An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/Crc Mathematical and Computational Biology Series)

Book Description

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 text avoids 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.

Customer Reviews:

Clear, rigorous, fascinating.......2007-01-20

I'm a Ph.D. student in biophysics. This is the best treatment of systems biology that I've encountered. It treats both the math and the biology with clarity, rigor, and respect. It simplifies without dumbing down. It's beautifully written. If you doubt that systems biology is a real scientific discipline, this book will change your mind.

Building Mathematical Models of Cells.......2006-09-25

The history of science over the past few centuries is to become ever more specialized. The physicists, becomming ever more concerned with the very large (stars, galaxies, the cosmos) or the very tiny (first atoms, then atomic components, now sub-components. The biologists on the other hand were studying much larger things, such as the cells that make up life. Both sciences developed techniques to facilitate their study.

In recent years, researchers have discovered that sometimes these specialized techniques can be used to develop greater insight into what is happening in other sciences.

In this book, Dr. Alon uses his training in physics to examine certain aspects of biology and to use the terminology and mathematics to describe the way these biological networks work.

The goal of the book is to begin the formulation of general laws that apply to biological networks. This is done by providing a mathematical framework in which some of the design principles of biological systems can help to understand biological networks. In looking at the results, an underlying simplicity not seen before appears in biological systems.

Great Job.......2006-09-09

A superb intro to the field. The math is moderate and helpful. Network concepts and their ties to examples and theory are clearly and succinctly presented. This is a textbook but reads easily like a book. Covers key elements while connecting them by at least mention to up-to-date further research. The basics and the grandeur of systems biology. I am trying to remember now anything on the negative side and cannot.

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Exposure Analysis

Manufacturer: CRC
ProductGroup: Book
Binding: Hardcover

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ASIN: 1566706637

Book Description

Written by experts, Exposure Analysis is the first complete resource in the emerging scientific discipline of exposure analysis. A comprehensive source on the environmental pollutants that affect human health, the book discusses human exposure through pathways including air, food, water, dermal absorption, and, for children, non-food ingestion. The book summarizes existing definitions of exposure, dose, and related concepts and provides the mathematical framework at the heart of these conceptual definitions. Using secondhand smoke as an example, the book illustrates how exposure analysis studies can change human behavior and improve public health. An extensive section on air pollutants considers volatile organic compounds (VOCs), carbon monoxide (CO), fine and ultrafine particles, and the latest personal air quality monitors for measuring individual exposure. Another detailed section examines exposures to pesticides, metals such as lead, and dioxin that may occur through multiple routes such as air, food, and dust ingestion. The book explores important aspects of dermal exposure such as the absorption of volatile organic compounds while showering or bathing and exposure through multiple carrier media. The authors describe quantitative methods that have been validated for predicting the concentrations in enclosed everyday locations, such as automobiles and rooms of the home. They also discuss existing laws and examine the relationship between exposure and national policies. Defining the new field of exposure analysis, this book provides the basic tools needed to identify sources, understand causes, measure exposures, and develop strategies for improving public health.

Stochastic Modelling for Systems Biology (Mathematical and Computational Biology)

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Correct title: Stochastic modeling of biological systems

Stochastic Modelling for Systems Biology (Mathematical and Computational Biology)
Darren J. Wilkinson
Manufacturer: Chapman & Hall/CRC
ProductGroup: Book
Binding: Hardcover

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An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/Crc Mathematical and Computational Biology Series)
Systems Biology: Properties of Reconstructed Networks
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts
Computational Systems Biology
Systems Biology in Practice: Concepts, Implementation and Application

ASIN: 1584885408

Book Description

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.

Customer Reviews:

Correct title: Stochastic modeling of biological systems.......2006-05-10

This is one of several recent books with system biology in the title, but first book with emphasis on statistics and stochastic approach. The book discusses some simple math models for biological systems, mostly biochemical models. Main focus is on statistical issues in differentail modeling, those as discussed in the nice Bower and Bolouri (2000) book, and the strong point is the use of Bayesian Markov chain Monte Carlo method for stochastic modeling. Weakness is that, the systems considered are too low-dimensional, and there is a long way toward real system biology issues, which will likely be much more complex, and involve potentially many high-dimensional interactions. Overall, it is simply a very straightforward introductory book, lacks depth and breadth. However, it should serve as a good starting point for people who want to learn something about stat and probabilistic methods relevant to bios system modelling.

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Using the free software on internet sites to help your research
Good
Yes, It's Really Written at the For Dummies Level.
Great introductory text
great beginner

Bioinformatics for Dummies
Jean-Michel Ph. D. Claverie , Cedric Ph.D. Notredame , Jean-Michel Claverie , and Cedric Notredame
Manufacturer: For Dummies
ProductGroup: Book
Binding: Paperback

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Genetics For Dummies (For Dummies (Math & Science))
Developing Bioinformatics Computer Skills
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Molecular Biology Made Simple and Fun, Third Edition
Discovering Genomics, Proteomics and Bioinformatics (2nd Edition) (The Genetics Place Series)

ASIN: 0764516965

Book Description

Bioinformatics – the process of searching biological databases, comparing sequences, examining protein structures, and researching biological questions with a computer – is one of the marvels of modern technology that can save you months of lab work. And the most amazing part is that, if you know how, you can use highly sophisticated programs over the Internet without paying a dime and sometimes, without installing anything new on your own computer. All you need to know is how to use these technological miracles.

That's where Bioinformatics For Dummies comes in. If you want to know what bioinformatics is all about and how to use it without wading through pages of computer gibberish or taking a course full of theory, this book has the answers in plain English. You'll find out how to

Use Internet resources
Understand bioinformatics jargon
Research biological databases
Locate the sequences you need
Perform specific tasks, step by step

Written by two experts who helped develop the science, Bioinformatics For Dummies is all about getting things done. If you're just getting your feet wet, start at the beginning with a quick review of those necessary parts of microbiology and an overview of the tools available. If you already know what you want to do, you can go directly to a chapter that shows you how. Get the lowdown on

Researching and analyzing DNA and protein sequences
Gathering information from all published sources
Searching databases for similar sequences and acquiring information about gene functions through sequence comparisons
Producing and editing multiple sequence comparisons for presentation
Predicting protein structures and RNA structures
Doing phylogenetic analysis

With an Internet connection and Bioinformatics For Dummies, you'll discover how to peruse databases that contain virtually everything known about human biology. It's like having access to the world's largest lab, right from your desk. This book is your lab assistant – one that never takes a day off, never argues when you ask it for help, and won't demand a benefits package.

Customer Reviews:

Using the free software on internet sites to help your research.......2007-03-14

The first chapter is a short review of DNA and RNA sequences, amino acids, and protein. The other chapters teach you to use the free software found on the Internet to work with your research. Information is also given which helps explain some biochemicals. My skills are in Software Development using C++ language, and I need more information on biochemicals to understand the problems and to develop algorithms to solve them.
My only criticism is that I would like the book to give more biochemical theory before taking up the subject of Internet software.
Overall, this is a good beginner's book on biochemistry.

Good.......2007-02-16

I am a couple years into a PhD in bioinformatics, but this is the book I started with. I knew some biology and some computer science, but I still found a lot of the databases, etc. confusing and the field has a decided lack of simplified documentation (though it is getting better).

Of course, bioinformatics is a pretty broad topic and no book could possibly cover everything.

If you do not know any biology at all you probably should also get a basic text on genetics/molecular biology (or read thema at the NCBI web site books section for free). You don't need anything in depth to read the dummies book, just at the level of an introductory biology book. Hint: DNA to RNA, RNA to Protein. And you want to know why proteins are similar because proteins with similar amino acid sequences often have similar chemical properties and therefore similar functions, so if you know what one protein does you can guess what a protein like it probably does.
:-)

And despite the name of the book the authors are REAL bioinformaticists (T-Coffee rocks!)

Yes, It's Really Written at the For Dummies Level........2007-01-18

This book kind of blew me away. Bioinformatics is such a big word.

Then in the second chapter they tell you 'How Most People Use Bioinformatics.' And all of a sudden they have you on line to the National Library of Medicine at the National Institute of Health. They have you looking at protein sequences, and you even understand what they are saying.

This is a 'For Dummies' book. It is written in their traditional style, assuming that you know very little -- well to be sure they say they are making the assumption that 'You likely have a background in molecular biology. If you don't - or if you need to brush up on your molecular biology - Chapter 1 gives you a brief overview of the basics.'

I found that the first few chapters went down pretty easily. By part IV it had gone further than I wanted to go, and I quit reading.

BUT if I were going to be taking a course in bioinformatics, or even thinking about taking such a course, or just looking at a degree in biology, I'd spend a week or two getting around this book. It's written a hell of a lot better than any text you're likely to get assigned, and at its price it's quite a deal.

Great introductory text.......2006-09-20

This is an excellent introduction to Bioinformatics. It does assume some very basic knowledge of biology- perhaps a couple of paragraphs could help the total newbies.

Have you noticed that reviews of bioinformatics books tend to follow certain patterns? The Computer Scientists and mathematicians complain that there is not enough detail about the algorithms, the biologists complain that they could not get through the math, and everyone complains that there is not enough detail about their favorite programs! Let us face the fact that this is a very broad field, and most people that want to learn about it will never design algorithms.

great beginner.......2005-12-16

In spite of the title (I don't know many dummies interested in multiple sequence alignments) this reference is written by experts in the field of bioinformatics and is very accessable for the beginner. I purchased this book as a beginning graduate student so that I could learn which programs to use to compare amino acid and nucleic acid sequences as well as prepare them for publication and this book was perfect for this end. This text doesn't delve into the algorithms or much theory (which is learned through practice and other sources), nevertheless, I recommend this for the researcher for a crash course or quick reference. This book really helped me get my feet wet in this area (and recently publish a nice alignment) and will certainly reduce my workload next semester for my bioinformatics course!

Historical Dynamics: Why States Rise and Fall (Princeton Studies in Complexity)

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Great read!
This is not a review it is only Table of Contents to help those who are intrested,
A new avenue for historical research

Historical Dynamics: Why States Rise and Fall (Princeton Studies in Complexity)
Peter Turchin
Manufacturer: Princeton University Press
ProductGroup: Book
Binding: Hardcover

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War and Peace and War: The Life Cycles of Imperial Nations
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Small Worlds: The Dynamics of Networks between Order and Randomness (Princeton Studies in Complexity)

ASIN: 0691116695

Book Description

Many historical processes are dynamic. Populations grow and decline. Empires expand and collapse. Religions spread and wither. Natural scientists have made great strides in understanding dynamical processes in the physical and biological worlds using a synthetic approach that combines mathematical modeling with statistical analyses. Taking up the problem of territorial dynamics--why some polities at certain times expand and at other times contract--this book shows that a similar research program can advance our understanding of dynamical processes in history.

Peter Turchin develops hypotheses from a wide range of social, political, economic, and demographic factors: geopolitics, factors affecting collective solidarity, dynamics of ethnic assimilation/religious conversion, and the interaction between population dynamics and sociopolitical stability. He then translates these into a spectrum of mathematical models, investigates the dynamics predicted by the models, and contrasts model predictions with empirical patterns. Turchin's highly instructive empirical tests demonstrate that certain models predict empirical patterns with a very high degree of accuracy. For instance, one model accounts for the recurrent waves of state breakdown in medieval and early modern Europe. And historical data confirm that ethno-nationalist solidarity produces an aggressively expansive state under certain conditions (such as in locations where imperial frontiers coincide with religious divides). The strength of Turchin's results suggests that the synthetic approach he advocates can significantly improve our understanding of historical dynamics.

Customer Reviews:

Great read!.......2006-12-30

This is a very good effort. The author goes through basic knowledge about complex systems and its basic math and then slowly brings historical trends and changes into the picture. This is a very good way to learn about history and a very easy way to remember historical events if the reader follows Turchin's approach.

Again a good read for those who want to learn history using the most natural approach.

This is not a review it is only Table of Contents to help those who are intrested,.......2006-12-27

Table of Contents
List of Figures
List of Tables
Preface
Ch. 1 Statement of the Problem 1
Ch. 2 Geopolitics 9
Ch. 3 Collective Solidarity 29
Ch. 4 The Metaethnic Frontier Theory 50
Ch. 5 An Empirical Test of the Metaethnic Frontier Theory 78
Ch. 6 Ethnokinetics 94
Ch. 7 The Demographic-Structural Theory 118
Ch. 8 Secular Cycles in Population Numbers 150
Ch. 9 Case Studies 170
Ch. 10 Conclusion 197
App. A: Mathematical Appendix 205
App. B Data Summaries for the Test of the Metaethnic Frontier Theory 214
Bibliography 226
Index 243

A new avenue for historical research.......2003-11-13

I remember that some years ago when I discovered
"Looking at History through Mathematics" by Nicolas Rashevsky
(published in 1968 by the MIT Press)
I was at first enthralled by the title but then fairly
disappointed by the book itself for in fact it contains very
little history: no solid statistical data, not even
qualitative historical trends that would illustrate some
of the theoretical curves. Instead of focusing on sharply
defined questions, Rashevsky raises broad issues such as for
instance (on p. 9 and 117)
why it took 10,000 years rather than a few hundred
for humanity to develop from its cultural state at the
beginning of early urban civilization to its present state.

This former experience explains why I read Peter Turchin's book
with so much pleasure. What a contrast indeed! In
every section stimulating models are blended with quantitative
historical data drawn from the best sources. From the rise of
Islam to the growth of the Mormon Church to Chinese dynastic
cycles "Historical Dynamics" offers a fascinating sample
of sharply defined problems for which models are able to provide
unified understanding.

Book Description

Biostatistics for the Biological and Health Sciences is the result of collaboration between the author of the #1 statistics book in the country and an expert in the biological sciences field. The major objective of this book is to provide a thorough, yet engaging introduction to statistics for students and professors in the biological, life, and health sciences. This text reflects the important features of a modern introductory statistics course and includes an abundance of real data and biological applications, and a variety of pedagogical components to help students succeed in their study of biological statistics. MARKET: It is the ideal introduction to statistics for students and professors in the biological, life, and health sciences.

Customer Reviews:

Great Resource.......2007-06-27

I have just completed my Biostatistics class and received an A by using this textbook. This is very concise, informative and easy to read.

Not good at all.......2006-11-03

I couldn't make heads or tails of this book... not enough practical application and way too much inconsequential detail. Other students complained about its format too. I found better information using Google searches.

Statistics for Biological and Health Science

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Statistics for Biological and Health Science
Joseph Inungu , and Felix Famoye
Manufacturer: Kendall/Hunt Publishing Company
ProductGroup: Book
Binding: Paperback

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ASIN: 0757532640

Sampling Rare or Elusive Species: Concepts, Designs, and Techniques for Estimating Population Parameters

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Very useful and illustrative!

Sampling Rare or Elusive Species: Concepts, Designs, and Techniques for Estimating Population Parameters

Manufacturer: Island Press
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Binding: Paperback

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Occupancy Estimation and Modeling: Inferring Patterns and Dynamics of Species Occurrence
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Analysis and Management of Animal Populations

ASIN: 1559634510

Book Description

Information regarding population status and abundance of rare species plays a key role in resource management decisions. Ideally, data should be collected using statistically sound sampling methods, but by their very nature, rare or elusive species pose a difficult sampling challenge.

Sampling Rare or Elusive Species describes the latest sampling designs and survey methods for reliably estimating occupancy, abundance, and other population parameters of rare, elusive, or otherwise hard-to-detect plants and animals. It offers a mixture of theory and application, with actual examples from terrestrial, aquatic, and marine habitats around the world.

Sampling Rare or Elusive Species is the first volume devoted entirely to this topic and provides natural resource professionals with a suite of innovative approaches to gathering population status and trend data. It represents an invaluable reference for natural resource professionals around the world, including fish and wildlife biologists, ecologists, biometricians, natural resource managers, and all others whose work or research involves rare or elusive species.

Customer Reviews:

Very useful and illustrative!.......2007-01-19

I usually work with very elusive animals like wild big cats, that's why I consider this book very useful and ilustrative if you are planning to work with rare species; in special the experimental desing section. Also the cited bibliography is a great tool to expand knowledge in this subjet. I really recomend it!!

Christian Estrada
Wildlife Biologist

Chance in Biology: Using Probability to Explore Nature

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Math Applied to Biology
Biology illuminated by physics

Chance in Biology: Using Probability to Explore Nature
Mark Denny , and Steven Gaines
Manufacturer: Princeton University Press
ProductGroup: Book
Binding: Paperback

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Random Walks in Biology
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Stochastic Modelling for Systems Biology (Mathematical and Computational Biology)
Dynamic Models in Biology
Air and Water

ASIN: 0691094942

Book Description

Life is a chancy proposition: from the movement of molecules to the age at which we die, chance plays a key role in the natural world. Traditionally, biologists have viewed the inevitable "noise" of life as an unfortunate complication. The authors of this book, however, treat random processes as a benefit. In this introduction to chance in biology, Mark Denny and Steven Gaines help readers to apply the probability theory needed to make sense of chance events--using examples from ocean waves to spiderwebs, in fields ranging from molecular mechanics to evolution.

Through the application of probability theory, Denny and Gaines make predictions about how plants and animals work in a stochastic universe. Is it possible to pack a variety of ion channels into a cell membrane and have each operate at near-peak flow? Why are our arteries rubbery? The concept of a random walk provides the necessary insight. Is there an absolute upper limit to human life span? Could the sound of a cocktail party burst your eardrums? The statistics of extremes allows us to make the appropriate calculations. How long must you wait to see the detail in a moonlit landscape? Can you hear the noise of individual molecules? The authors provide answers to these and many other questions.

After an introduction to the basic statistical methods to be used in this book, the authors emphasize the application of probability theory to biology rather than the details of the theory itself. Readers with an introductory background in calculus will be able to follow the reasoning, and sets of problems, together with their solutions, are offered to reinforce concepts. The use of real-world examples, numerous illustrations, and chapter summaries--all presented with clarity and wit--make for a highly accessible text. By relating the theory of probability to the understanding of form and function in living things, the authors seek to pique the reader's curiosity about statistics and provide a new perspective on the role of chance in biology.

Customer Reviews:

Math Applied to Biology.......2002-10-10

*Chance in Biology* is one of the best science books I have ever read (and I have read quite a few of them). This book applies probability theory (along with other topics in math and physics) to biological phenomena. A big PLUS for this book is that the authors intentionally wrote the book to be accessible to an educated but nonspecialized audience.

I really enjoyed the authors' discussion of random walks applied to 'genetic drift' (the likelihood that offsprings' genomes will be different than their parents') and a surprising application of probability theory to elastic materials found in nature.

I also enjoyed their chapter on the probability of extreme phenomena -- which is an obviously useful topic that gets short shrift in many probability and statistics books I have seen. They even use baseball statistics in that chapter!

Another interesting part of this book was the discussion and the practice problems dealing with Bayes' Theorem. The concepts discussed in this book is something that all health care officials and lawyers should familiarize themselves with.

Some caveats about the book:

(a) The reader should be familiar with the 1st year of college calculus. While it is is possible that someone with only an understanding of algebra can get a lot out of the book, the calculus would help. I should note that you do not need to know a lot of calculus and someone who is 'mathophobic' could still get a lot out of the book.

(b) This book does not deal too much with inferential statistics. This book focuses in on probability, which is the cornerstone of statistics. However, when it does touch upon inferential statistics, it does a superb job.

(c) I wish the authors spent a little bit of time going over Markov Chains (random walks is a type of Markov Chain and the book does deal with that but without talking about MC explicitly). But that is a minor complaint.

Rounding out my praise for this book is the fact that most of the chapters have practice problems and ALL of the problems have solutions to them at the back of the book. I can't even begin to tell you how great having all of the solutions for all of the problems is for self-study/comprehension. The problems provided are no 'toy problems' either ... they are actually extremely helpful in not only testing one's grasps of the materials but also in illuminating and extending the points made in the particular chapter.

Other miscellanous positive things about *Chance in Biology*:

- a sample MATLAB program to simulate random phenomenon (in the solution to one of the practice problems)

- a chapter that deals with 'noise' .... interesting for those interested in Chaos

- authors make an excellent distinction between non-deterministic random/stochastic phenomena vs. deterministic Chaos

- many more good things!!!

Bottom-line: If you are at all interested in probability, applied math, physics, chemistry, or biology, you should buy this book.

Biology illuminated by physics.......2001-11-18

Biology progressed from natural history to its great depth and breadth in part from the inclusion of truly quantitative ideas from math, physics, and chemistry. The mantle of greatest expositor of these ideas in recent times may have passed from Stephen Vogel (his excellent books are well worth reading) to Mark Denny. Here, with Steven Gaines, he takes us into extreme events, the limits of our ability to hear and to see, the elasticity of spider silk, and more. The math is demanding, but it should be; Denny and Gaines make no bones about it, but reward the reader. Denny's book, Air and Water, is equally a pleasure to read.

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Handbook of Capture-Recapture Analysis

Manufacturer: Princeton University Press
ProductGroup: Book
Binding: Paperback

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Model Selection and Multi-Model Inference

ASIN: 069108968X

Book Description

Every day, biologists in parkas, raincoats, and rubber boots go into the field to capture and mark a variety of animal species. Back in the office, statisticians create analytical models for the field biologists' data. But many times, representatives of the two professions do not fully understand one another's roles. This book bridges this gap by helping biologists understand state-of-the-art statistical methods for analyzing capture-recapture data. In so doing, statisticians will also become more familiar with the design of field studies and with the real-life issues facing biologists.

Reliable outcomes of capture-recapture studies are vital to answering key ecological questions. Is the population increasing or decreasing? Do more or fewer animals have a particular characteristic? In answering these questions, biologists cannot hope to capture and mark entire populations. And frequently, the populations change unpredictably during a study. Thus, increasingly sophisticated models have been employed to convert data into answers to ecological questions. This book, by experts in capture-recapture analysis, introduces the most up-to-date methods for data analysis while explaining the theory behind those methods. Thorough, concise, and portable, it will be immensely useful to biologists, biometricians, and statisticians, students in both fields, and anyone else engaged in the capture-recapture process.

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