Bioinformatics for Dummies (For Dummies Series)

Book Description

Were you always curious about biology but were afraid to sit through long hours of dense reading? Did you like the subject when you were in high school but had other plans after you graduated? Now you can explore the human genome and analyze DNA without ever leaving your desktop!

Bioinformatics for Dummies is packed with valuable information that introduces you to this exciting new discipline. This easy-to-follow guide leads you step by step through every bioinformatics task that can be done over the Internet. Forget long equations, computer-geek gibberish, and installing bulky programs that slow down your computer. You’ll be amazed at all the things you can accomplish just by logging on and following these trusty directions. You get the tools you need to:

Analyze all types of sequences
Use all types of databases
Work with DNA and protein sequences
Conduct similarity searches
Build a multiple sequence alignment
Edit and publish alignments
Visualize protein 3-D structures
Construct phylogenetic trees

This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. It provides tips for using servers and places to seek resources to find out about what’s going on in the bioinformatics world. Bioinformatics for Dummies will show you how to get the most out of your PC and the right Web tools so you’ll be searching databases and analyzing sequences like a pro!

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!

Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics)

Average customer rating:

Strong on subject matter
I know it was written by the Father of Informatics but.....
Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics)

Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics)

Manufacturer: Springer
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Binding: Hardcover

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Accessories:

ASIN: 0387289860

Book Description

The practice of modern medicine requires sophisticated information technologies with which to manage patient information, plan diagnostic procedures, interpret laboratory results, and conduct research. This book, inspired by a Stanford University training program developed to introduce health professionals to computer applications in modern medical care, fills the need for a high quality text in computers and medicine, and meets the growing demand by practitioners, researchers, and students for a comprehensive introduction to key topics in the field. The work is designed for a broad audience interested in the intersection of computer science and medicine.

Completely revised and expanded, the Third Edition (previously titled "Medical Informatics") includes several new chapters filled with brand new material. This book will provide both a conceptual framework and a practical approach for the implementation and management of IT used to improve the delivery of health care. Designed for use by professors and students of medical informatics and for practicing professionals, this book will focus on the role of computers in the provision of medical services. Biomedial Informatics, Third Edition, provides the conceptual base needed to comprehend and utilize medical informatics through easy to understand examples that demonstrate how computers assist in the delivery of health care. This text also includes pointers to additional literature, chapter summaries, and concise definition of recurring terms for self-study or classroom use.

Customer Reviews:

Strong on subject matter.......2007-10-18

I didn't think I'd like this book very much when I found I had to order it for a class I'm taking (Introduction to Medical Informatics). It's fairly dense, but I found that it is dense in a good kind of way. Each chapter reads like a good overview of the subject. As I've progressed through the book I find very little lacking. It offers nearly complete information on every aspect of the subject matter. Someone who didn't know something ever existed before reading this book could come away with a good grasp of the subject and have references to follow up for a more complete view. It doesn't read like literature, but thankfully it is broken up into small easily digestible sections.

There are probably other texts that are easier to read because of style. This one is very strong on content and won't leave gaps. It might have you asking the right kind of question when finished, but that is the whole point, isn't it?

I know it was written by the Father of Informatics but............2007-07-01

Everyone in the field of medical informatics knows Ed Shortliffe. He has done a lot of pioneering work in the field. However, I think this book was just so-so. It is a brief overview of the field of informatics. I found it difficult to read - nothing in the book "grabs" me.

I wouldn't recommend it, really. It may be worth a look because it is authored by Shortliffe.

Biomedical Informatics: Computer Applications in Health Care and Biomedicine (Health Informatics).......2007-02-05

This Book is a Bible in Biomedical Informatics.

Developing Bioinformatics Computer Skills

Average customer rating:

horrible
Good introduction, somewhat uneven
Useful only for a reference book
Quite good introduction
A Great Book For Exploring the Bioinformatics Field

Developing Bioinformatics Computer Skills
Cynthia Gibas , and Per Jambeck
Manufacturer: O'Reilly Media, Inc.
ProductGroup: Book
Binding: Paperback

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ASIN: 1565926641

Book Description

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. It's impossible for even the most zealous researcher to stay on top of necessary information in the field without the aid of computer-based tools. Bioinformatics is all about building these tools. Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, and data visualization. Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

Customer Reviews:

horrible.......2004-06-11

This book is the worst I've ever purchased. It has been no help whatsoever. It had a couple examples of PERL programming...big deal.

The 5-star ratings are obvious shills (one reviewer wrote a very long review and has never reviewed anything else)

Good introduction, somewhat uneven.......2003-12-18

This book is a good introduction to Bioinformatics and to what it takes to get started in the field. Some reviewers deride it as too superficial or as too Unix-centric, but I think those are two of its strengths. The authors lay no claim to having written the definitive work on the subject of Bioinformatics, and they freely admit that they come in with a certain bias. If you are serious about Bioinformatics this won't be your last book anyway, but it'll get you started.

That said, I found the material a bit uneven. The authors tend to jump from almost trivial stuff to very complex in a heartbeat, and they sometimes use a concept or command before it can be properly understood One example: Introducing the Unix commands head and tail, then moving on to split and csplit. The introduction to regular expressions as needed by csplit follows a few pages later.

Nevertheless, I plan to use this book as a companion text to my own sequence of computer classes for biologists, and I think it will serve that purpose very well.

Useful only for a reference book.......2003-12-03

We are all well aware that it is impossible to write a book on bioinformatics satisfying all types of readers. That is the reason why we are spending much time on finding a book that we can say "This book is just for me!"

Well, this book is not a self-teaching book by itself. Don't expect that things will become clear to understand after reading this book.

If your expectation is just to taste flavor of bioinformatics and to use it as a reference book, then this book is right for you.

Quite good introduction.......2003-10-03

This is a quite good book for people who have little background in Bioinformatics or Computer Science. I have to say it was pretty good in introducing basic ideas in Bioinformatics, and online resources.

However, I think the authors can do a better job in providing more details in certain areas, for example, in Perl programming, and in sequence alignment. Some parts of the book is so simple that the contents in those parts are not quite useful.

I would recommend this book to people who are new to Bioinformatics. But not to people who have taken one or two
introductory classes.

A Great Book For Exploring the Bioinformatics Field.......2003-04-16

It's no deep secret many Information Technology (IT) professionals today are facing a rough road finding gainful employment. In fact, according to Information Week, nearly 10% of the US IT workforce vanished in the last two months of 2002. More aptly put, some 272,530 American IT professionals in October were unemployed by December. This data is corroborated by the Bureau of Labor Statistics. Where did they all go? Many almost certainly got jobs in other professions and many still could be seeking employment. Employment counselors are encouraging IT professionals to "repurpose" those hard earned tech skills.

Bioinformatics is a ripe apple waiting to be eaten. Bioinformatics simply stated is the computational and analytical methods to biological problems. If this sounds like an open ended explanation, it is. In fact, according to O'Reilly's definitive publication on the topic, "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck, there are several different definitions to Bioinformatics, but suffice to say all revolve around applying IT to the management of biological data.

Chapters one through six delineate the basics including the typical and common software and hardware requirements for Bioinformatics. I will tell you right now if you want to be successful in this fresh field, you must learn Unix. The book points out why. Unix is used extensively in universities and academia where the abundance of software for scientific data analysis is developed. Not to mention in the mid nineties, the only workstations able to visualize protein data structure in real-time were Silicon Graphics and Sun Unix workstations. Linux fans rejoice! As the book points out, "Linux is an excellent platform for developing software, so there's a rich library of tools available for computational biology and research in general."

Sound interesting? At this point you could be overwhelmed and ask yourself, "Where do I start?" Well, you may want to purchase O'Reilly's "Developing Bioinformatics Computer Skills" to see what the fuss is all about, determine whether you have what it takes to succeed in this new field, and most importantly, get an introduction to the software tools for biological applications from the inside out. Bioinformatics is a growing field that will continue for the unforeseeable future.

Book Description

The Handbook of Computational Statistics - Concepts and Methods is divided into 4 parts. It begins with an overview of the field of Computational Statistics, how it emerged as a seperate discipline, how it developed along the development of hard- and software, including a discussion of current active research.

The second part presents several topics in the supporting field of statistical computing. Emphasis is placed on the need for fast and accurate numerical algorithms, and it discusses some of the basic methodologies for transformation, data base handling and graphics treatment.

The third part focuses on statistical methodology. Special attention is given to smoothing, iterative procedures, simulation and visualization of multivariate data.

Finally a set of selected applications like Bioinformatics, Medical Imaging, Finance and Network Intrusion Detection highlight the usefulness of computational statistics.

Data Mining in Bioinformatics (Advanced Information and Knowledge Processing)

Average customer rating:

Data Mining in Bioinformatics (Advanced Information and Knowledge Processing)
J. T. L. Wang
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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Accessories:

ASIN: 1852336714

Book Description

The goal of this book is to help readers understand state-of-the-art techniques in biological data mining and data management and includes topics such as:

- preprocessing tasks such as data cleaning and data integration as applied to biological data

- classification and clustering techniques for microarrays

- comparison of RNA structures based on string properties and energetics

- discovery of the sequence characteristics of different parts of the genome

- mining of haplotypes to find disease markers

- sequencing of events leading to the folding of a protein

- inference of the subcellular location of protein activity

- classification of chemical compounds based on structure

- special purpose metrics and index structures for phylogenetic applications

- a new query language for protein searching based on the shape of proteins

- very fast indexing schemes for sequences and pathways

Aimed at computer scientists, necessary biology is explained.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health)

Average customer rating:

technically accurate but pedagogically flawed
Book contains many chapters to help get you started

Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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Accessories:

ASIN: 0387251464

Book Description

Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R.

This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms:

Curation and delivery of biological metadata for use in statistical modeling and interpretation

Statistical analysis of high-throughput data, including machine learning and visualization

Modeling and visualization of graphs and networks

The developers of the software, who are in many cases leading academic researchers, jointly authored chapters. All methods are illustrated with publicly available data, and a major section of the book is devoted to exposition of fully worked case studies.

This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

Customer Reviews:

technically accurate but pedagogically flawed.......2007-02-09

If you're like me, you came upon this book because you decided to use R for analysis of microarray data, but you're mired in its gory and frustrating details.

Yes, you need a reference book. But not this one, and certainly not this edition. Better documentation can be found elsewhere (dare I say online?).

The code examples given are technically accurate and run as advertised, but they are of the "monkey see, monkey do" variety. They provide little intuition for how to use R for oneself, outside the covers of this text. For example, Chapter 23 discusses linear models for microarray data (using the "limma" package), and several code examples contain the parameter 'adjust = "fdr"'. The reader is never enlightened that this refers to a "false discovery rate" adjustment.

In other cases, example code is simply missing. Chapter 21 covers the Rgraphviz graphing library, with a figure showing the three common graphical layouts -- but no example code for producing these graphs is given (I had to find it outside the book).

For those trying to use R for computational biology, I recommend getting an overview of the R programming language first (Venables and Ripley's book "Modern Applied Statistics with S" is a great text), and only then wading into references such as this one, if at all.

Book contains many chapters to help get you started.......2006-06-30

I purchased this book to learn specific details and look at applications for the functions present in bioconductor. I have had trouble applying some of the chapters to custom data because they are written for specific microarray/data formats. Overall, this book is a good value because it contains examples of how bioconductor can be used to aid in hypothesis testing, but I struggle to apply what I have read to the different types of data I have. The section on Statistical analysis for genomic experiments and the section on gaphs and networks should be the reason you purchase this book. They are very helpful and interesting. The case studies were not very helpful in my opinion.

Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure

Average customer rating:

Good introduction for undergraduates or as reference.
Good intro, but light presentation

Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure
Ingvar Eidhammer
Manufacturer: John Wiley & Sons
ProductGroup: Book
Binding: Hardcover

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ASIN: 0470848391

Book Description

Genomics and bioinformatics play an increasingly important and transformative role in medicine, society and agriculture. The mapping of the human genome has revealed 35,000 or so genes which might code for more than one protein, resulting in 100,000 proteins for the humans alone. Since proteins are attractive targets for developing drugs, efforts are now underway to map sequences and assign functions to many novel proteins. This book takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an algorithmic perspective.

Key features of the book include:

Provides a comprehensive introduction to the analysis of protein sequence and structure analysis.
Takes an algorithmic approach, relying on computational methods rather than theoretical.
Provides an integrated presentation of theory, examples, exercises and applications.
Includes coverage of both protein structure, and sequence, analysis.
Accessible enough for biologists, yet rigorous enough for computer scientists and mathematicians.
Supported by a Web site featuring exercises, solutions, images, and computer programs.

Visit this website for exercises with solutions, computer programs, errata and additional material:

http://www.ii.uib.no/proteinbioinformatics/

Customer Reviews:

Good introduction for undergraduates or as reference........2005-02-24

The book 'Protein Bioinformatics' tries to cover all aspects of proteins, from sequence to structure. This is of course a very wide field and the difficulty of the algorithms involved in this analysis increases from sequence to structure investigations. From the preface of the book one can read, that this is still not enough for the authors because additionally they are trying to write this book for a broad audience, for researchers and students.
After reading this book I think it could be used by undergraduate students in Bioinformatics or related fields or as reference. It does not give deep and clear explanations but rather provides short summaries of articles. The good thing is after reading this book you know of the existence of these articles and can consult them to understand the working mechanism of the algorithms in detail.

There is certainly a lack in good books about proteins and especially about protein structure analysis which can partly filled by this book.

Good intro, but light presentation.......2004-12-02

This book gives good, basic coverage of the concepts important in understanding protein sequence and structure.

There are three major sections in this book: sequence, structure, and the relatinship between the two. The sequence section covers all the basics: dynamic programming for string matching, scoring matrices, trees and classification, and profiles of various sorts. The sequence discussion is a bit shorter, but goes over substructures, similarity searching and scoring, and kinds of structures and domains. The third section is even shorter and unites the two areas: predicting structure from sequence, with a good introduction to threading.

The book's strength is its breadth. It sacrifices depth to get that breadth, though. A few analytic techniques are sketched in the text or presented in psuedocode. Most often, however, a programmer will have a hard time gleaning enough detail from this to implement any of the algorithms described.

The authors aim at readers who already understand the significance of protein structure and who are comfortable with ideas like hydrogen bonding. Lots of programmers will have a hard time understanding why problems are important or what the driving phenomena are. Biologists won't be put off by an excessively mathematical treatment, but won't get a detailed understanding of the algorithms or mathematical foundations either. This book comes close to under-serving both kinds of reader.

This book is good for conceptual understanding of the algorithms, where implementable details don't matter, and gives good coverage to protein-specific issues. It's decidedly for someone who wants more than just the how-to of running BLAST or strucuture analysis tools. I think this book will help most if you want more understanding of what goes on inside the tools, or if you want an easy start to a deep and complex topic. Advanced readers may not like it, though - detail and real understanding just aren't there. I give this one four stars, but I had to round up to four.

//wiredwerid

Average customer rating:

Good book for beginners
Essential Bioinformatics for Life Scientists.
Good Introductory Book for the Student or Researcher

Essential Bioinformatics
Jin Xiong
Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Paperback

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ASIN: 0521600820

Book Description

Essential Bioinformatics is a concise yet comprehensive textbook of bioinformatics, which provides a broad introduction to the entire field. Written specifically for a life science audience, the basics of bioinformatics are explained, followed by discussions of the state-of-the-art computational tools available to solve biological research problems. All key areas of bioinformatics are covered including biological databases, sequence alignment, genes and promoter prediction, molecular phylogenetics, structural bioinformatics, genomics and proteomics. The book emphasizes how computational methods work and compares the strengths and weaknesses of different methods. This balanced yet easily accessible text will be invaluable to students who do not have sophisticated computational backgrounds. Technical details of computational algorithms are explained with a minimum use of mathematical formulae; graphical illustrations are used in their place to aid understanding. The effective synthesis of existing literature as well as in-depth and up-to-date coverage of all key topics in bioinformatics make this an ideal textbook for all bioinformatics courses taken by life science students and for researchers wishing to develop their knowledge of bioinformatics to facilitate their own research.

Customer Reviews:

Good book for beginners.......2007-01-06

The book is written in an easy and concise way. It is a very useful book for beginners. If the reader knows the basics, he needs a more advanced book.

Essential Bioinformatics for Life Scientists........2006-08-20

This compact, economical book (at least for bioinformatics) covers the usual basics of bioinformatics (Databases, alignments, phylogeny, gene prediction, structure prediction, transcriptome analysis, proteome analysis) but is unique in its approach. Recognizing most life scientists need to understand basic bioinformatis, but lack extensive mathematical modeling, computer command line or programming experience Jin Xiong has written a text that describes common bioinformatics tools to perform each of the above studies. Using diagrams and figures in lieu of complex mathematical formulas, Xiong explains how the tools work. Each task in bioinformatics has many comoputing tools - the strengths and weaknesses of each, and guidance in critical evaluation of the output are explained. There are capstone problems at the end of the book that are extremely helpful in enhancing understanding of the tools. The text is easy to read.

In the preface. Xiong describes that the book is a compilation of notes from several years of teaching bioinformatics. Therefore they presumably have been revised based on student review. However, this is a first edition - there are a lot of typos, misspellings, and some figures have errors. Hopefully these will be fixed for this is a fine introductory book.

The text is for those new to bioinformatics. Unlike many bioinformatics books, there is no coverage of programming (PERL or SQL for ex,). Therefore, those who are already skilled in this area will likely not find this particularly useful. Familiarity with the UNIX operating system will help readers do the problems.

Good Introductory Book for the Student or Researcher.......2006-04-17

The author gives a pretty good summary of this book in the preface: 'I needed a text that was comprehensive enough to cover all major aspects in the field [bioinformatics], technical enough for a college level course, and sufficiently up to date to include most current algorithms while at the same time being logical and easy to understand... The book is aimed at graduate and undergraduate students in biology, or any practicing molecular biologise, who has no background in computer algorithms but wishes to understand the fundamental principles of bioinformatics and use this knowledge to tackle his or her own research problems.'

The book was developed over several years, first being issued in the form of Xerox'd lecture notes to test the acceptability by students. Subsequently the notes were revised, expanded and now assembled into book form.

There are now a large number of standard software packages designed for use in the bioinformatics area. Many of these are discussed. However, it is not intended for this book to be a manual on these packages. Instead it discusses the software from a standpoint of when and where specific packages can be used to solve your problem of the moment.

As a field, bioinformatics is expanding and developing at an extremely rapid rate. This book is up to date as of early 2006.

Genomic Perl: From Bioinformatics Basics to Working Code

Average customer rating:

Not a good perl programming book period!
Develops effective genomic toolkits for UNIX, Windows & Mac

Genomic Perl: From Bioinformatics Basics to Working Code
Rex A. Dwyer
Manufacturer: Cambridge University Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 052180177X

Book Description

In this introduction to computational molecular biology, Rex Dwyer explains many basic computational problems and gives concise, working programs to solve them in the Perl programming language. With minimal prerequisites, he covers the biological background for each problem, develops a model for the solution, and then introduces the Perl concepts needed to implement the solution. The chapters discuss pairwise and multiple sequence alignment, fast database searches for homologous sequences, protein motif identification, genome rearrangement, physical mapping, phylogeny reconstruction, satellite identification, sequence assembly, gene finding, and RNA secondary structure. Concrete examples and a step-by-step approach enable readers to grasp the computational and statistical methods.

Customer Reviews:

Not a good perl programming book period!.......2003-12-18

This books tries to combine and explain both bioinformatics and perl programming yet fails miserably at both. Though I have taken a class on learning perl this code is difficult to read and poorly explained. The bioinformatics is useless because the examples are simply stupid. For example instead of using free energy to determine RNA folding the author uses hydrogen bonding which is completely irrelavent or predicting species by using %gc or %at content between two organsims also useless. If you are looking for bioinformatics programming tips this book will not help you.
Variables are introduced that are not explained and the program is written in the most condensed possible way making it difficult to read and leaving you wading through each line. I am thankful I have taken programming perl and bioinformatics or this book would be of zero value. If I could I would give this book a -5 stars. Check it out at a library before you BUY!!!!!!! Even if perl.com reviews the book favorably the biology is at best completely WRONG!!! Buy O'Riely's advanced bioinformatics.

Develops effective genomic toolkits for UNIX, Windows & Mac.......2003-03-23

Combines intuitive derivations of most key algorithms, thoughtful use of key references to illustrate solutions of main problems with a detailed example, and develop well documented, carefully programmed,perl toolkit. The 65 routines on the CD in UNIX, Windows, and Mac formats perform most of the essential maipulations of GenBank sequences. I only miss Hidden Markov Model routines.

Average customer rating:

An introduction, but very little computing
Comprehensive Introduction to the filed of Bioinformatics
Solid introduction to this field of biology
A must read!
Bioinformatics for now and the future

Bioinformatics Computing
Bryan Bergeron
Manufacturer: Prentice Hall PTR
ProductGroup: Book
Binding: Paperback

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ASIN: 0131008250

Customer Reviews:

An introduction, but very little computing.......2005-10-19

While the book does an adequate job of explaining the purpose to bioinformatics, it wasn't very technical. I had it as a text for a graduate course, and many of us whose background was in computing found a need to find outside references. It's not a bad book for some high level coverage, but it never seems to get to the meat of a subject in much depth or detail. It is more for someone interested in existing tools and databases, but not for a developer who wants to get started in this field. If you're in that category you may want to look at some other text books such as "Bioinformatics in the Post Genomic Era" by Augen or "Fundamental Concepts of Bioinformatics" by Krane and Raymer. Another potential source is Lesk's "Introduction to Bioinformatics" (a bit older, but it does talk about specific computational skills).

Comprehensive Introduction to the filed of Bioinformatics.......2004-12-08

Bergeron wrote this book such that if you have a computer background, you can relate to the topic at hand, and if you have a biology background, you can pick up the material quickly. He uses one to teach the other, and does so rather comprehensively. Major topics and areas of interests in bioinformatics are covered, such as:
* Databases
* Networks and the Internet
* Bioinformatics search engines
* Data mining techniques
* Statistics
* Pattern Matching
* Simulation techniques and modeling

Any of these topics deserve a volume of books dedicated to them, but the author gives the readers enough information that can be useful in determining where to go next. Even though the topics are mostly computing related, the author takes a great care at talking about these topics in the context of Bioinformatics. He even lists the specific applications of each topic at the beginning of each chapter to aid the reader in relating to the topic at hand. For example, after reading the chapter on modeling and simulation, you would know that modeling is used to determine the efficacy of drugs and to determine drug side effects during the drug discovery process.

Databases are probably one of the most important and well known tools in Bioinformatics. The enormous amount of data available for analysis requires large and fast databases. In fact, the amount of data in bioinformatics doubles every eighteen months, so databases and database design is an integral part of bioinformatics computing. In addition to the vast amount of raw data (sequence data and protein data for example) that is stores in databases, the analysis such as pattern matching, simulation and visualization of data requires constant access to databases. The author talks about what are know as primary databases, databases that are used to store raw data, and other value added databases, the one's that store analyzed and/or verified data. One thing that reader gets out databases is the realization of what the data life cycle is in the bioinformatics world, and how it affects all the application areas of bioinformatics.

The databases around the world are either somehow integrated together ease the task of data discovery and data mining. Due to the vast amount of information available, various data mining techniques have been developed over the years to assist in finding the data that a researcher is looking for. Tasks such as data enrichment, missing value analysis for sequence data, data characterization and data distribution analysis mark some of the tasks that data mining techniques needs to accomplish. A number of data mining techniques such as hidden Markov Models, Decision Trees, Neural Networks and Genetic Algorithms are talked about and the pro's and con's of each one is discusses in detail. A bioinformatician needs to be at least aware of the various data mining techniques and should have an overview how they work and why they work in general.

After the data has been discovered, a method of visualization that can get the point across, per se, needs to be used. Visualization and simulation techniques are talked about to show the reader what a bioinformatician needs to do with the information found. There are a number of graphical tools available out there, some free and some not, that are used heavily in this business to aid the understanding of the vast amount of information that is available. Various modeling techniques are being used today to aid with the drug discovery process and figuring out the side effect of newly developed drugs. I would say that this area of bioinformatics will see the most growth in the coming years, and the author, Bryan Bergeron, does a great job discussing this topic.

Statistics is another technique used heavily in bioinformatics computing. Even though most of the statistical tools, Matlab and many others, have been used for a number of years, one must know the theory and reason behind using numerous statistical techniques in Bioinformatics. These techniques are integrated into bioinformatics search engines and the software applications for modeling and simulations, but one still needs to know how they work. Bioinformatics is a new field of study, and not by any means been perfected, so there are still a number research track and advancements that are still untapped, thus making the theory behind how some of the available tools work very important in this field.

Bryn Bergeron in Bioinformatics Computing gives the necessary background for anyone interested in the field of bioinformatics. After reading this book, a reader can get a good idea of which area s/he wants to pursue further. The topics are broken into logical units that can aid the reader in realizing what specific field of bioinformatics is more interesting than others.

Even if you don't decide to pickup one of many advanced books in this topic, you should know about an industry that is growing rapidly, and Bergeron's book can aid you to do just that.

Solid introduction to this field of biology.......2004-06-30

Ok, I'm not done yet with the book but after two chapters, I could already share with people something: this book is a solid introduction to the field of biocomputing. It cover many aspects in 10 differents chapters (database, data mining, collaboration, read the table of contents).

The autor is enthousiast about his field of research but he doesn't miss an important thing: criticism!! At the end of chapter, you have a small dose of concerns he have about biocomputing. Where we could make mystakes, what we should do?

I'm about to choose if I want to do my master degree in this discipline and this book is great to introduce me with a large perspective to this branch of science.

If you working in this industry, this book might be a little bit boring but even for me who work 5 years with computers networks and databases, both chapters about those technologies learned me something interesting so... I'm quite happy about my decision to acquire this book.

A must read!.......2003-01-10

This book was a pleasant surprise. It's one of the few books on bioinformatics that I've read that doesn't assume the reader has a PhD in biochemistry or mathematics. It's a gentle but thorough introduction to many of the problems faced by life scientists who are trying to get a handle on this thing called bioinformatics. I've been working in the life sciences for years, and this is the first book I've read that explains how I can make use of the various search engines, genomic analysis tools, and the dozens of genomics databases worldwide in my day-to-day life.

I especially appreciate the author's frank analysis of the state of the art at the end of each chapter. He seems to put a balanced spin on the field, pointing out the vast potential of bioinformatics computing in practical medicine and materials synthesis, while grounding the reader in current political and economic realities that are limiting many aspects of the field.

I consider it a must read.

Bioinformatics for now and the future.......2002-12-19

Dr, Beregeron ofers a sensible yet visionary exposition of the field. For me, the future direction of this field is most compelling. It is a primer that can be challenging to the most sophisticated afficionado, also.

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