Systems Biology Modelling And Analysis

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Systems Biology

Author : Andreas Kremling
Publisher : CRC Press
ISBN 13 : 1466567899
Total Pages : 382 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Systems Biology by : Andreas Kremling

Download or read book Systems Biology written by Andreas Kremling and published by CRC Press. This book was released on 2013-11-12 with total page 382 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.

Mathematical Modeling in Systems Biology

Author : Brian P. Ingalls
Publisher : MIT Press
ISBN 13 : 0262545829
Total Pages : 423 pages
Book Rating : 4.2/5 (625 download)

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Book Synopsis Mathematical Modeling in Systems Biology by : Brian P. Ingalls

Download or read book Mathematical Modeling in Systems Biology written by Brian P. Ingalls and published by MIT Press. This book was released on 2022-06-07 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Systems Biology

Author : Jinzhi Lei
Publisher : Springer Nature
ISBN 13 : 3030730336
Total Pages : 308 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis Systems Biology by : Jinzhi Lei

Download or read book Systems Biology written by Jinzhi Lei and published by Springer Nature. This book was released on 2021-05-13 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses the mathematical simulation of biological systems, with a focus on the modeling of gene expression, gene regulatory networks and stem cell regeneration. The diffusion of morphogens is addressed by introducing various reaction-diffusion equations based on different hypotheses concerning the process of morphogen gradient formation. The robustness of steady-state gradients is also covered through boundary value problems. The introduction gives an overview of the relevant biological concepts (cells, DNA, organism development) and provides the requisite mathematical preliminaries on continuous dynamics and stochastic modeling. A basic understanding of calculus is assumed. The techniques described in this book encompass a wide range of mechanisms, from molecular behavior to population dynamics, and the inclusion of recent developments in the literature together with first-hand results make it an ideal reference for both new students and experienced researchers in the field of systems biology and applied mathematics.

Modeling in Systems Biology

Author : Ina Koch
Publisher : Springer Science & Business Media
ISBN 13 : 1849964742
Total Pages : 378 pages
Book Rating : 4.8/5 (499 download)

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Book Synopsis Modeling in Systems Biology by : Ina Koch

Download or read book Modeling in Systems Biology written by Ina Koch and published by Springer Science & Business Media. This book was released on 2010-10-21 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Author : Bernhard Palsson
Publisher : Cambridge University Press
ISBN 13 : 1107038855
Total Pages : 551 pages
Book Rating : 4.1/5 (7 download)

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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.

Systems Biology

Author : Andreas Kremling
Publisher : CRC Press
ISBN 13 : 1466567902
Total Pages : 379 pages
Book Rating : 4.4/5 (665 download)

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Book Synopsis Systems Biology by : Andreas Kremling

Download or read book Systems Biology written by Andreas Kremling and published by CRC Press. This book was released on 2013-11-12 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are sy

A Guide to Numerical Modelling in Systems Biology

Author : Peter Deuflhard
Publisher : Springer
ISBN 13 : 3319200593
Total Pages : 168 pages
Book Rating : 4.3/5 (192 download)

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Book Synopsis A Guide to Numerical Modelling in Systems Biology by : Peter Deuflhard

Download or read book A Guide to Numerical Modelling in Systems Biology written by Peter Deuflhard and published by Springer. This book was released on 2015-07-06 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks and identification of model parameters by means of comparisons with real data. Throughout the text, the strengths and weaknesses of numerical algorithms with respect to various systems biological issues are discussed. Web addresses for downloading the corresponding software are also included.

Computational Modeling of Biological Systems

Author : Nikolay V Dokholyan
Publisher : Springer Science & Business Media
ISBN 13 : 1461421454
Total Pages : 360 pages
Book Rating : 4.4/5 (614 download)

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Book Synopsis Computational Modeling of Biological Systems by : Nikolay V Dokholyan

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Modeling Methods for Medical Systems Biology

Author : María Elena Álvarez-Buylla Roces
Publisher : Springer
ISBN 13 : 3319893548
Total Pages : 258 pages
Book Rating : 4.3/5 (198 download)

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Book Synopsis Modeling Methods for Medical Systems Biology by : María Elena Álvarez-Buylla Roces

Download or read book Modeling Methods for Medical Systems Biology written by María Elena Álvarez-Buylla Roces and published by Springer. This book was released on 2018-08-03 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contributes to better understand how lifestyle modulations can effectively halt the emergence and progression of human diseases. The book will allow the reader to gain a better understanding of the mechanisms by which the environment interferes with the bio-molecular regulatory processes underlying the emergence and progression of complex diseases, such as cancer. Focusing on key and early cellular bio-molecular events giving rise to the emergence of degenerative chronic disease, it builds on previous experience on the development of multi-cellular organisms, to propose a mathematical and computer based framework that allows the reader to analyze the complex interplay between bio-molecular processes and the (micro)-environment from an integrative, mechanistic, quantitative and dynamical perspective. Taking the wealth of empirical evidence that exists it will show how to build and analyze models of core regulatory networks involved in the emergence and progression of chronic degenerative diseases, using a bottom-up approach.

Biological Modeling and Simulation

Author : Russell Schwartz
Publisher : MIT Press
ISBN 13 : 0262195844
Total Pages : 403 pages
Book Rating : 4.2/5 (621 download)

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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.

Stochastic Modelling for Systems Biology

Author : Darren J. Wilkinson
Publisher : CRC Press
ISBN 13 : 9781584885405
Total Pages : 296 pages
Book Rating : 4.8/5 (854 download)

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Book Synopsis Stochastic Modelling for Systems Biology by : Darren J. Wilkinson

Download or read book Stochastic Modelling for Systems Biology written by Darren J. Wilkinson and published by CRC Press. This book was released on 2006-04-18 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although stochastic kinetic models are increasingly accepted as the best way to represent and simulate genetic and biochemical networks, most researchers in the field have limited knowledge of stochastic process theory. The stochastic processes formalism provides a beautiful, elegant, and coherent foundation for chemical kinetics and there is a wealth of associated theory every bit as powerful and elegant as that for conventional continuous deterministic models. The time is right for an introductory text written from this perspective. Stochastic Modelling for Systems Biology presents an accessible introduction to stochastic modelling using examples that are familiar to systems biology researchers. Focusing on computer simulation, the author examines the use of stochastic processes for modelling biological systems. He provides a comprehensive understanding of stochastic kinetic modelling of biological networks in the systems biology context. The text covers the latest simulation techniques and research material, such as parameter inference, and includes many examples and figures as well as software code in R for various applications. While emphasizing the necessary probabilistic and stochastic methods, the author takes a practical approach, rooting his theoretical development in discussions of the intended application. Written with self-study in mind, the book includes technical chapters that deal with the difficult problems of inference for stochastic kinetic models from experimental data. Providing enough background information to make the subject accessible to the non-specialist, the book integrates a fairly diverse literature into a single convenient and notationally consistent source.

Networks in Systems Biology

Author : Fabricio Alves Barbosa da Silva
Publisher : Springer Nature
ISBN 13 : 3030518620
Total Pages : 381 pages
Book Rating : 4.0/5 (35 download)

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Book Synopsis Networks in Systems Biology by : Fabricio Alves Barbosa da Silva

Download or read book Networks in Systems Biology written by Fabricio Alves Barbosa da Silva and published by Springer Nature. This book was released on 2020-10-03 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a range of current research topics in biological network modeling, as well as its application in studies on human hosts, pathogens, and diseases. Systems biology is a rapidly expanding field that involves the study of biological systems through the mathematical modeling and analysis of large volumes of biological data. Gathering contributions from renowned experts in the field, some of the topics discussed in depth here include networks in systems biology, the computational modeling of multidrug-resistant bacteria, and systems biology of cancer. Given its scope, the book is intended for researchers, advanced students, and practitioners of systems biology. The chapters are research-oriented, and present some of the latest findings on their respective topics.

Modeling in Computational Biology and Biomedicine

Author : Frédéric Cazals
Publisher : Springer Science & Business Media
ISBN 13 : 364231208X
Total Pages : 333 pages
Book Rating : 4.6/5 (423 download)

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Book Synopsis Modeling in Computational Biology and Biomedicine by : Frédéric Cazals

Download or read book Modeling in Computational Biology and Biomedicine written by Frédéric Cazals and published by Springer Science & Business Media. This book was released on 2012-11-06 with total page 333 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational biology, mathematical biology, biology and biomedicine are currently undergoing spectacular progresses due to a synergy between technological advances and inputs from physics, chemistry, mathematics, statistics and computer science. The goal of this book is to evidence this synergy by describing selected developments in the following fields: bioinformatics, biomedicine and neuroscience. This work is unique in two respects - first, by the variety and scales of systems studied and second, by its presentation: Each chapter provides the biological or medical context, follows up with mathematical or algorithmic developments triggered by a specific problem and concludes with one or two success stories, namely new insights gained thanks to these methodological developments. It also highlights some unsolved and outstanding theoretical questions, with a potentially high impact on these disciplines. Two communities will be particularly interested in this book. The first one is the vast community of applied mathematicians and computer scientists, whose interests should be captured by the added value generated by the application of advanced concepts and algorithms to challenging biological or medical problems. The second is the equally vast community of biologists. Whether scientists or engineers, they will find in this book a clear and self-contained account of concepts and techniques from mathematics and computer science, together with success stories on their favorite systems. The variety of systems described represents a panoply of complementary conceptual tools. On a practical level, the resources listed at the end of each chapter (databases, software) offer invaluable support for getting started on a specific topic in the fields of biomedicine, bioinformatics and neuroscience.

Computational Systems Biology

Author : Andres Kriete
Publisher : Elsevier
ISBN 13 : 9780080459349
Total Pages : 424 pages
Book Rating : 4.4/5 (593 download)

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Book Synopsis Computational Systems Biology by : Andres Kriete

Download or read book Computational Systems Biology written by Andres Kriete and published by Elsevier. This book was released on 2005-11-10 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology is concerned with the quantitative study of complex biosystems at the molecular, cellular, tissue, and systems scales. Its focus is on the function of the system as a whole, rather than on individual parts. This exciting new arena applies mathematical modeling and engineering methods to the study of biological systems. This book is the first of its kind to focus on the newly emerging field of systems biology with an emphasis on computational approaches. The work covers new concepts, methods for information storage, mining and knowledge extraction, reverse engineering of gene and metabolic networks, as well as modelling and simulation of multi-cellular systems. Central themes include strategies for predicting biological properties and methods for elucidating structure-function relationships.

An Introduction to Computational Systems Biology

Author : Karthik Raman
Publisher : CRC Press
ISBN 13 : 0429944527
Total Pages : 359 pages
Book Rating : 4.4/5 (299 download)

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Book Synopsis An Introduction to Computational Systems Biology by : Karthik Raman

Download or read book An Introduction to Computational Systems Biology written by Karthik Raman and published by CRC Press. This book was released on 2021-05-30 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Emphasises a hands-on approach to modelling Strong emphasis on 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 Current chapters on exciting new developments like whole-cell modelling and community modelling

Modeling Dynamic Biological Systems

Author : Bruce Hannon
Publisher : Springer Science & Business Media
ISBN 13 : 1461206510
Total Pages : 399 pages
Book Rating : 4.4/5 (612 download)

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Book Synopsis Modeling Dynamic Biological Systems by : Bruce Hannon

Download or read book Modeling Dynamic Biological Systems written by Bruce Hannon and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models help us understand the dynamics of real-world processes by using the computer to mimic the actual forces that are known or assumed to result in a system's behavior. This book does not require a substantial background in mathematics or computer science.

Systems Biology Modelling and Analysis

Author : Elisabetta De Maria
Publisher : John Wiley & Sons
ISBN 13 : 1119716586
Total Pages : 468 pages
Book Rating : 4.1/5 (197 download)

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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 2022-11-18 with total page 468 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology Modelling and Analysis 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. Edited by a highly qualified expert 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.