systems; middleware, meta-architectures, and systems; Maude and rewriting logic; and computational biology. The 21 papers presented are organized in topical sections named: Essays on Carolyn Talcott; actors and programming languages; cyberphysical systems; middleware and meta-architectures; formal methods and reasoning tools; and computational biology.

Formal Methods for Dynamical Systems
Formal Methods for Dynamical Systems

Author: Marco Bernardo

Publisher: Springer

Published: 2013-06-12

Total Pages: 186

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.

Leveraging Applications of Formal Methods, Verification and Validation: Discussion, Dissemination, Applications
Leveraging Applications of Formal Methods, Verification and Validation: Discussion, Dissemination, Applications

Author: Tiziana Margaria

Publisher: Springer

Published: 2016-10-04

Total Pages: 874

ISBN-13: 3319471694

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The two-volume set LNCS 9952 and LNCS 9953 constitutes the refereed proceedings of the 7th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, ISoLA 2016, held in Imperial, Corfu, Greece, in October 2016. The papers presented in this volume were carefully reviewed and selected for inclusion in the proceedings. Featuring a track introduction to each section, the papers are organized in topical sections named: statistical model checking; evaluation and reproducibility of program analysis and verification; ModSyn-PP: modular synthesis of programs and processes; semantic heterogeneity in the formal development of complex systems; static and runtime verification: competitors or friends?; rigorous engineering of collective adaptive systems; correctness-by-construction and post-hoc verification: friends or foes?; privacy and security issues in information systems; towards a unified view of modeling and programming; formal methods and safety certification: challenges in the railways domain; RVE: runtime verification and enforcement, the (industrial) application perspective; variability modeling for scalable software evolution; detecting and understanding software doping; learning systems: machine-learning in software products and learning-based analysis of software systems; testing the internet of things; doctoral symposium; industrial track; RERS challenge; and STRESS.