Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology PDF Download
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Author: Paola Lecca
Publisher: Elsevier
ISBN: 1908818212
Category : Mathematics
Languages : en
Pages : 411
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Book Description
Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples Presents recently developed discrete stochastic formalisms for modelling biological systems and processes Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics
Author: Paola Lecca
Publisher: Elsevier
ISBN: 1908818212
Category : Mathematics
Languages : en
Pages : 411
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Book Description
Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples Presents recently developed discrete stochastic formalisms for modelling biological systems and processes Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics
Author: Howard M. Taylor
Publisher: Academic Press
ISBN: 1483269272
Category : Mathematics
Languages : en
Pages : 410
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Book Description
An Introduction to Stochastic Modeling provides information pertinent to the standard concepts and methods of stochastic modeling. This book presents the rich diversity of applications of stochastic processes in the sciences. Organized into nine chapters, this book begins with an overview of diverse types of stochastic models, which predicts a set of possible outcomes weighed by their likelihoods or probabilities. This text then provides exercises in the applications of simple stochastic analysis to appropriate problems. Other chapters consider the study of general functions of independent, identically distributed, nonnegative random variables representing the successive intervals between renewals. This book discusses as well the numerous examples of Markov branching processes that arise naturally in various scientific disciplines. The final chapter deals with queueing models, which aid the design process by predicting system performance. This book is a valuable resource for students of engineering and management science. Engineers will also find this book useful.
Author: Marco Pellegrini
Publisher: Frontiers Media SA
ISBN: 288963650X
Category :
Languages : en
Pages : 270
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Book Description
Network science has accelerated a deep and successful trend in research that influences a range of disciplines like mathematics, graph theory, physics, statistics, data science and computer science (just to name a few) and adapts the relevant techniques and insights to address relevant but disparate social, biological, technological questions. We are now in an era of 'big biological data' supported by cost-effective high-throughput genomic, transcriptomic, proteomic, metabolomic data collection techniques that allow one to take snapshots of the cells' molecular profiles in a systematic fashion. Moreover recently, also phenotypic data, data on diseases, symptoms, patients, etc. are being collected at nation-wide level thus giving us another source of highly related (causal) 'big data'. This wealth of data is usually modeled as networks (aka binary relations, graphs or webs) of interactions, (including protein-protein, metabolic, signaling and transcription-regulatory interactions). The network model is a key view point leading to the uncovering of mesoscale phenomena, thus providing an essential bridge between the observable phenotypes and 'omics' underlying mechanisms. Moreover, network analysis is a powerful 'hypothesis generation' tool guiding the scientific cycle of 'data gathering', 'data interpretation, 'hypothesis generation' and 'hypothesis testing'. A major challenge in contemporary research is the synthesis of deep insights coming from network science with the wealth of data (often noisy, contradictory, incomplete and difficult to replicate) so to answer meaningful biological questions, in a quantifiable way using static and dynamic properties of biological networks.
Author: Ne-Zheng Sun
Publisher: Springer
ISBN: 1493923234
Category : Mathematics
Languages : en
Pages : 638
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Book Description
This three-part book provides a comprehensive and systematic introduction to these challenging topics such as model calibration, parameter estimation, reliability assessment, and data collection design. Part 1 covers the classical inverse problem for parameter estimation in both deterministic and statistical frameworks, Part 2 is dedicated to system identification, hyperparameter estimation, and model dimension reduction, and Part 3 considers how to collect data and construct reliable models for prediction and decision-making. For the first time, topics such as multiscale inversion, stochastic field parameterization, level set method, machine learning, global sensitivity analysis, data assimilation, model uncertainty quantification, robust design, and goal-oriented modeling, are systematically described and summarized in a single book from the perspective of model inversion, and elucidated with numerical examples from environmental and water resources modeling. Readers of this book will not only learn basic concepts and methods for simple parameter estimation, but also get familiar with advanced methods for modeling complex systems. Algorithms for mathematical tools used in this book, such as numerical optimization, automatic differentiation, adaptive parameterization, hierarchical Bayesian, metamodeling, Markov chain Monte Carlo, are covered in details. This book can be used as a reference for graduate and upper level undergraduate students majoring in environmental engineering, hydrology, and geosciences. It also serves as an essential reference book for professionals such as petroleum engineers, mining engineers, chemists, mechanical engineers, biologists, biology and medical engineering, applied mathematicians, and others who perform mathematical modeling.
Author: Anthony Almudevar
Publisher: Springer Nature
ISBN: 3030346757
Category : Medical
Languages : en
Pages : 361
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Book Description
This book commemorates the scientific contributions of distinguished statistician, Andrei Yakovlev. It reflects upon Dr. Yakovlev’s many research interests including stochastic modeling and the analysis of micro-array data, and throughout the book it emphasizes applications of the theory in biology, medicine and public health. The contributions to this volume are divided into two parts. Part A consists of original research articles, which can be roughly grouped into four thematic areas: (i) branching processes, especially as models for cell kinetics, (ii) multiple testing issues as they arise in the analysis of biologic data, (iii) applications of mathematical models and of new inferential techniques in epidemiology, and (iv) contributions to statistical methodology, with an emphasis on the modeling and analysis of survival time data. Part B consists of methodological research reported as a short communication, ending with some personal reflections on research fields associated with Andrei and on his approach to science. The Appendix contains an abbreviated vitae and a list of Andrei’s publications, complete as far as we know. The contributions in this book are written by Dr. Yakovlev’s collaborators and notable statisticians including former presidents of the Institute of Mathematical Statistics and of the Statistics Section of the AAAS. Dr. Yakovlev’s research appeared in four books and almost 200 scientific papers, in mathematics, statistics, biomathematics and biology journals. Ultimately this book offers a tribute to Dr. Yakovlev’s work and recognizes the legacy of his contributions in the biostatistics community.
Author: Michael Stumpf
Publisher: John Wiley & Sons
ISBN: 1119952042
Category : Science
Languages : en
Pages : 624
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Book Description
Systems Biology is now entering a mature phase in which the key issues are characterising uncertainty and stochastic effects in mathematical models of biological systems. The area is moving towards a full statistical analysis and probabilistic reasoning over the inferences that can be made from mathematical models. This handbook presents a comprehensive guide to the discipline for practitioners and educators, in providing a full and detailed treatment of these important and emerging subjects. Leading experts in systems biology and statistics have come together to provide insight in to the major ideas in the field, and in particular methods of specifying and fitting models, and estimating the unknown parameters. This book: Provides a comprehensive account of inference techniques in systems biology. Introduces classical and Bayesian statistical methods for complex systems. Explores networks and graphical modeling as well as a wide range of statistical models for dynamical systems. Discusses various applications for statistical systems biology, such as gene regulation and signal transduction. Features statistical data analysis on numerous technologies, including metabolic and transcriptomic technologies. Presents an in-depth presentation of reverse engineering approaches. Provides colour illustrations to explain key concepts. This handbook will be a key resource for researchers practising systems biology, and those requiring a comprehensive overview of this important field.
Author: Péter Érdi
Publisher: Manchester University Press
ISBN: 9780719022081
Category : Science
Languages : en
Pages : 296
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Book Description
Author: Henry Han
Publisher: Springer Nature
ISBN: 3031618165
Category : Application software
Languages : en
Pages : 264
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Book Description
Zusammenfassung: This book constitutes the refereed proceedings of the Sescond Southwest Data Science Conference, SDSC 2023, held in Waco, TX, USa, during March 24-25, 2023. The 16 full and 1 short paper included in this book were carefully reviewed and selected from 72 submissions. They were oragnized in topical sections named: Business social and foundation data science; and applied data science, artifiicial intelligence and data engineering.
Author: Jacques Istas
Publisher: Springer Science & Business Media
ISBN: 354027877X
Category : Mathematics
Languages : en
Pages : 170
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Book Description
Provides a wide range of mathematical models currently used in the life sciences Each model is thoroughly explained and illustrated by example Includes three appendices to allow for independent reading
Author: Klaus Schittkowski
Publisher: Springer Science & Business Media
ISBN: 9781402010798
Category : Computers
Languages : en
Pages : 416
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Book Description
Real life phenomena in engineering, natural, or medical sciences are often described by a mathematical model with the goal to analyze numerically the behaviour of the system. Advantages of mathematical models are their cheap availability, the possibility of studying extreme situations that cannot be handled by experiments, or of simulating real systems during the design phase before constructing a first prototype. Moreover, they serve to verify decisions, to avoid expensive and time consuming experimental tests, to analyze, understand, and explain the behaviour of systems, or to optimize design and production. As soon as a mathematical model contains differential dependencies from an additional parameter, typically the time, we call it a dynamical model. There are two key questions always arising in a practical environment: 1 Is the mathematical model correct? 2 How can I quantify model parameters that cannot be measured directly? In principle, both questions are easily answered as soon as some experimental data are available. The idea is to compare measured data with predicted model function values and to minimize the differences over the whole parameter space. We have to reject a model if we are unable to find a reasonably accurate fit. To summarize, parameter estimation or data fitting, respectively, is extremely important in all practical situations, where a mathematical model and corresponding experimental data are available to describe the behaviour of a dynamical system.
