Download or read book Combined Discrete and Continual Approaches in Biological Modelling written by Alexander E. Filippov and published by Springer Nature. This book was released on 2020-06-30 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: Basic laws of nature are rather simple, but observed biological structures and their dynamic behaviors are unbelievably complicated. This book is devoted to a study of this “strange” relationship by applying mathematical modeling to various structures and phenomena in biology, such as surface patterns, bioadhesion, locomotion, predator-prey behavior, seed dispersal, etc. and revealing a kind of self-organization in these phenomena. In spite of diversity of biological systems considered, two main questions are (1) what does self-organization in biology mean mathematically and (2) how one can apply this knowledge to generate new knowledge about behavior of particular biological system? We believe that this kind of “biomimetics” in computer will lead to better understanding of biological phenomena and possibly towards development of technical implications based on our modeling.
Download or read book Continuous Time Modeling in the Behavioral and Related Sciences written by Kees van Montfort and published by Springer. This book was released on 2018-10-11 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book provides an overview of continuous time modeling in the behavioral and related sciences. It argues that the use of discrete time models for processes that are in fact evolving in continuous time produces problems that make their application in practice highly questionable. One main issue is the dependence of discrete time parameter estimates on the chosen time interval, which leads to incomparability of results across different observation intervals. Continuous time modeling by means of differential equations offers a powerful approach for studying dynamic phenomena, yet the use of this approach in the behavioral and related sciences such as psychology, sociology, economics and medicine, is still rare. This is unfortunate, because in these fields often only a few discrete time (sampled) observations are available for analysis (e.g., daily, weekly, yearly, etc.). However, as emphasized by Rex Bergstrom, the pioneer of continuous-time modeling in econometrics, neither human beings nor the economy cease to exist in between observations. In 16 chapters, the book addresses a vast range of topics in continuous time modeling, from approaches that closely mimic traditional linear discrete time models to highly nonlinear state space modeling techniques. Each chapter describes the type of research questions and data that the approach is most suitable for, provides detailed statistical explanations of the models, and includes one or more applied examples. To allow readers to implement the various techniques directly, accompanying computer code is made available online. The book is intended as a reference work for students and scientists working with longitudinal data who have a Master's- or early PhD-level knowledge of statistics.
Download or read book Discrete and Topological Models in Molecular Biology written by Nataša Jonoska and published by Springer Science & Business Media. This book was released on 2013-12-23 with total page 522 pages. Available in PDF, EPUB and Kindle. Book excerpt: Theoretical tools and insights from discrete mathematics, theoretical computer science, and topology now play essential roles in our understanding of vital biomolecular processes. The related methods are now employed in various fields of mathematical biology as instruments to "zoom in" on processes at a molecular level. This book contains expository chapters on how contemporary models from discrete mathematics – in domains such as algebra, combinatorics, and graph and knot theories – can provide perspective on biomolecular problems ranging from data analysis, molecular and gene arrangements and structures, and knotted DNA embeddings via spatial graph models to the dynamics and kinetics of molecular interactions. The contributing authors are among the leading scientists in this field and the book is a reference for researchers in mathematics and theoretical computer science who are engaged with modeling molecular and biological phenomena using discrete methods. It may also serve as a guide and supplement for graduate courses in mathematical biology or bioinformatics, introducing nontraditional aspects of mathematical biology.
Download or read book Continuous Time Modeling in the Behavioral and Related Sciences written by Kees van Montfort and published by . This book was released on 2018 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: This unique book provides an overview of continuous time modeling in the behavioral and related sciences. It argues that the use of discrete time models for processes that are in fact evolving in continuous time produces problems that make their application in practice highly questionable. One main issue is the dependence of discrete time parameter estimates on the chosen time interval, which leads to incomparability of results across different observation intervals. Continuous time modeling by means of differential equations offers a powerful approach for studying dynamic phenomena, yet the use of this approach in the behavioral and related sciences such as psychology, sociology, economics and medicine, is still rare. This is unfortunate, because in these fields often only a few discrete time (sampled) observations are available for analysis (e.g., daily, weekly, yearly, etc.). However, as emphasized by Rex Bergstrom, the pioneer of continuous-time modeling in econometrics, neither human beings nor the economy cease to exist in between observations. In 16 chapters, the book addresses a vast range of topics in continuous time modeling, from approaches that closely mimic traditional linear discrete time models to highly nonlinear state space modeling techniques. Each chapter describes the type of research questions and data that the approach is most suitable for, provides detailed statistical explanations of the models, and includes one or more applied examples. To allow readers to implement the various techniques directly, accompanying computer code is made available online. The book is intended as a reference work for students and scientists working with longitudinal data who have a Master's- or early PhD-level knowledge of statistics.--
Download or read book Transactions on Computational Systems Biology I written by Corrado Priami and published by Springer Science & Business Media. This book was released on 2005-03-30 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt: The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena. This first volume of the Transactions on Computational Systems Biology is made up of papers by members of the journal's Editorial Board to provide a representative and smart start-up to the new journal.
Download or read book A Systems Theoretic Approach to Systems and Synthetic Biology I Models and System Characterizations written by Vishwesh V. Kulkarni and published by Springer. This book was released on 2014-07-03 with total page 338 pages. Available in PDF, EPUB and Kindle. Book excerpt: The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume I provides a panoramic view that illustrates the potential of such mathematical methods in systems and synthetic biology. Recent advances in systems and synthetic biology have clearly demonstrated the benefits of a rigorous and systematic approach rooted in the principles of systems and control theory - not only does it lead to exciting insights and discoveries but it also reduces the inordinately lengthy trial-and-error process of wet-lab experimentation, thereby facilitating significant savings in human and financial resources. In Volume I, some of the leading researchers in the field of systems and synthetic biology demonstrate how systems and control theoretic concepts and techniques can be useful, or should evolve to be useful, in order to understand how biological systems function. As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.
Download or read book Understanding the Dynamics of Biological Systems written by Werner Dubitzky and published by Springer Science & Business Media. This book was released on 2011-01-07 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended as a communication platform to bridge the cultural, conceptual, and technological gap among the key systems biology disciplines of biology, mathematics, and information technology. To support this goal, contributors were asked to adopts an approach that appeals to audiences from different backgrounds.
Download or read book Models and Methods for Biological Evolution written by Gilles Didier and published by John Wiley & Sons. This book was released on 2024-04-10 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biological evolution is the phenomenon concerning how species are born, are transformed or disappear over time. Its study relies on sophisticated methods that involve both mathematical modeling of the biological processes at play and the design of efficient algorithms to fit these models to genetic and morphological data. Models and Methods for Biological Evolution outlines the main methods to study evolution and provides a broad overview illustrating the variety of formal approaches used, notably including combinatorial optimization, stochastic models and statistical inference techniques. Some of the most relevant applications of these methods are detailed, concerning, for example, the study of migratory events of ancient human populations or the progression of epidemics. This book should thus be of interest to applied mathematicians interested in central problems in biology, and to biologists eager to get a deeper understanding of widely used techniques of evolutionary data analysis.
Download or read book Algebraic and Discrete Mathematical Methods for Modern Biology written by Raina Robeva and published by Academic Press. This book was released on 2015-05-09 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experts in both mathematics and biology, Algebraic and Discrete Mathematical Methods for Modern Biology offers a bridge between math and biology, providing a framework for simulating, analyzing, predicting, and modulating the behavior of complex biological systems. Each chapter begins with a question from modern biology, followed by the description of certain mathematical methods and theory appropriate in the search of answers. Every topic provides a fast-track pathway through the problem by presenting the biological foundation, covering the relevant mathematical theory, and highlighting connections between them. Many of the projects and exercises embedded in each chapter utilize specialized software, providing students with much-needed familiarity and experience with computing applications, critical components of the "modern biology" skill set. This book is appropriate for mathematics courses such as finite mathematics, discrete structures, linear algebra, abstract/modern algebra, graph theory, probability, bioinformatics, statistics, biostatistics, and modeling, as well as for biology courses such as genetics, cell and molecular biology, biochemistry, ecology, and evolution. Examines significant questions in modern biology and their mathematical treatments Presents important mathematical concepts and tools in the context of essential biology Features material of interest to students in both mathematics and biology Presents chapters in modular format so coverage need not follow the Table of Contents Introduces projects appropriate for undergraduate research Utilizes freely accessible software for visualization, simulation, and analysis in modern biology Requires no calculus as a prerequisite Provides a complete Solutions Manual Features a companion website with supplementary resources
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 474 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
Download or read book The SAGE Handbook of Multilevel Modeling written by Marc A. Scott and published by SAGE. This book was released on 2013-08-31 with total page 954 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this important new Handbook, the editors have gathered together a range of leading contributors to introduce the theory and practice of multilevel modeling. The Handbook establishes the connections in multilevel modeling, bringing together leading experts from around the world to provide a roadmap for applied researchers linking theory and practice, as well as a unique arsenal of state-of-the-art tools. It forges vital connections that cross traditional disciplinary divides and introduces best practice in the field. Part I establishes the framework for estimation and inference, including chapters dedicated to notation, model selection, fixed and random effects, and causal inference. Part II develops variations and extensions, such as nonlinear, semiparametric and latent class models. Part III includes discussion of missing data and robust methods, assessment of fit and software. Part IV consists of exemplary modeling and data analyses written by methodologists working in specific disciplines. Combining practical pieces with overviews of the field, this Handbook is essential reading for any student or researcher looking to apply multilevel techniques in their own research.
Download or read book Quantitative Biology written by Brian Munsky and published by MIT Press. This book was released on 2018-08-21 with total page 729 pages. Available in PDF, EPUB and Kindle. Book excerpt: An introduction to the quantitative modeling of biological processes, presenting modeling approaches, methodology, practical algorithms, software tools, and examples of current research. The quantitative modeling of biological processes promises to expand biological research from a science of observation and discovery to one of rigorous prediction and quantitative analysis. The rapidly growing field of quantitative biology seeks to use biology's emerging technological and computational capabilities to model biological processes. This textbook offers an introduction to the theory, methods, and tools of quantitative biology. The book first introduces the foundations of biological modeling, focusing on some of the most widely used formalisms. It then presents essential methodology for model-guided analyses of biological data, covering such methods as network reconstruction, uncertainty quantification, and experimental design; practical algorithms and software packages for modeling biological systems; and specific examples of current quantitative biology research and related specialized methods. Most chapters offer problems, progressing from simple to complex, that test the reader's mastery of such key techniques as deterministic and stochastic simulations and data analysis. Many chapters include snippets of code that can be used to recreate analyses and generate figures related to the text. Examples are presented in the three popular computing languages: Matlab, R, and Python. A variety of online resources supplement the the text. The editors are long-time organizers of the Annual q-bio Summer School, which was founded in 2007. Through the school, the editors have helped to train more than 400 visiting students in Los Alamos, NM, Santa Fe, NM, San Diego, CA, Albuquerque, NM, and Fort Collins, CO. This book is inspired by the school's curricula, and most of the contributors have participated in the school as students, lecturers, or both. Contributors John H. Abel, Roberto Bertolusso, Daniela Besozzi, Michael L. Blinov, Clive G. Bowsher, Fiona A. Chandra, Paolo Cazzaniga, Bryan C. Daniels, Bernie J. Daigle, Jr., Maciej Dobrzynski, Jonathan P. Doye, Brian Drawert, Sean Fancer, Gareth W. Fearnley, Dirk Fey, Zachary Fox, Ramon Grima, Andreas Hellander, Stefan Hellander, David Hofmann, Damian Hernandez, William S. Hlavacek, Jianjun Huang, Tomasz Jetka, Dongya Jia, Mohit Kumar Jolly, Boris N. Kholodenko, Markek Kimmel, Michał Komorowski, Ganhui Lan, Heeseob Lee, Herbert Levine, Leslie M Loew, Jason G. Lomnitz, Ard A. Louis, Grant Lythe, Carmen Molina-París, Ion I. Moraru, Andrew Mugler, Brian Munsky, Joe Natale, Ilya Nemenman, Karol Nienałtowski, Marco S. Nobile, Maria Nowicka, Sarah Olson, Alan S. Perelson, Linda R. Petzold, Sreenivasan Ponnambalam, Arya Pourzanjani, Ruy M. Ribeiro, William Raymond, William Raymond, Herbert M. Sauro, Michael A. Savageau, Abhyudai Singh, James C. Schaff, Boris M. Slepchenko, Thomas R. Sokolowski, Petr Šulc, Andrea Tangherloni, Pieter Rein ten Wolde, Philipp Thomas, Karen Tkach Tuzman, Lev S. Tsimring, Dan Vasilescu, Margaritis Voliotis, Lisa Weber
Download or read book Identification Analysis and Control of Discrete and Continuous Models of Gene Regulation Networks written by Christian Breindl and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: A systems biological approach towards cellular networks promises a better understanding of how these systems work. The development of mathematical models is however inherently complicated, as the involved molecules and their interactions are mostly difficult to measure. Focusing on gene regulation networks, this work therefore intends to provide systems theoretic tools that support the process of model development and analysis in presence of such incomplete knowledge. The contributions are threefold. First, the problem of identifying interconnections between genes from noisy data is addressed. Existing solutions formulated in a discrete framework are reviewed and simplified significantly with the help of tools from convex optimization theory. Second, a novel method for model verification and discrimination is introduced. It is based on concepts from robust control theory and allows to quantify the capability of a model to reproduce experimentally observed stationary behaviors. As the proposed formalism only requires a vague knowledge about the interactions between the molecules, the method is intended to test and compare early modeling hypotheses. Third, the problem of controlling gene regulation networks in presence of qualitative information only is studied. Methods from discrete event systems theory are adapted to obtain stimulation strategies that will steer the network toward a desired attractor. The benefits of all contributions are illustrated with examples in the individual chapters.
Download or read book Discrete Event Modeling and Simulation written by Gabriel A. Wainer and published by CRC Press. This book was released on 2017-12-19 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt: Complex artificial dynamic systems require advanced modeling techniques that can accommodate their asynchronous, concurrent, and highly non-linear nature. Discrete Event systems Specification (DEVS) provides a formal framework for hierarchical construction of discrete-event models in a modular manner, allowing for model re-use and reduced development time. Discrete Event Modeling and Simulation presents a practical approach focused on the creation of discrete-event applications. The book introduces the CD++ tool, an open-source framework that enables the simulation of discrete-event models. After setting up the basic theory of DEVS and Cell-DEVS, the author focuses on how to use the CD++ tool to define a variety of models in biology, physics, chemistry, and artificial systems. They also demonstrate how to map different modeling techniques, such as Finite State Machines and VHDL, to DEVS. The in-depth coverage elaborates on the creation of simulation software for DEVS models and the 3D visualization environments associated with these tools. A much-needed practical approach to creating discrete-event applications, this book offers world-class instruction on the field’s most useful modeling tools.
Download or read book Kicks and Maps a Different Approach to Modeling Biological Systems written by Stephen Anthony Ippolito and published by . This book was released on 2015 with total page 60 pages. Available in PDF, EPUB and Kindle. Book excerpt: Modeling a biological systems, is a cyclic process which involves constructing a model from current theory and beliefs and then validating that model against the data. If the data does not match, qualitatively or quantitatively then there may be a problem with either our beliefs or the current theory. At the same time directly finding a model from the existing data would make generalizing results difficult. A considerable dicultly in this process is how to specify the model in the rst place. There is a need to be practice which accounts for the growing use of mathematical and statistical methods. However, as a systems becomes more complex, standard mathematical approaches may not be sufficient. In the field of ecology, the standard techniques involve discrete maps, and continuous models such as ODE's. The intent of this work is to present the mathematics necessary to study hybrids of these two models, then consider two case studies. In first case we consider a coral reef with continuous change, except in the presence of hurricanes. The results of the data are compared quantitatively and qualitatively with simulation results. For the second case we consider a model for rabies with a periodic birth pulse. Here the analysis is qualitative as we demonstrate the existence of a strange attractor by looking at the intersections of the stable and unstable manifold for the saddle point generating the attractor. For both cases studies the introduction of a discrete event into a continuous system is done via a Dirac Distribution or Measure.
Download or read book Cancer Systems Biology written by Edwin Wang and published by CRC Press. This book was released on 2010-05-04 with total page 456 pages. Available in PDF, EPUB and Kindle. Book excerpt: The unprecedented amount of data produced with high-throughput experimentation forces biologists to employ mathematical representation and computation methods to glean meaningful information in systems-level biology. Applying this approach to the underlying molecular mechanisms of tumorigenesis, cancer researchers can uncover a series of new discov
Download or read book A Guided Tour of Artificial Intelligence Research written by Pierre Marquis and published by Springer Nature. This book was released on 2020-05-08 with total page 584 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of this book is to provide an overview of AI research, ranging from basic work to interfaces and applications, with as much emphasis on results as on current issues. It is aimed at an audience of master students and Ph.D. students, and can be of interest as well for researchers and engineers who want to know more about AI. The book is split into three volumes: - the first volume brings together twenty-three chapters dealing with the foundations of knowledge representation and the formalization of reasoning and learning (Volume 1. Knowledge representation, reasoning and learning) - the second volume offers a view of AI, in fourteen chapters, from the side of the algorithms (Volume 2. AI Algorithms) - the third volume, composed of sixteen chapters, describes the main interfaces and applications of AI (Volume 3. Interfaces and applications of AI). This third volume is dedicated to the interfaces of AI with various fields, with which strong links exist either at the methodological or at the applicative levels. The foreword of this volume reminds us that AI was born for a large part from cybernetics. Chapters are devoted to disciplines that are historically sisters of AI: natural language processing, pattern recognition and computer vision, and robotics. Also close and complementary to AI due to their direct links with information are databases, the semantic web, information retrieval and human-computer interaction. All these disciplines are privileged places for applications of AI methods. This is also the case for bioinformatics, biological modeling and computational neurosciences. The developments of AI have also led to a dialogue with theoretical computer science in particular regarding computability and complexity. Besides, AI research and findings have renewed philosophical and epistemological questions, while their cognitive validity raises questions to psychology. The volume also discusses some of the interactions between science and artistic creation in literature and in music. Lastly, an epilogue concludes the three volumes of this Guided Tour of AI Research by providing an overview of what has been achieved by AI, emphasizing AI as a science, and not just as an innovative technology, and trying to dispel some misunderstandings.
