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Formal Methods In Systems Biology
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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.
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.
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.
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.
Book Synopsis PROCEEDINGS OF THE 20TH CONFERENCE ON FORMAL METHODS IN COMPUTER-AIDED DESIGN – FMCAD 2020 by : Alexander Ivrii
Download or read book PROCEEDINGS OF THE 20TH CONFERENCE ON FORMAL METHODS IN COMPUTER-AIDED DESIGN – FMCAD 2020 written by Alexander Ivrii and published by TU Wien Academic Press. This book was released on 2020-09-11 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Systems Biology Modelling and Analysis by : Elisabetta De Maria
Download or read book Systems Biology Modelling and Analysis written by Elisabetta De Maria and published by John Wiley & Sons. This book was released on 2022-12-13 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis FM 2009: Formal Methods by : Ana Cavalcanti
Download or read book FM 2009: Formal Methods written by Ana Cavalcanti and published by Springer. This book was released on 2009-11-04 with total page 836 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Formal Modeling: Actors; Open Systems, Biological Systems by : Gul Agha
Download or read book Formal Modeling: Actors; Open Systems, Biological Systems written by Gul Agha and published by Springer. This book was released on 2011-10-30 with total page 465 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 186 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.
Book Synopsis Leveraging Applications of Formal Methods, Verification and Validation: Discussion, Dissemination, Applications by : Tiziana Margaria
Download or read book Leveraging Applications of Formal Methods, Verification and Validation: Discussion, Dissemination, Applications written by Tiziana Margaria and published by Springer. This book was released on 2016-10-04 with total page 874 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Automated Reasoning for Systems Biology and Medicine by : Pietro Liò
Download or read book Automated Reasoning for Systems Biology and Medicine written by Pietro Liò and published by Springer. This book was released on 2019-06-11 with total page 471 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents outstanding contributions in an exciting, new and multidisciplinary research area: the application of formal, automated reasoning techniques to analyse complex models in systems biology and systems medicine. Automated reasoning is a field of computer science devoted to the development of algorithms that yield trustworthy answers, providing a basis of sound logical reasoning. For example, in the semiconductor industry formal verification is instrumental to ensuring that chip designs are free of defects (or “bugs”). Over the past 15 years, systems biology and systems medicine have been introduced in an attempt to understand the enormous complexity of life from a computational point of view. This has generated a wealth of new knowledge in the form of computational models, whose staggering complexity makes manual analysis methods infeasible. Sound, trusted, and automated means of analysing the models are thus required in order to be able to trust their conclusions. Above all, this is crucial to engineering safe biomedical devices and to reducing our reliance on wet-lab experiments and clinical trials, which will in turn produce lower economic and societal costs. Some examples of the questions addressed here include: Can we automatically adjust medications for patients with multiple chronic conditions? Can we verify that an artificial pancreas system delivers insulin in a way that ensures Type 1 diabetic patients never suffer from hyperglycaemia or hypoglycaemia? And lastly, can we predict what kind of mutations a cancer cell is likely to undergo? This book brings together leading researchers from a number of highly interdisciplinary areas, including: · Parameter inference from time series · Model selection · Network structure identification · Machine learning · Systems medicine · Hypothesis generation from experimental data · Systems biology, systems medicine, and digital pathology · Verification of biomedical devices “This book presents a comprehensive spectrum of model-focused analysis techniques for biological systems ...an essential resource for tracking the developments of a fast moving field that promises to revolutionize biology and medicine by the automated analysis of models and data.”Prof Luca Cardelli FRS, University of Oxford
Book Synopsis Formal Methods. FM 2019 International Workshops by : Emil Sekerinski
Download or read book Formal Methods. FM 2019 International Workshops written by Emil Sekerinski and published by Springer Nature. This book was released on 2020-08-12 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the workshops which complemented the 23rd Symposium on Formal Methods, FM 2019, held in Porto, Portugal, in October 2019. This volume presents the papers that have been accepted for the following workshops: Third Workshop on Practical Formal Verification for Software Dependability, AFFORD 2019; 8th International Symposium From Data to Models and Back, DataMod 2019; First Formal Methods for Autonomous Systems Workshop, FMAS 2019; First Workshop on Formal Methods for Blockchains, FMBC 2019; 8th International Workshop on Formal Methods for Interactive Systems, FMIS 2019; First History of Formal Methods Workshop, HFM 2019; 8th International Workshop on Numerical and Symbolic Abstract Domains, NSAD 2019; 9th International Workshop on Open Community Approaches to Education, Research and Technology, OpenCERT 2019; 17th Overture Workshop, Overture 2019; 19th Refinement Workshop, Refine 2019; First International Workshop on Reversibility in Programming, Languages, and Automata, RPLA 2019; 10th International Workshop on Static Analysis and Systems Biology, SASB 2019; and the 10th Workshop on Tools for Automatic Program Analysis, TAPAS 2019.
Book Synopsis Modern Formal Methods and Applications by : Hossam A. Gabbar
Download or read book Modern Formal Methods and Applications written by Hossam A. Gabbar and published by Springer Science & Business Media. This book was released on 2006-06-28 with total page 217 pages. Available in PDF, EPUB and Kindle. Book excerpt: Formal methods are a robust approach for problem solving. It is based on logic and algebraic methods where problems can be formulated in a way that can help to find an appropriate solution. This book shows the basic concepts of formal methods and highlights modern modifications and enhancements to provide a more robust and efficient problem solving tool. Applications are presented from different disciplines such as engineering where the operation of chemical plants is synthesized using formal methods. Computational biology becomes easier and systematic using formal methods. Also, hardware compilation and systems can be managed using formal methods. This book will be helpful for both beginners and experts to get insights and experience on modern formal methods by viewing real applications from different domains.
Book Synopsis Computational Methods in Systems Biology by :
Download or read book Computational Methods in Systems Biology written by and published by . This book was released on 2003 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Systems Biology by : Bernhard Palsson
Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.
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 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.
Book Synopsis Biological Modeling and Simulation by : Russell Schwartz
Download or read book Biological Modeling and Simulation written by Russell Schwartz and published by MIT Press. This book was released on 2008-07-25 with total page 403 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
