Developing Bioinformatics Computer Skills

by Per Jambeck and Cynthia Gibas

Book Overview

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...

• Format: Paperback
• Language: English
• ISBN: 1565926641
• ISBN13: 9781565926646
• Release Date: May 2001
• Publisher: O'Reilly Media
• Length: 448 Pages
• Weight: 1.65 lbs.
• Dimensions: 0.9" x 6.7" x 9.4"

Customer Reviews

A Great Book For Exploring the Bioinformatics Field

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.If you're serious about turning around that stagnant IT career and expanding your education, you may find yourself in the same enviable position you were three years ago...needed and wanted! But don't let me mislead you. As the book points out, Bioinformatics is first and foremost a biological science.

Very Useful, Excellent Value

I've seen quite a few reviews on bioinformatics books, and I think it's important to mention that this book is NOT for those people who really know their way around bioinformatics. It's NOT for people who have a pretty good idea WHY they're doing bioinformatics. These people usually know what they want to do, whether it's molecular phylogenetics, or developing search algorithm software....... whatever. They have a better feel for the field (which is a diverse one, by the way), and have high, sometimes arrogant, expectations of any book that deals with bioinformatics because they are always on the lookout for specific answers to their specific questions. They want books like Pierre Baldi's or the (in)famous Durbin textbook on sequence analysis algorithms, books which for the most part, are pretty damn inaccessible at first and downright scary to look at to people like myself who want to familiarise with bioinformatics and see what all the hype is about. Those are NOT texts to check out if you are totally new to all this. Now for people who don't really know anything significant about the field and, who for all intensive purposes, are generally CLUELESS about what it deals with in particular, like myself before I bought this book, it's worth buying this text to get an excellent intro on what bioinformatics is all about, and the kind of biological problems it addresses. The text is neither a programming bible, nor a manual on pairwise alignment techniques or RNA structure/function prediction. What it does do well is to give you a very good feel for what this field is about, as well as the confidence to start hitting the 'real' bioinformatics books that are aplenty out there. It will help you decide whether you are willing to do computational biology and really interested in it. It's the only book I know that does that, that can serve as a proper primer on bioinformatics. I suspect Gibas and Jambeck's book can also serve as a decent reference guide for the more seasoned bioinformaticians out there. It's a handy book and covers a little of everything, and I recommend reading it along with Attwood and Parry-Smith's introductory text, maybe following it up with Kanehisa's Post-Genome Informatics (2000). In any case, finally somebody came up with a book explaining the field that's actually from Planet Earth. It's very accessible, reasonably priced, and for that I am grateful to the authors.

Excellent BooK

This is an excellent book. The authors know their audience. I work at a biotech company in Silicon Valley and use this book everyday. It is written in plain English and covers all the skills needed for the bioinformatics environment that I work in. Section II covers the Bioinformatics workstation as well as the tools needed to have a functional system up and running. Bioinformatics Computer Skills is the best and only book on this subject. Whenever a new field in science emerges there needs to be one book that puts it all together for people to get an understanding of what that field is all about, what you need to know to be good in that field (pg 14), what tools you need, what matters and this book does that. This book is not a bible of bioinformatics, but a blueprint of how such systems work and what skills are need as well as where one should seek out further knowledge. O'reilly press, Cynthia Gibas and Per Jambeck have done an excellent job with this first book and I hope there will be other books to follow. They have begun to define this new field. The other reviews (on this web site) that criticize this book do not understand the purpose of the book. It is to shed light on a field that is new and undefined. People who may not have known what bioinformatics is, or what skills one needs to have in order to enter this new field, now have a refrence point. The problem with many scientist today is they really believe they are more important then the people they are trying to save with their great discoveries. Everything having to do with science does not have to be written in the same context of the Journal Of Science etc... Regular people have a right to understand what is being written and how it will affect them in the future. The attacks of ("too superficial, misleading" etc..) are unfair. Those critics should write their own book so that the rest of us can be more informed. This is a great book on the subject.

HIGHLY recommended for those entering bioinformatics

This book is an excellent introduction to bioinformatics for a person entering the field or deciding to enter. The author's introduction to UNIX in the second part of the book is better written than most books devoted completely to UNIX. The discussion would be even better if some words were said about the new MAC OS X operating system. With its UNIX flavor, and the ease of use of a MAC, it will no doubt make its presence known in bioinformatics. Publication timing may have prevented a discussion of it however since OS X has just been released in the last few months. A non-mathematical but very informative overview of sequence analysis is given in part three of the book. A mathematician who might be deciding to enter this exciting field will the discussion good preparation for further technical reading in computational biology and sequence algorithms. The authors even include a discussion of mathematical physiology and give URLs and a list of companies attempting to create user applications in this area of computational biology. This is a further example of the book's merits, as it shows what areas in bioinformatics need more application tools to be developed. Even the rather short chapter on PERL programming still suffices to create an appreciation of the power of PERL in bioinformatics. What takes sometimes many weeks of development time and many lines of code can frequently be done in a matter of hours and a few lines of code in PERL. The book ends with an introduction to databases and data mining, and, even though the discussion is short, the authors explain the concepts well. Data mining in this field, as in others, is a subject that will take on further importance in the near future. In addition, the book is just plain fun to read. A large set of references is given along with many URLs throughout the book. I visited all of these Websites and with their content and the book at hand....I had a BLAST.

New to the field? This is your book!

As a research scientist at a major pharmaceutical company, I became involved with microbial genomics four years ago. I have become familar with bioinformatics by talking and working with colleagues in my company, but on more than one occasion in the past, I found myself baffled by some detail or aspect of this new and rapidly evolving field. This book, Developing Bioinformatics Computer Skills is an outstanding introduction for the biologist attempting to become broadly familar with the basics of the bioinformatics field. The authors begin with a highly informative introduction to the Unix operating system, and then proceed to describe many of the basic tools for sequence analysis, database searching, multiple sequence alignments and phylogenetic analysis. This section has an outstanding non-mathematical explanation of scoring matrices and dynamic programming for alignments. This is followed by chapters on protein structure and predicting protein structure and function from sequence. They also discuss tools for sequence assembly, annotating genomes, proteomics and biochemical pathway databases. There is an excellent chapter on analysis of large data sets using Perl scripts. The book closes with chapters on building relational databases and data visualization. The material is well written and clearly presented, and can serve as an excellent springboard to more advanced texts in the field. I highly recommend it to those who are beginning to use bioinformatics, as well as to those more experienced who would like a ready reference with the basics all under one cover. Well worth the modest price!!