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Author: Jinzhi Lei Publisher: ISBN: 9783030730345 Category : Languages : en Pages : 0
Book Description
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.
Author: Jinzhi Lei Publisher: ISBN: 9783030730345 Category : Languages : en Pages : 0
Book Description
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.
Author: Brian P. Ingalls Publisher: MIT Press ISBN: 0262545829 Category : Science Languages : en Pages : 423
Book Description
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.
Author: Andreas Kremling Publisher: CRC Press ISBN: 1466567902 Category : Mathematics Languages : en Pages : 379
Book Description
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
Author: Ina Koch Publisher: Springer Science & Business Media ISBN: 1849964742 Category : Computers Languages : en Pages : 378
Book Description
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.
Author: Peter Deuflhard Publisher: Springer ISBN: 3319200593 Category : Mathematics Languages : en Pages : 185
Book Description
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.
Author: Nikolay V Dokholyan Publisher: Springer Science & Business Media ISBN: 1461421454 Category : Science Languages : en Pages : 360
Book Description
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.
Author: Fabricio Alves Barbosa da Silva Publisher: Springer Nature ISBN: 3030518620 Category : Computers Languages : en Pages : 381
Book Description
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.
Author: Russell Schwartz Publisher: MIT Press ISBN: 0262303396 Category : Science Languages : en Pages : 403
Book Description
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.
Author: Jinzhi Lei
Author: Jinzhi Lei
Author: Brian P. Ingalls
Author: Andreas Kremling
Author: Ina Koch
Author: Bernhard Palsson
Author: Peter Deuflhard
Author: Nikolay V Dokholyan
Author: Fabricio Alves Barbosa da Silva
Author: James W. Haefner
Author: Russell Schwartz