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on May 12, 2001
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.
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on September 18, 2001
I have been examining my career and looking around to see what else interests me. I am a unix and perl hacker. I never took a whole lot of math or bio in college, and worried that a text like this would be as difficult to understand as _Biological Sequence Analysis_ (which I purchased at the same time) was. To put it more clearly, in order to begin understanding _Biological Sequence Analysis_, I am going to have to study Statistics and Discrete Mathematics. Coming from a programming background, I already understand matrix-based math, and I understand string algorithms and algorithms in general.
This book allowed me to take a look at what Bioinformatics is all about, and see if I am interested.
I can also say, as a perl programmer and general unix guy, that the unix and perl taught in this book are quite good, and concise while still being comprehensive.
This is definitely one of the better OReilly books I have read lately.
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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 July 27, 2001
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.
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on July 15, 2001
This is a good place to start for the computer person who wants to get into Bioinformatics. There are overviews of the many biological issues involved, and URLs aplenty to get more information and download software. However, the emphasis on Unix as the platform of choice is becoming less and less relevant. Very few bioinformatics programs are available only on Unix, and many are available only on Windows and not Unix. Researchers who already know Windows and/or have access to departmental support for their Windows systems are ill-advised to get into the morass of setting up and supporting a Linux or other Unix machine.
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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 October 2, 2003
This is a quite good book for people who have little background in Bioinformatics or Computer Science. I have to say it was pretty good in introducing basic ideas in Bioinformatics, and online resources.
However, I think the authors can do a better job in providing more details in certain areas, for example, in Perl programming, and in sequence alignment. Some parts of the book is so simple that the contents in those parts are not quite useful.
I would recommend this book to people who are new to Bioinformatics. But not to people who have taken one or two
introductory classes.
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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 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 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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