Cynthia GibasDeveloping Bioinformatics Computer Skills: An Introduction to Software Tools for Biological Applications

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.

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.

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!!

I'm still starting out in the field of bioinformatics and two chapters into this book gives the impression that this book is worth the money I paid for it. I know it's 12 years old (by copyright) but I can use this material as a good starting point. Text is clearly written with just enough detail for the reader to know what to dig into more. Thanks CG and PJ!

Es un libro indispensable para empezar en la bioinformática. Explicaciones muy claras, lenguaje ameno y directo. Sin duda un indispensable.

Und selbst fuer die ist es didaktisch schlecht organisiert. Ich habe den Kauf dieses Buchs selbst ~ 2000 sehr schnell bereut - heutzutage ist es sicher noch dazu veraltet.

Good

分子生物学の実験をしているけどコンピューターにはあまり興味が無い、という人にはよいマニュアルになるであろう。　　あくまで実践的でリナックスのインストールの仕方や簡単なコマンドまで載っている。他に、役立つウェブサイトや、ソフトの使い方、特徴などの説明が多い。読み物としてはまったくつまらないもので、コンピューターの前で格闘しながらマニュアル的に使うのがよいであろう。ncbiのホームページの使い方など、正直分子生物学の実験をしている人には常識となっているようなことが多い。だが、背景となっている理論抜きに実際に使うときの注意点を述べるなど、数学やコンピューターが嫌いな生物学者には適切なアドバイスが期待できる。

絵が少ない、紹介している内容がやや古いなどの欠点はあるものの、普段使っているツールやその原型が、どのような理屈のもとに解析を行なっているのかについて、比較的平易に説明されている。UNIXベースの解析について述べられているが、そこを読み飛ばしても読む価値はある一冊だと思う。