An Introduction to Systems Biology

Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks.

An Introduction to Systems Biology

Author: Uri Alon

Publisher: CRC Press

ISBN: 1584886420

Page: 320

View: 119

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.

Introduction to Systems Biology

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems.

Introduction to Systems Biology

Author: Sangdun Choi

Publisher: Springer Science & Business Media

ISBN: 1597455318

Page: 542

View: 714

This book provides an introductory text for undergraduate and graduate students who are interested in comprehensive biological systems. The authors offer a broad overview of the field using key examples and typical approaches to experimental design. The volume begins with an introduction to systems biology and then details experimental omics tools. Other sections introduce the reader to challenging computational approaches. The final sections provide ideas for theoretical and modeling optimization in systemic biological researches. The book is an indispensable resource, providing a first glimpse into the state-of-the-art in systems biology.

Mathematical Modeling in Systems Biology

This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology.

Mathematical Modeling in Systems Biology

Author: Brian P. Ingalls

Publisher: MIT Press

ISBN: 0262018888

Page: 408

View: 738

An introduction to the mathematical concepts and techniques needed for the construction and analysis of models in molecular systems biology. Systems techniques are integral to current research in molecular cell biology, and system-level investigations are often accompanied by mathematical models. These models serve as working hypotheses: they help us to understand and predict the behavior of complex systems. This book offers an introduction to mathematical concepts and techniques needed for the construction and interpretation of models in molecular systems biology. It is accessible to upper-level undergraduate or graduate students in life science or engineering who have some familiarity with calculus, and will be a useful reference for researchers at all levels. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials. Chapters 3–8 end with optional sections that address more specialized modeling topics. Exercises, solvable with pen-and-paper calculations, appear throughout the text to encourage interaction with the mathematical techniques. More involved end-of-chapter problem sets require computational software. Appendixes provide a review of basic concepts of molecular biology, additional mathematical background material, and tutorials for two computational software packages (XPPAUT and MATLAB) that can be used for model simulation and analysis.

An Introduction to Computational Systems Biology

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks--a fundamental aspect of computational systems biology.

An Introduction to Computational Systems Biology

Author: KARTHIK. RAMAN

Publisher: CRC Press

ISBN: 9781138597327

Page: 360

View: 577

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks: a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity which will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling. Coding and software tools for systems biology. Covers the entire spectrum of modelling, from static networks, to dynamic models. Thoughtful exercises to test and enable student understanding of concepts. State-of-the-art chapters on exciting new developments, like whole-cell modelling and community modelling. The book is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.

Life An Introduction to Complex Systems Biology

This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally ...

Life  An Introduction to Complex Systems Biology

Author: Kunihiko Kaneko

Publisher: Springer

ISBN: 3540326677

Page: 374

View: 944

This book examines life not from the reductionist point of view, but rather asks the questions: what are the universal properties of living systems, and how can one construct from there a phenomenological theory of life that leads naturally to complex processes such as reproductive cellular systems, evolution and differentiation? The presentation is relatively non-technical to appeal to a broad spectrum of students and researchers.

Systems Biology A Very Short Introduction

ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly.

Systems Biology  A Very Short Introduction

Author: Eberhard O. Voit

Publisher: Oxford University Press

ISBN: 0192563459

Page: 144

View: 749

Systems biology came about as growing numbers of engineers and scientists from other fields created algorithms which supported the analysis of biological data in incredible quantities. Whereas biologists of the past had been forced to study one item or aspect at a time, due to technical and biological limitations, it suddenly became possible to study biological phenomena within their natural contexts. This interdisciplinary field offers a holistic approach to interpreting these processes, and has been responsible for some of the most important developments in the science of human health and environmental sustainability. This Very Short Introduction outlines the exciting processes and possibilities in the new field of systems biology. Eberhard O. Voit describes how it enabled us to learn how intricately the expression of every gene is controlled, how signaling systems keep organisms running smoothly, and how complicated even the simplest cells are. He explores what this field is about, why it is needed, and how it will affect our understanding of life, particularly in the areas of personalized medicine, drug development, food and energy production, and sustainable stewardship of our environments. Throughout he considers how new tools are being provided from the fields of mathematics, computer science, engineering, physics, and chemistry to grasp the complexity of the countless interacting processes in cells which would overwhelm the cognitive and analytical capabilities of the human mind. ABOUT THE SERIES: The Very Short Introductions series from Oxford University Press contains hundreds of titles in almost every subject area. These pocket-sized books are the perfect way to get ahead in a new subject quickly. Our expert authors combine facts, analysis, perspective, new ideas, and enthusiasm to make interesting and challenging topics highly readable.

Systems Biology

This book is an introduction to control in biochemical pathways.

Systems Biology

Author: Herbert Sauro

Publisher:

ISBN: 9780982477366

Page: 278

View: 351

This book is an introduction to control in biochemical pathways. Itintroduces students to some of the most important concepts in modern metabolic control principles. It covers the basics of metabolic controlanalysis that helps us think about how biochemical networks operate. The book should be suitable for undergraduates in their early (Junior, USA, second year UK) to mid years at college.

Modeling Biomolecular Networks

This book describes the essentials of a mathematical description of the dynamics of biochemical networks.

Modeling Biomolecular Networks

Author: Anirvan M. Sengupta

Publisher:

ISBN: 9780198568049

Page: 208

View: 208

This book describes the essentials of a mathematical description of the dynamics of biochemical networks. It covers both deterministic and stochastic aspects of the dynamics. After providing a brief introduction to basic molecular biology, the book describes fundamentals of chemical kinetics. The chapter on signal transduction makes contact with ideas from feedback circuit analysis and signal processing. The chapter on switches and oscillators analyses in detail biological examples, both natural and synthetic. Excitable systems are introduced and contrasted with oscillators. The last chapter deals with pattern formation and development and brings us to current questions of robustness of performance of developmental networks. The book provides brief introductions to some of the mathematical tools required in the main text and in a dedicated appendix. The emphasis, throughout, is on understanding of the essential dynamical aspects rather than just on recipes to build complex models.

Systems Biology

This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies.

Systems Biology

Author: Lilia Alberghina

Publisher: Springer Science & Business Media

ISBN: 9783540742692

Page: 408

View: 418

For life to be understood and disease to become manageable, the wealth of postgenomic data now needs to be made dynamic. This development requires systems biology, integrating computational models for cells and organisms in health and disease; quantitative experiments (high-throughput, genome-wide, living cell, in silico); and new concepts and principles concerning interactions. This book defines the new field of systems biology and discusses the most efficient experimental and computational strategies. The benefits for industry, such as the new network-based drug-target design validation, and testing, are also presented.

Systematic

SYSTEMATIC is the first book to introduce general readers to systems biology, which is improving medical treatments and our understanding of living things.

Systematic

Author: James R. Valcourt

Publisher: Bloomsbury Publishing USA

ISBN: 1632860317

Page: 288

View: 537

A brilliant young scientist introduces us to the fascinating field that is changing our understanding of how the body works and the way we can approach healing. SYSTEMATIC is the first book to introduce general readers to systems biology, which is improving medical treatments and our understanding of living things. In traditional bottom-up biology, a biologist might spend years studying how a single protein works, but systems biology studies how networks of those proteins work together--how they promote health and how to remedy the situation when the system isn't functioning properly. Breakthroughs in systems biology became possible only when powerful computer technology enabled researchers to process massive amounts of data to study complete systems, and has led to progress in the study of gene regulation and inheritance, cancer drugs personalized to an individual's genetically unique tumor, insights into how the brain works, and the discovery that the bacteria and other microbes that live in the gut may drive malnutrition and obesity. Systems biology is allowing us to understand more complex phenomena than ever before. In accessible prose, SYSTEMATIC sheds light not only on how systems within the body work, but also on how research is yielding new kinds of remedies that enhance and harness the body's own defenses.

Systems Biology Introduction to Pathway Modeling

This is revision 1.17 (April 2020) and includes reworded chapters on model fitting including a completely new chapter on Bayesian Infernece.

Systems Biology  Introduction to Pathway Modeling

Author: Herbert Sauro

Publisher: Future Skill Software

ISBN: 9780982477373

Page: 416

View: 650

Computer models of biochemical systems are starting to play an increasingly important role in modern systems and synthetic biology. This monograph introduces students to some of the essential topics in biochemical modeling using differential equations and stochastic models. The book includes many hands-on modeling exercises using Python and examples that illustrate many important concepts, including the stoichiometric networks, building models, running simulations, model fitting, stability of systems and multicompartment systems.

The Inner Workings of Life

An easy-to-read introductory text, comprised of concise vignettes that explain key concepts within systems biology without using jargon.

The Inner Workings of Life

Author: Eberhard O. Voit

Publisher: Cambridge University Press

ISBN: 1107149959

Page: 222

View: 740

An easy-to-read introductory text, comprised of concise vignettes that explain key concepts within systems biology without using jargon.

A First Course in Systems Biology

New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law ...

A First Course in Systems Biology

Author: Eberhard Voit

Publisher: Garland Science

ISBN: 1351332945

Page: 480

View: 172

A First Course in Systems Biology is an introduction for advanced undergraduate and graduate students to the growing field of systems biology. Its main focus is the development of computational models and their applications to diverse biological systems. The book begins with the fundamentals of modeling, then reviews features of the molecular inventories that bring biological systems to life and discusses case studies that represent some of the frontiers in systems biology and synthetic biology. In this way, it provides the reader with a comprehensive background and access to methods for executing standard systems biology tasks, understanding the modern literature, and launching into specialized courses or projects that address biological questions using theoretical and computational means. New topics in this edition include: default modules for model design, limit cycles and chaos, parameter estimation in Excel, model representations of gene regulation through transcription factors, derivation of the Michaelis-Menten rate law from the original conceptual model, different types of inhibition, hysteresis, a model of differentiation, system adaptation to persistent signals, nonlinear nullclines, PBPK models, and elementary modes. The format is a combination of instructional text and references to primary literature, complemented by sets of small-scale exercises that enable hands-on experience, and large-scale, often open-ended questions for further reflection.

Aging and Health A Systems Biology Perspective

Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging.

Aging and Health   A Systems Biology Perspective

Author: A.I. Yashin

Publisher: Karger Medical and Scientific Publishers

ISBN: 3318027308

Page: 206

View: 732

Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its application to biological aging. Key pathways and processes that impinge on aging are reviewed, and how they contribute to health and disease during aging is discussed. The evolution of this situation is analyzed, and the consequences for the study of genetic effects on aging are presented. Epigenetic programming of aging, as a continuation of development, creates an interface between the genome and the environment. New research into the gut microbiome describes how this interface may operate in practice with marked consequences for a variety of disorders. This analysis is bolstered by a view of the aging organism as a whole, with conclusions about the mechanisms underlying resilience of the organism to change, and is expanded with a discussion of circadian rhythms in aging. Finally, the book presents an outlook for the development of interventions to delay or to reverse the features of aging. The publication is recommended to students, researchers as well as professionals dealing with public health and public policy related to an aging society.

Modeling in Systems Biology

This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Modeling in Systems Biology

Author: Ina Koch

Publisher: Springer Science & Business Media

ISBN: 9781849964746

Page: 364

View: 356

The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.

Systems Biology and Synthetic Biology

This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Systems Biology and Synthetic Biology

Author: Pengcheng Fu

Publisher: John Wiley & Sons

ISBN: 9780470437971

Page: 672

View: 484

The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Systems Biology in Toxicology and Environmental Health

Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are ...

Systems Biology in Toxicology and Environmental Health

Author: Rebecca Fry

Publisher: Academic Press

ISBN: 0128015683

Page: 284

View: 904

Systems Biology in Toxicology and Environmental Health uses a systems biological perspective to detail the most recent findings that link environmental exposures to human disease, providing an overview of molecular pathways that are essential for cellular survival after exposure to environmental toxicants, recent findings on gene-environment interactions influencing environmental agent-induced diseases, and the development of computational methods to predict susceptibility to environmental agents. Introductory chapters on molecular and cellular biology, toxicology and computational biology are included as well as an assessment of systems-based tools used to evaluate environmental health risks. Further topics include research on environmental toxicants relevant to human health and disease, various high-throughput technologies and computational methods, along with descriptions of the biological pathways associated with disease and the developmental origins of disease as they relate to environmental contaminants. Systems Biology in Toxicology and Environmental Health is an essential reference for undergraduate students, graduate students, and researchers looking for an introduction in the use of systems biology approaches to assess environmental exposures and their impacts on human health. Provides the first reference of its kind, demonstrating the application of systems biology in environmental health and toxicology Includes introductions to the diverse fields of molecular and cellular biology, toxicology, and computational biology Presents a foundation that helps users understand the connections between the environment and health effects, and the biological mechanisms that link them

Stochastic Modelling for Systems Biology Third Edition

Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book.

Stochastic Modelling for Systems Biology  Third Edition

Author: Darren J. Wilkinson

Publisher: CRC Press

ISBN: 1351000896

Page: 384

View: 764

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. Having been thoroughly updated to reflect this, this third edition covers everything necessary for a good appreciation of stochastic kinetic modelling of biological networks in the systems biology context. New methods and applications are included in the book, and the use of R for practical illustration of the algorithms has been greatly extended. There is a brand new chapter on spatially extended systems, and the statistical inference chapter has also been extended with new methods, including approximate Bayesian computation (ABC). Stochastic Modelling for Systems Biology, Third Edition is now supplemented by an additional software library, written in Scala, described in a new appendix to the book. New in the Third Edition New chapter on spatially extended systems, covering the spatial Gillespie algorithm for reaction diffusion master equation models in 1- and 2-d, along with fast approximations based on the spatial chemical Langevin equation Significantly expanded chapter on inference for stochastic kinetic models from data, covering ABC, including ABC-SMC Updated R package, including code relating to all of the new material New R package for parsing SBML models into simulatable stochastic Petri net models New open-source software library, written in Scala, replicating most of the functionality of the R packages in a fast, compiled, strongly typed, functional language Keeping with the spirit of earlier editions, 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. An effective introduction to the area of stochastic modelling in computational systems biology, this new edition adds additional detail and computational methods that will provide a stronger foundation for the development of more advanced courses in stochastic biological modelling.