Customer Reviews

Developing Bioinformatics Computer Skills

5 star:		(11)
4 star:		(4)
3 star:		(6)
2 star:		(3)
1 star:		(6)

 

 

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!!

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.

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.

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.

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.

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.

I'd been looking forward to getting ahold of this book for awhile but am somewhat disappointed. To echo what some of the above have said, _Developing Bioinformatics Computer Skills_ is at once too detailed for the absolute beginner yet insufficiently detailed for someone who wants to take the next steps.

Beyond elaborating on the "necessary" skills, it might have been better to point readers to the wealth of existing books (many also published by O'Reilly). However, I strongly disagree with those who think Unix and Perl *are not* needed skills. If bioinformatics folk are to be more than data entry workers using black box programs, understanding the mechanics is a good thing. So Gibas and Jambeck are right in pointing out these topic.

I am torn whether I think this is a must-have book for the lab library. I think Rashidi and Buehler's _Bioinformatics Basics_ is better as a compendium of existing resources and for giving a flavor of what one can do.

It is a cardinal sin to tack an inaccurate title to a piece scientific writing, but that's what happened here. The title "Bioinformatics Computer Skills" seems to imply that the book will teach *skills.* It would be better titled "Bioinformatics Computer Resources," and it does a pretty good job of trying to describe the areas where IT and biology overlap, although that is a vast undertaking for a slim book. And this book does not replace any standard reference in either field.

For the programmer, this book will steer them towards major resources for bioinformatics. For the biologist, there are thumbnail descriptions of important programming tools, minus the IT handwaving argle-bargle.

But in no sense does it build "skills." There's not enough biology here to benefit a programmer, and there's not enough IT to benefit a biologist. This book will not prepare either a biolist or programmer to do even simple tasks.

I too was eagerly looking forward to this book , and by the time I finished it, I asked myself , "Isn't there more?". I would say this book tries to be too many things for too many people. If you are a biologist and have little/no experience with programming, especially in a Unix/Linux environment this would offer a fairly concise but maybe too brief intro to bioinformatics. THere are some nice chapters on how to setup a Linux system and learning some basic commands , but there are other O'reilly books to help with that (Learning the unix operating system comes to mind). On the other hand, for a computer programmer/IT person, if you were sharp and could stand to wade through some of the references the author suggests for learning more about molecular biology, you could probably apply what you learn in this book pretty well. Perhaps they should have named this Intro to Bioinformatics skills. However, there are some glaring errors in the book, most notably in the intro chapters to molecular biology, esp. the diagrams for how DNA is converted into RNA and is in turn translated into a polypeptide. I hope the authors have corrected this by the next printing. ... ... ... There is a vast and thriving unix community developing tools that are as good or better than any Windows based tools out there, plus they're free ! Most of the bioinformatics firms I know of use Linux/Unix , so that ... ...

Not a bad introductory book. But did not cater to all my expectations. The style of writing is impressive in a sense, not obscured by lot of scientific jargon. However many of important concepts were glossed over and made to appear over simplistic. Readers may be misled by wrong title. Other than introductory chapters on unix/perl hacks there isn'tmuch in computer skills to be gained. Biologist who want to learn about introductory bioinformatics may be satisfied but definitely I think one needs more "introductory computer skills" than what is stated in the book and of course deeper understanding of algorithms/bioinformatics methods! Some of the works were not even properly referenced. For example the chapter on protein modeling metions "allergen modeling" as a recent acheivement without any reference to scientific journal. She must have included some interesting biological case studies towards the end of the chapter, that may have helped beginners to appreciate the knowledge gained thorough the book. Any way good place to begin! Nothing is better than something....