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Developing Bioinformatics Computer Skills Paperback – 3 May 2001

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Product details

  • Paperback: 448 pages
  • Publisher: O'Reilly Media; 1 edition (3 May 2001)
  • Language: English
  • ISBN-10: 1565926641
  • ISBN-13: 978-1565926646
  • Product Dimensions: 17.8 x 2.4 x 23.3 cm
  • Average Customer Review: 3.0 out of 5 stars  See all reviews (2 customer reviews)
  • Amazon Bestsellers Rank: 1,016,389 in Books (See Top 100 in Books)
  • See Complete Table of Contents

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Product Description


An invaluable aid, this book has much to offer the novice bioinformaticist and should be strongly considered by those who are new to the field. -- Darryl Nishamura, Biotech Software & Internet report, Vol 2 No 5, 2001

Overall, I HIGHLY recommend this book to Computer Scientists, Biologists, and even people already involved in Bioinformatics. -- Brandon King, Cerritos Linux Users Group, April 2002

Well written, properly organized, and a worthwhile investment for those interested in the field from a purely academic sense or applied. -- Bryan William Jones, Applelust.com, August 2002

From the Publisher

Developing Bioinformatics Computer Skills will help biologists, researchers, and students develop a structured approach to biological data and the computer tools they'll need to analyze it. 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, data visualization, and tips for tailoring data analysis software to individual research needs.

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18 of 18 people found the following review helpful By Amazon Customer on 23 July 2002
Format: Paperback
I found this book to be little more than a very basic introduction to bioinformatics. If you want a book to tell you what can be done then it useful, but it goes into very little detail. The ground it attempts to cover is far too large, it runs through an introduction to databases, LINUX and PERL. If you are interested in these you will need to buy a proper book for each subject.
The book would have been a lot better if they had run through some examples of what you can do, showing you what can be done along the way.
The authors should also acknowledge that most biologists only use Windows PCs and Macs rather than just concentrate on LINUX. It should have also mentioned that OS-X is based upon UNIX and lots of the LINUX things can be done on that OS too.
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17 of 17 people found the following review helpful By A Customer on 5 Jun. 2001
Format: Paperback
Firstly this book is entirely Unix/Linux based, which may cut out many casual laboratory users. This is par for the course in bioinformatics but not strictly necessary. It has a few chapters to get you started on Linux set-up, and a very, very light grounding in molecular biology. The brief explanation of Perl programming, and databases is hardly sufficient other than as an eye-opener. It is a probable time saver as a good current reference to the available free bioinformatics web-sites and tools.
Possibly the authors are trying to cater to people who either know very little molecular biology (computing students), or very little computing (biologists). Perhaps there are two books yet to be written: one for each group.
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Most Helpful Customer Reviews on Amazon.com (beta)

Amazon.com: 35 reviews
56 of 63 people found the following review helpful
New to the field? This is your book! 9 May 2001
By Thomas J. Dougherty - Published on Amazon.com
Format: Paperback Verified Purchase
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!!
28 of 30 people found the following review helpful
Rating depends on what you purpose is 27 Dec. 2002
By Steven Marks - Published on Amazon.com
Format: Paperback Verified Purchase
My purpose in ordering this book is to see if I can make the transision into this new field. From that perspective, I would rank this book 5 stars. It really satisfied my need to understand what is required to make the leap into this area.
This book is a real broad swatch of all the different skills that one needs to know to assume a basic competency in bioinformatics. On page 14, they actually list core essential skills and "nice to have skills". molecular biology, Unix, Perl, algorithms, major biology software packages are all on the essential core list. The auuthors really take the viewpoint on here is how to set your computer up (on a budget!), web sites to go to and so on. Not knowing Unix and not having it currently on my computer made the two Unix/Linux chapters academic.
The book is great from the perspective of seeing the big picture. Where it falls down is in the depth department. "Predicting Protein Structure and Function from Sequence" is covered in 35 pages! It is impossible to understand this subject in 35 pages - yet the authors conveyed a sense of the subject and how it fits into a larger picture.
If you are familiar with the subject and want in depth treatment, this is not the book.
if you want an introduction "big picture" book this could serve your needs.
45 of 53 people found the following review helpful
Useful but can be misleading 18 Jun. 2001
By A Customer - Published on Amazon.com
Format: Paperback
Bioinformatics as we know it today is a conglomerate of quasi-scientific activity, software development and data management. Of course the field is still in making and the concepts of "scientific activity", "software development" and "data management" are neither well defined nor universally agreed upon by their practitioners.
Gibas and Jambeck attempted to expose an impression about bioinformatics to the readers who want to be employed as bioinformaticians. I am not sure the authors' impression about the skills of bioinformaticians is universally correct. As a bioinformatics manager myself I like computer literate biologists collaborating with professional programmers. I would gladly train seasoned programmers according to Gibas and Jambeck book. However I think biologists would be better prepared for bioinformatics if they wrote some computer programs themselves. It does not matter that routine programs for computing in molecular biology already exist. If a self-learning student would write a primitive version of the program she is going to use, it would prepare her to understand what the program is capable of doing.
I like the book as a potential text for good programmers who want to get a job in bioinformatics. However I think the book will mislead all readers who want to become computer-literate biologists. Unix and Perl are really not important in a long range (operating systems and scripting languages will evolve and change anyway.) Understanding principles of programming and computing does matter infinitely more for these readers even if they are unaware of this reality.
34 of 40 people found the following review helpful
Very Useful, Excellent Value 17 Nov. 2001
By LOODY - Published on Amazon.com
Format: Paperback
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.
11 of 11 people found the following review helpful
Useful only for a reference book 2 Dec. 2003
By Seungwoo Hwang - Published on Amazon.com
Format: Paperback
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.
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