Developing Bioinformatics Computer Skills (Paperback)

by Cynthia Gibas (Author), Per Jambeck (Author)

Editorial Reviews

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

Product Description
Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. As a result of advances in gene sequencing, biological databases are growing exponentially. 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. Written in a clear, engaging style, Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology, 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, data visualization, and tips for tailoring existing data analysis software to individual research needs. Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze it.

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Product Details

• Paperback: 442 pages
• Publisher: O'Reilly Media, Inc.; 1 edition (April 15, 2001)
• Language: English
• ISBN-10: 1565926641
• ISBN-13: 978-1565926646
• Product Dimensions: 9 x 7 x 1 inches
• Shipping Weight: 1.6 pounds (View shipping rates and policies)
• Average Customer Review: 3.3 out of 5 stars See all reviews (29 customer reviews)
• Amazon.com Sales Rank: #254,702 in Books (See Bestsellers in Books)

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  #56 in	Books > Science > Biological Sciences > Bioinformatics
  #99 in	Books > Computers & Internet > Databases > Data Mining

Customer Reviews

Most Helpful Customer Reviews

54 of 63 people found the following review helpful:

5.0 out of 5 stars New to the field? This is your book!, May 8, 2001

By	Thomas J. Dougherty (Ayer, Ma. USA) - See all my reviews (REAL NAME)

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!!

38 of 44 people found the following review helpful:

3.0 out of 5 stars Useful but can be misleading, June 18, 2001

By A Customer

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.

25 of 28 people found the following review helpful:

4.0 out of 5 stars Rating depends on what you purpose is, December 26, 2002

By	Steven Marks "Prog Harpo" (Petaluma, CA United States) - See all my reviews (REAL NAME)

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.