Modeling Biological Systems

Principles and Applications

Author: James W. Haefner

Publisher: Springer Science & Business Media

ISBN: 1461541190

Category: Science

Page: 473

View: 8401

This book is intended as a text for a first course on creating and analyzing computer simulation models of biological systems. The expected audience for this book are students wishing to use dynamic models to interpret real data mueh as they would use standard statistical techniques. It is meant to provide both the essential principles as well as the details and equa tions applicable to a few particular systems and subdisciplines. Biological systems, however, encompass a vast, diverse array of topics and problems. This book discusses only a select number of these that I have found to be useful and interesting to biologists just beginning their appreciation of computer simulation. The examples chosen span classical mathematical models of well-studied systems to state-of-the-art topics such as cellular automata and artificial life. I have stressed the relationship between the models and the biology over mathematical analysis in order to give the reader a sense that mathematical models really are useful to biologists. In this light, I have sought examples that address fundamental and, I think, interesting biological questions. Almost all of the models are directly COIIl pared to quantitative data to provide at least a partial demonstration that some biological models can accurately predict.

A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations

Author: Vishwesh V. Kulkarni,Guy-Bart Stan,Karthik Raman

Publisher: Springer

ISBN: 9401790418

Category: Medical

Page: 332

View: 6233

The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume I provides a panoramic view that illustrates the potential of such mathematical methods in systems and synthetic biology. Recent advances in systems and synthetic biology have clearly demonstrated the benefits of a rigorous and systematic approach rooted in the principles of systems and control theory - not only does it lead to exciting insights and discoveries but it also reduces the inordinately lengthy trial-and-error process of wet-lab experimentation, thereby facilitating significant savings in human and financial resources. In Volume I, some of the leading researchers in the field of systems and synthetic biology demonstrate how systems and control theoretic concepts and techniques can be useful, or should evolve to be useful, in order to understand how biological systems function. As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Principles and Models of Biological Transport

Author: Morton H. Friedman

Publisher: Springer Science & Business Media

ISBN: 9780387792408

Category: Technology & Engineering

Page: 510

View: 9804

Focus, Organization, and Content This book, like the first edition, deals with the mass transport processes that take place in living systems, with a focus on the normal behavior of eukaryotic cells and the - ganisms they constitute, in their normal physiological environment. As a consequence of this focus, the structure and content of the book differ from those of traditional transport texts. We do not start with the engineering principles of mass transport (which are well presented elsewhere) and then seek biological applications of these principles; rather, we begin with the biological processes themselves, and then - velop the models and analytical tools that are needed to describe them. This approach has several consequences. First of all, it drives the content of the text in a direction distinctively different from conventional transport texts. This is - cause the tools and models needed to describe complex biological processes are often different from those employed to describe more well-characterized inanimate systems. Many biological processes must still be described phenomenologically, using me- odologies like nonequilibrium thermodynamics. Simple electrical analogs employing a paucity of parameters can be more useful for characterization and prediction than complex theories based on the behavior of more well-defined systems on a laboratory bench. By allowing the biology to drive the choice of analysis tools and models, the latter are consistently presented in the context of real biological systems, and analysis and biology are interwoven throughout.

Modelling Nutrient Digestion and Utilisation in Farm Animals

Author: D. Sauvant,J. van Milgen,P. Faverdin,N. Friggens

Publisher: Springer Science & Business Media

ISBN: 908686712X

Category: Science

Page: 430

View: 8520

For more than 30 years, modelling has been an important method for integrating, in a flexible, comprehensive and widely applicable way, basic knowledge and biological concepts on digestion and metabolism in farm animals. The purpose of this book is to present the 'state of art' in this area. The chapters are written by leading teams and researchers in this field of study, mainly from Europe, North America and Australasia. Considerable progress has been made in topics dealing with: modelling methods, feeding behaviour, digestion and metabolic processes in ruminants and monogastric animals. This progress is clearly illustrated by the emergence of a new paradigm in animal nutrition, which has moved from the aim to cover the requirements of the animal to explaining and predicting the responses of the animals to diets (e.g., productivity and efficiency, impact on quality of products, environmental aspects, health and well-being). In this book several chapters illustrate that through empirical models, meta-analysis is an efficient tool to synthesize information gathered over recent decades. In addition, compared with other books on modelling farm animal nutrition, two new aspects received particular attention: expanding knowledge of the individual animal to understanding the functioning and management of herds, and the consideration of the environmental impact of animal production. This book is a valuable source of information for researchers, nutritionists, advisors, and graduate students who want to have up-to-date and concise information on mathematical modelling applied to farm animals.

Kompendium Systembiologie

Mathematische Modellierung und Modellanalyse

Author: Andreas Kremling

Publisher: Springer-Verlag

ISBN: 3834886076

Category: Science

Page: 300

View: 2898

Das Buch beschreibt die Grundlagen der mathematischen Modellierung zellulärer Systeme. Nach einer Klassifikation von Modellen wird schwerpunktmäßig auf deterministische Modelle eingegangen und für alle relevanten zellulären Prozesse entsprechende Gleichungen angegeben. Anschließend werden eine Reihe von Verfahren zur Modellanalyse vorgestellt. Etwas kürzer werden Verfahren zum Reverse Engineering und zur Analyse von Netzwerkgraphen abgehandelt. Am Ende werden noch Verfahren der Parameteridentifikation besprochen.

Computational Chemistry and Molecular Modeling

Principles and Applications

Author: K. I. Ramachandran,Gopakumar Deepa,Krishnan Namboori

Publisher: Springer Science & Business Media

ISBN: 3540773045

Category: Science

Page: 398

View: 6755

The gap between introductory level textbooks and highly specialized monographs is filled by this modern textbook. It provides in one comprehensive volume the in-depth theoretical background for molecular modeling and detailed descriptions of the applications in chemistry and related fields like drug design, molecular sciences, biomedical, polymer and materials engineering. Special chapters on basic mathematics and the use of respective software tools are included. Numerous numerical examples, exercises and explanatory illustrations as well as a web site with application tools (http://www.amrita.edu/cen/ccmm) support the students and lecturers.

Plagues and Epidemics

Infected Spaces Past and Present

Author: D. Ann Herring,Alan C. Swedlund

Publisher: Berg

ISBN: 1847887554

Category: Social Science

Page: 416

View: 2205

Until recently, plagues were thought to belong in the ancient past. Now there are deep worries about global pandemics. This book presents views from anthropology about this much publicized and complex problem. The authors take us to places where epidemics are erupting, waning, or gone, and to other places where they have not yet arrived, but where a frightening story line is already in place. They explore public health bureaucracies and political arenas where the power lies to make decisions about what is, and is not, an epidemic. They look back into global history to uncover disease trends and look ahead to a future of expanding plagues within the context of climate change. The chapters are written from a range of perspectives, from the science of modeling epidemics to the social science of understanding them. Patterns emerge when people are engulfed by diseases labeled as epidemics but which have the hallmarks of plague. There are cycles of shame and blame, stigma, isolation of the sick, fear of contagion, and end-of-the-world scenarios. Plague, it would seem, is still among us.

Kinetic Modelling in Systems Biology

Author: Oleg Demin,Igor Goryanin

Publisher: CRC Press

ISBN: 9781420011661

Category: Mathematics

Page: 360

View: 5653

With more and more interest in how components of biological systems interact, it is important to understand the various aspects of systems biology. Kinetic Modelling in Systems Biology focuses on one of the main pillars in the future development of systems biology. It explores both the methods and applications of kinetic modeling in this emerging field. The book introduces the basic biological cellular network concepts in the context of cellular functioning, explains the main aspects of the Edinburgh Pathway Editor (EPE) software package, and discusses the process of constructing and verifying kinetic models. It presents the features, user interface, and examples of DBSolve as well as the principles of modeling individual enzymes and transporters. The authors describe how to construct kinetic models of intracellular systems on the basis of models of individual enzymes. They also illustrate how to apply the principles of kinetic modeling to collect all available information on the energy metabolism of whole organelles, construct a kinetic model, and predict the response of the organelle to changes in external conditions. The final chapter focuses on applications of kinetic modeling in biotechnology and biomedicine. Encouraging readers to think about future challenges, this book will help them understand the kinetic modeling approach and how to apply it to solve real-life problems. CD-ROM Features Extensively used throughout the text for pathway visualization and illustration, the EPE software is available on the accompanying CD-ROM. The CD also includes pathway diagrams in several graphical formats, DBSolve installation with examples, and all models from the book with dynamic visualization of simulation results, allowing readers to perform in silico simulations and use the models as templates for further applications.

Mathematical Models in Population Biology and Epidemiology

Author: Fred Brauer,Carlos Castillo-Chavez

Publisher: Springer Science & Business Media

ISBN: 1475735162

Category: Science

Page: 417

View: 3066

The goal of this book is to search for a balance between simple and analyzable models and unsolvable models which are capable of addressing important questions on population biology. Part I focusses on single species simple models including those which have been used to predict the growth of human and animal population in the past. Single population models are, in some sense, the building blocks of more realistic models -- the subject of Part II. Their role is fundamental to the study of ecological and demographic processes including the role of population structure and spatial heterogeneity -- the subject of Part III. This book, which will include both examples and exercises, is of use to practitioners, graduate students, and scientists working in the field.

Systems Biology

Definitions and Perspectives

Author: Lilia Alberghina,Hans V. Westerhoff

Publisher: Springer Science & Business Media

ISBN: 9783540742692

Category: Computers

Page: 408

View: 3314

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.

Dynamic Models and Control of Biological Systems

Author: Vadrevu Sree Hari Rao,Ponnada Raja Sekhara Rao

Publisher: Springer Science & Business Media

ISBN: 1441903593

Category: Science

Page: 275

View: 4922

Mathematical Biology has grown at an astonishing rate and has established itself as a distinct discipline. Mathematical modeling is now being applied in every major discipline in the biological sciences. Though the field has become increasingly large and specialized, this book remains important as a text that introduces some of the exciting problems which arise in the biological sciences and gives some indication of the wide spectrum of questions that modeling can address.

Systems Biology in Practice

Concepts, Implementation and Application

Author: Edda Klipp,Ralf Herwig,Axel Kowald,Christoph Wierling,Hans Lehrach

Publisher: John Wiley & Sons

ISBN: 352760488X

Category: Medical

Page: 486

View: 2581

Presenting the main concepts, this book leads students as well as advanced researchers from different disciplines to an understanding of current ideas in the complex field of comprehensive experimental investigation of biological objects, analysis of data, development of models, simulation, and hypothesis generation. It provides readers with guidance on how a specific complex biological question may be tackled: - How to formulate questions that can be answered - Which experiments to perform - Where to find information in databases and on the Internet - What kinds of models are appropriate - How to use simulation tools - What can be learned from the comparison of experimental data and modeling results - How to make testable predictions. The authors demonstrate how mathematical concepts can illuminate the principles underlying biology at a genetic, molecular, cellular and even organism level, and how to use mathematical tools for analysis and prediction.

Principles of Mathematical Modeling

Author: Clive L. Dym

Publisher: Academic Press

ISBN: 9780122265518

Category: Mathematics

Page: 303

View: 9014

This book provides a readable and informative introduction to the development and application of mathematical models in science and engineering. The first half of the book begins with a clearly defined set of modeling principles, and then introduces a set of foundational tools (dimensional analysis, scaling techniques, and approximation and validation techniques). The second half then applies these foundational tools to a broad variety of subjects, including exponenttial growth and decay in fields ranging from biology to economics, traffic flow, free and forced vibration of mechanical and other systems, and optimization problems in biology, structures, and social decision making. An extensive collection of more than 360 problems offer ample opportunity in both a formal course and for the individual reader. (Midwest).

Modeling and Simulation

Author: Hartmut Bossel

Publisher: Springer-Verlag

ISBN: 3663108228

Category: Technology & Engineering

Page: 484

View: 570

This book is the the English Language Version of the very successful German textbook, "Modellbildung und Simulation". It provides a self-contained and complete guide to the methods and mathematical background of modeling and simulation software of dynamic systems. Furthermore, an appropriate simulation software and a collection of dynamic system models (on the accompanying disk) are highlights of the book/software-Package.Dies ist die englischsprachige Ausgabe des sehr erfolgreichen Lehrbuches "Modellbildung und Simulation". Geboten wird eine vollständige Einführung in die Methoden der Simulation dynamischer Systeme, wobei auch der notwendige mathematische Hintergrund vermittelt wird. Außerdem ist eine Simulationssoftware Bestandteil des Werkes; auf der beiliegenden Diskette befinden sich ferner 50 Beispielsysteme ("Systemzoo"), die zur spielerischen Einübung der verwendeten Verfahren hilfreich sind.

Models for Planning Wildlife Conservation in Large Landscapes

Author: Joshua J. Millspaugh,Frank Richard Thompson

Publisher: Academic Press

ISBN: N.A

Category: Nature

Page: 688

View: 5920

Intended to provide a recipe for successful development of wildlife habitat models and their implementation in conservation planning, the book could be used in studying wildlife habitat models, conservation planning, and management techniques. Additionally it may be a supplemental text in courses dealing with quantitative assessment of wildlife populations. Additionally, the length of the book would be ideal for graduate student seminar course. Using wildlife habitat models in conservation planning is of considerable interest to wildlife biologists. With ever tightening budgets for wildlife research and planning activities, there is a growing need to use computer methods. Use of simulation models represents the single best alternative. However, it is imperative that these techniques be described in a single source. Moreover, biologists should be made aware of alternative modeling techniques.-

Systems Biology

Author: Jens Nielsen,Stefan Hohmann,Sang Yup Lee,Gregory Stephanopoulos

Publisher: John Wiley & Sons

ISBN: 3527335587

Category: Computers

Page: 432

View: 1551

Comprehensive coverage of the many different aspects of systems biology, resulting in an excellent overview of the experimental and computational approaches currently in use to study biological systems. Each chapter represents a valuable introduction to one specific branch of systems biology, while also including the current state of the art and pointers to future directions. Following different methods for the integrative analysis of omics data, the book goes on to describe techniques that allow for the direct quantification of carbon fluxes in large metabolic networks, including the use of 13C labelled substrates and genome-scale metabolic models. The latter is explained on the basis of the model organism Escherichia coli as well as the human metabolism. Subsequently, the authors deal with the application of such techniques to human health and cell factory engineering, with a focus on recent progress in building genome-scale models and regulatory networks. They highlight the importance of such information for specific biological processes, including the ageing of cells, the immune system and organogenesis. The book concludes with a summary of recent advances in genome editing, which have allowed for precise genetic modifications, even with the dynamic control of gene expression. This is part of the Advances Biotechnology series, covering all pertinent aspects of the field with each volume prepared by eminent scientists who are experts on the topic in question.

Modeling in natural resource management

development, interpretation, and application

Author: Tanya M. Shenk,Alan B. Franklin

Publisher: Island Pr

ISBN: N.A

Category: Mathematics

Page: 223

View: 1608

The natural environment is so complex that simplification through abstraction is necessary to communicate concepts and relationships, to comprehend possible reactions, and to decide upon a course of action for management. Today, nearly every decision concerning the management of natural resources is based on a model of one kind or another. Modeling in Natural Resource Managementoffers a much-needed overview of the basic principles for understanding and evaluating models. Focusing on the fundamental components of model creation, interpretation, and application, the book provides a wealth of information on how models are developed and used in natural resource management, as it: defines what models are explores how the different classes of models fit into the scientific process discusses how to determine the appropriateness and usefulness of a particular model provides examples of how models are used (and misused) considers how further progress might be achieved Chapters written by leading experts -- including Mark S. Boyce, William T. Clark, Michael J. Conroy, Donald L. DeAngelis, Douglas H. Johnson, William L. Kendall, Lyman L. McDonald, Marc Mangel, James D. Nichols, Gary C. White, and others -- describe how models should be constructed and interpreted, and highlight how they can be and have been used. Modeling in Natural Resource Managementbrings together in a single volume the best and most current information about natural resource modeling and its on-the-ground application, providing a valuable reference both for scientists involved with issues of natural resource management and for managers who apply the science to real-world problems.

Environmental Reviews

Author: N.A

Publisher: N.A

ISBN: N.A

Category: Environmental sciences

Page: N.A

View: 8345