stochastic modelling for systems biology second edition

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Stochastic Modelling For Systems Biology Second Edition

Author : Darren J. Wilkinson
ISBN : 9781439837764
Genre : Mathematics
File Size : 33. 33 MB
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Since the first edition of Stochastic Modelling for Systems Biology, there have been many interesting developments in the use of "likelihood-free" methods of Bayesian inference for complex stochastic models. Re-written to reflect this modern perspective, this second edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. Keeping with the spirit of the first edition, all of the new theory is presented in a very informal and intuitive manner, keeping the text as accessible as possible to the widest possible readership. New in the Second Edition All examples have been updated to Systems Biology Markup Language Level 3 All code relating to simulation, analysis, and inference for stochastic kinetic models has been re-written and re-structured in a more modular way An ancillary website provides links, resources, errata, and up-to-date information on installation and use of the associated R package More background material on the theory of Markov processes and stochastic differential equations, providing more substance for mathematically inclined readers Discussion of some of the more advanced concepts relating to stochastic kinetic models, such as random time change representations, Kolmogorov equations, Fokker-Planck equations and the linear noise approximation Simple modelling of "extrinsic" and "intrinsic" noise An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional mathematical detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.

Markov Processes For Stochastic Modeling

Author : Oliver Ibe
ISBN : 9780080922454
Genre : Mathematics
File Size : 55. 74 MB
Format : PDF
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Markov processes are used to model systems with limited memory. They are used in many areas including communications systems, transportation networks, image segmentation and analysis, biological systems and DNA sequence analysis, random atomic motion and diffusion in physics, social mobility, population studies, epidemiology, animal and insect migration, queueing systems, resource management, dams, financial engineering, actuarial science, and decision systems. This book, which is written for upper level undergraduate and graduate students, and researchers, presents a unified presentation of Markov processes. In addition to traditional topics such as Markovian queueing system, the book discusses such topics as continuous-time random walk,correlated random walk, Brownian motion, diffusion processes, hidden Markov models, Markov random fields, Markov point processes and Markov chain Monte Carlo. Continuous-time random walk is currently used in econophysics to model the financial market, which has traditionally been modelled as a Brownian motion. Correlated random walk is popularly used in ecological studies to model animal and insect movement. Hidden Markov models are used in speech analysis and DNA sequence analysis while Markov random fields and Markov point processes are used in image analysis. Thus, the book is designed to have a very broad appeal. - Provides the practical, current applications of Markov processes - Coverage of HMM, Point processes, and Monte Carlo - Includes enough theory to help students gain throrough understanding of the subject - Principles can be immediately applied in many specific research projects, saving researchers time - End of chapter exercises provide reinforcement, practice and increased understanding to the student

Stochastic Dynamics For Systems Biology

Author : Christian Mazza
ISBN : 9781466514942
Genre : Mathematics
File Size : 32. 66 MB
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Stochastic Dynamics for Systems Biology is one of the first books to provide a systematic study of the many stochastic models used in systems biology. The book shows how the mathematical models are used as technical tools for simulating biological processes and how the models lead to conceptual insights on the functioning of the cellular processing system. Most of the text should be accessible to scientists with basic knowledge in calculus and probability theory. The authors illustrate the relevant Markov chain theory using realistic models from systems biology, including signaling and metabolic pathways, phosphorylation processes, genetic switches, and transcription. A central part of the book presents an original and up-to-date treatment of cooperativity. The book defines classical indexes, such as the Hill coefficient, using notions from statistical mechanics. It explains why binding curves often have S-shapes and why cooperative behaviors can lead to ultrasensitive genetic switches. These notions are then used to model transcription rates. Examples cover the phage lambda genetic switch and eukaryotic gene expression. The book then presents a short course on dynamical systems and describes stochastic aspects of linear noise approximation. This mathematical framework enables the simplification of complex stochastic dynamics using Gaussian processes and nonlinear ODEs. Simple examples illustrate the technique in noise propagation in gene networks and the effects of network structures on multistability and gene expression noise levels. The last chapter provides up-to-date results on stochastic and deterministic mass action kinetics with applications to enzymatic biochemical reactions and metabolic pathways.

An Introduction To Systems Biology

Author : Uri Alon
ISBN : 9781584886426
Genre : Mathematics
File Size : 30. 90 MB
Format : PDF, Kindle
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Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles. An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

Game Theoretical Models In Biology

Author : Mark Broom
ISBN : 9781439853214
Genre : Mathematics
File Size : 32. 41 MB
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Covering the major topics of evolutionary game theory, Game-Theoretical Models in Biology presents both abstract and practical mathematical models of real biological situations. It discusses the static aspects of game theory in a mathematically rigorous way that is appealing to mathematicians. In addition, the authors explore many applications of game theory to biology, making the text useful to biologists as well. The book describes a wide range of topics in evolutionary games, including matrix games, replicator dynamics, the hawk-dove game, and the prisoner’s dilemma. It covers the evolutionarily stable strategy, a key concept in biological games, and offers in-depth details of the mathematical models. Most chapters illustrate how to use MATLAB® to solve various games. Important biological phenomena, such as the sex ratio of so many species being close to a half, the evolution of cooperative behavior, and the existence of adornments (for example, the peacock’s tail), have been explained using ideas underpinned by game theoretical modeling. Suitable for readers studying and working at the interface of mathematics and the life sciences, this book shows how evolutionary game theory is used in the modeling of these diverse biological phenomena.

Modeling And Analysis Of Stochastic Systems

Author : Vidyadhar G. Kulkarni
ISBN : 0412049910
Genre : Business & Economics
File Size : 68. 73 MB
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This practical text aims to enable students in engineering, business, operations research, public policy, and computer science to model and analyze stochastic systems. The major classes of useful stochastic processes - discrete and continuous time Markov chains, renewal processes, regenerative processes, and Markov regenerative processes - are presented, with an emphasis on modelling real-life situations with stochastic elements and analyzing the resulting stochastic model.

An Introduction To Stochastic Processes With Applications To Biology

Author : Linda J. S. Allen
ISBN : 0130352187
Genre : Mathematics
File Size : 49. 10 MB
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Plenty of examples, diagrams, and figures take readers step-by-step through well-known classical biological models to ensure complete understanding of stochastic formulation. Probability, Markov Chains, discrete time branching processes, population genetics, and birth and death chains. For biologists and other professionals who want a comprehensive, easy-to-follow introduction to stochastic formulation as it pertains to biology.

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