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on April 15, 2003
It's no deep secret many Information Technology (IT) professionals today are facing a rough road finding gainful employment. In fact, according to Information Week, nearly 10% of the US IT workforce vanished in the last two months of 2002. More aptly put, some 272,530 American IT professionals in October were unemployed by December. This data is corroborated by the Bureau of Labor Statistics. Where did they all go? Many almost certainly got jobs in other professions and many still could be seeking employment. Employment counselors are encouraging IT professionals to "repurpose" those hard earned tech skills.
Bioinformatics is a ripe apple waiting to be eaten. Bioinformatics simply stated is the computational and analytical methods to biological problems. If this sounds like an open ended explanation, it is. In fact, according to O'Reilly's definitive publication on the topic, "Developing Bioinformatics Computer Skills" by Cynthia Gibas and Per Jambeck, there are several different definitions to Bioinformatics, but suffice to say all revolve around applying IT to the management of biological data.
Chapters one through six delineate the basics including the typical and common software and hardware requirements for Bioinformatics. I will tell you right now if you want to be successful in this fresh field, you must learn Unix. The book points out why. Unix is used extensively in universities and academia where the abundance of software for scientific data analysis is developed. Not to mention in the mid nineties, the only workstations able to visualize protein data structure in real-time were Silicon Graphics and Sun Unix workstations. Linux fans rejoice! As the book points out, "Linux is an excellent platform for developing software, so there's a rich library of tools available for computational biology and research in general."
Sound interesting? At this point you could be overwhelmed and ask yourself, "Where do I start?" Well, you may want to purchase O'Reilly's "Developing Bioinformatics Computer Skills" to see what the fuss is all about, determine whether you have what it takes to succeed in this new field, and most importantly, get an introduction to the software tools for biological applications from the inside out. Bioinformatics is a growing field that will continue for the unforeseeable future.
If you're serious about turning around that stagnant IT career and expanding your education, you may find yourself in the same enviable position you were three years ago...needed and wanted! But don't let me mislead you. As the book points out, Bioinformatics is first and foremost a biological science.
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on December 17, 2003
This book is a good introduction to Bioinformatics and to what it takes to get started in the field. Some reviewers deride it as too superficial or as too Unix-centric, but I think those are two of its strengths. The authors lay no claim to having written the definitive work on the subject of Bioinformatics, and they freely admit that they come in with a certain bias. If you are serious about Bioinformatics this won't be your last book anyway, but it'll get you started.
That said, I found the material a bit uneven. The authors tend to jump from almost trivial stuff to very complex in a heartbeat, and they sometimes use a concept or command before it can be properly understood One example: Introducing the Unix commands head and tail, then moving on to split and csplit. The introduction to regular expressions as needed by csplit follows a few pages later.
Nevertheless, I plan to use this book as a companion text to my own sequence of computer classes for biologists, and I think it will serve that purpose very well.
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on December 26, 2002
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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on November 16, 2001
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.
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on August 29, 2001
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 ... ...
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on August 12, 2001
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....
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on July 4, 2001
This is one more book written by new and enthusiastic bioinformaticians and published by a prominent publisher of computer books. The content is trivial and superficial at best. Moreover it is potentially confusing and misleading for newcomers. The authors play with names of computer programs and databases but cannot even correctly identify the reasons why those programs have been written in the first place. I believe the focus on Unix and perl is misguided as well. It does not serve any educational purpose except for demonstrating that the authors know about Unix and perl (which they certainly do.) There exist fuller and better treatments of these topics and there are fuller and better introductory texts of bioinformatics. The only good think I have noticed about the book is its low price. But the book is not worth buying even though. A bioinformatics newcomer will be better off buying Durbin and co-authors "Biological Sequence Analysis" and reading search results for keywords *bioinformatics*, *computational biology*, and *genomics* on the Internet.
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on July 3, 2001
This is an excellent book. The authors know their audience. I work at a biotech company in Silicon Valley and use this book everyday. It is written in plain English and covers all the skills needed for the bioinformatics environment that I work in. Section II covers the Bioinformatics workstation as well as the tools needed to have a functional system up and running. Bioinformatics Computer Skills is the best and only book on this subject. Whenever a new field in science emerges there needs to be one book that puts it all together for people to get an understanding of what that field is all about, what you need to know to be good in that field (pg 14), what tools you need, what matters and this book does that. This book is not a bible of bioinformatics, but a blueprint of how such systems work and what skills are need as well as where one should seek out further knowledge. O'reilly press, Cynthia Gibas and Per Jambeck have done an excellent job with this first book and I hope there will be other books to follow. They have begun to define this new field. The other reviews (on this web site) that criticize this book do not understand the purpose of the book. It is to shed light on a field that is new and undefined. People who may not have known what bioinformatics is, or what skills one needs to have in order to enter this new field, now have a refrence point. The problem with many scientist today is they really believe they are more important then the people they are trying to save with their great discoveries. Everything having to do with science does not have to be written in the same context of the Journal Of Science etc... Regular people have a right to understand what is being written and how it will affect them in the future. The attacks of ("too superficial, misleading" etc..) are unfair. Those critics should write their own book so that the rest of us can be more informed. This is a great book on the subject.
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on June 18, 2001
While I agree that this book is very pleasant to read I really miss substantial information. The authors try to cover a large number of tools and techniques and even the UNIX operating system and Perl in one volume. Unfortunately everything stays very much on the surface. There are plenty of excellent introductory books on UNIX - why not refer to those and talk about algorithms instead? This leads us to the main weakness of the book (in my opinion): Lots of things are touched but none of them are really explained or illustrated by actual code or algorithms.
Of cause a book on applying bioinformatics tools in every day lab-life would also be very usefull. But most tools are presented on extremly limited space so all the reader gets is a rough idea what the tool is for. Many popular and/or important packages are not described or even mentioned at all: e.g. there is just a tiny reference to GCG and EMBOSS is non-existant in the book.
If you are in biology and would like to hear about some of the tools available on the net for free this book is for you: The book will get you curious about many things and give you some keywords to feed the search engine with along with a bunch of URLs.
If you want to learn about computational biology and its foundations and methods you will be disappointed.
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on June 18, 2001
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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