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Developing Bioinformatics Computer Skills 1st Edition

36 customer reviews
ISBN-13: 978-1565926646
ISBN-10: 1565926641
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Editorial Reviews


'... the authors have produced a book which really is a 'must read' for the newcomer to bioinformatics'. European Bioinformatics Institute

About the Author

Cynthia Gibas is an assistant professor of biology at Virginia Tech, in Blacksburg, Virginia. She's been a computational biologist since before computational biology was cool, and is currently learning to drive her spankin' new home-built Linux cluster. Her research interests include the structure and evolution of genomes, the properties of protein surfaces and interfaces, and prediction of protein structure. She teaches introductory courses in bioinformatics methods for biologists and is looking forward to her next real vacation, sometime in 2006.

Per Jambeck is a Ph.D. student in the bioengineering department at the University of California, San Diego. He has worked on computational biology problems since 1994, concentrating on machine learning applications in understanding multidimensional biological data. Per smiles wistfully at the mention of free time, but he manages to host shows at community and student-run radio stations anyway.


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Product Details

  • Paperback: 448 pages
  • Publisher: O'Reilly Media; 1 edition (May 3, 2001)
  • Language: English
  • ISBN-10: 1565926641
  • ISBN-13: 978-1565926646
  • Product Dimensions: 7 x 1 x 9.2 inches
  • Shipping Weight: 1.7 pounds (View shipping rates and policies)
  • Average Customer Review: 3.4 out of 5 stars  See all reviews (36 customer reviews)
  • Amazon Best Sellers Rank: #905,281 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

56 of 63 people found the following review helpful By Thomas J. Dougherty on May 8, 2001
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!!
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28 of 30 people found the following review helpful By Steven Marks on December 26, 2002
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.
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45 of 53 people found the following review helpful By A Customer on June 18, 2001
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.
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34 of 40 people found the following review helpful By LOODY on November 16, 2001
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.Read more ›
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