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Developing Bioinformatics Computer Skills [Paperback]

Cynthia Gibas , Per Jambeck
3.3 out of 5 stars  See all reviews (30 customer reviews)
Price: CDN$ 43.95 & FREE Shipping. Details
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Book Description

April 2001 1600330290 978-1600330292 1

Bioinformatics--the application of computational and analytical methods to biological problems--is a rapidly evolving scientific discipline. Genome sequencing projects are producing vast amounts of biological data for many different organisms, and, increasingly, storing these data in public databases. Such biological databases are growing exponentially, along with the biological literature. 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. Bioinformatics is all about building these tools.Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, 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, and data visualization.Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

--This text refers to an alternate Paperback edition.

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An invaluable aid, this book has much to offer the novice bioinformaticist and should be strongly considered by those who are new to the field. -- Darryl Nishamura, Biotech Software & Internet report, Vol 2 No 5, 2001

Overall, I HIGHLY recommend this book to Computer Scientists, Biologists, and even people already involved in Bioinformatics. -- Brandon King, Cerritos Linux Users Group, April 2002 --This text refers to an alternate Paperback edition.

From the Publisher

Developing Bioinformatics Computer Skills will help biologists, researchers, and students develop a structured approach to biological data and the computer tools they'll need to analyze it. 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 data analysis software to individual research needs. --This text refers to an alternate Paperback edition.

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Customer Reviews

Most helpful customer reviews
2 of 2 people found the following review helpful
5.0 out of 5 stars A Great Book For Exploring the Bioinformatics Field 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!
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4.0 out of 5 stars Good introduction, somewhat uneven Dec 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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4.0 out of 5 stars Rating depends on what you purpose is Dec 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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5.0 out of 5 stars Very Useful, Excellent Value Nov. 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. Read more ›
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Most recent customer reviews
1.0 out of 5 stars horrible
This book is the worst I've ever purchased. It has been no help whatsoever. It had a couple examples of PERL programming...big deal. Read more
Published on June 10 2004
3.0 out of 5 stars Useful only for a reference book
We are all well aware that it is impossible to write a book on bioinformatics satisfying all types of readers. Read more
Published on Dec 2 2003 by Seungwoo Hwang
4.0 out of 5 stars Quite good introduction
This is a quite good book for people who have little background in Bioinformatics or Computer Science. Read more
Published on Oct. 2 2003 by doudou1229
3.0 out of 5 stars Brief coverage of many topics
No indepth analysis in the topics presented. But this book could be really useful for those people who would like a quick review of many topics overnight for an interview or so. Read more
Published on June 30 2002 by B. John
2.0 out of 5 stars Very simplistic book.
The book is at a level of a magazine article overview, just longer. With some editing it probably could have made it into a magazine.
Published on May 18 2002 by Hisashi T. Fujinaka
1.0 out of 5 stars AWFUL! SAVE YOUR MONEY
Published on April 29 2002
1.0 out of 5 stars THE WRITERS SHOULD BE SHOT!
Published on April 29 2002
4.0 out of 5 stars Useful for individuals migrating from structured systems
Most biological scientists are comfortable in Windows-based environments (Mac or Wintel) and can migrate from one to the other. They are also happy on the web. Read more
Published on Sept. 27 2001 by Peter J. Neame
5.0 out of 5 stars Totally acessible to Computer geeks looking into Biology.
I have been examining my career and looking around to see what else interests me. I am a unix and perl hacker. Read more
Published on Sept. 18 2001 by Jane Avriette
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