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Bioinformatics, Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice (Life Sciences) Paperback – 23 Jun 2004


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Product details

  • Paperback: 508 pages
  • Publisher: John Wiley & Sons; 1 edition (23 Jun. 2004)
  • Language: English
  • ISBN-10: 047085331X
  • ISBN-13: 978-0470853313
  • Product Dimensions: 19.2 x 3.1 x 22.3 cm
  • Average Customer Review: 4.0 out of 5 stars  See all reviews (1 customer review)
  • Amazon Bestsellers Rank: 1,439,885 in Books (See Top 100 in Books)
  • See Complete Table of Contents

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Product Description

Review

"...such a helpful and relevant book...I am following [an] MSc distance learning course in Bioinformatics...I would have been at a complete loss without your book!" (Susan Tzotzos MSc, PhD, Vienna, Austria)

"...such a helpful and relevant book...I would have been at a complete loss without your book!" (Susan Tzotzos MSc, PhD, Vienna, Austria)

From the Author

We (the authors, Michael Moorhouse and Paul Barry) wrote Bioinformatics Biocomputing and Perl to be a comprehensive, modern and, above all, realistic introduction to the world of Bioinformatics. One author is a Computer Scientist by training; the other has a background in Biochemistry.
Together, we draw on our experience as practising professionals to cover a wide range of Biological and Informatics concepts, practice and ‘traps to be avoided’.

Our aim was not only to transfer a set of skills or programming tricks but also a mindset for how to think as Bioinformaticians. Hence, we included a collection of ‘Maxims’ which offer general guidance on key concepts - imparting the skills useful in judging the approaches to apply and those to avoid.

We wrote this book for three broad categories of readers:

(1) students who are embarking on a formal taught Bioinformatics course and require a good, all-round course text;

(2) Bioscientists whose background is in a non-computationally based research field but who need to use Bioinformatics tools;

and (3) those whose background is in Informatics or Computer Science who need to know something about (computational) Biology.

The book helps readers address two questions often asked by newcomers to the field:

(1) ‘What is possible?’,

and (2) ‘How do I use it to solve my particular problem?’
These are the classic ‘What’ and ‘How’ questions.

Our book also outlines the science underlying the major applications and techniques which Bioinformaticians use and also explains ‘Why’ a particular method is used.

Throughout the book we use well maintained and ‘free to use’ WWW ‘portals’ in preference to propriety software. This, in our opinion, lowers the financial and legal barriers that could otherwise be a deterrent to the reader/researcher.

The use of pre-formed WWW interfaces will only take the reader so far (though in many cases far enough), after which some type of automation of mundane processing operations is required.
To address this need, a large part of the book covers the learning and application of programming skills (we use the Perl programming language in all examples).

Readers are assumed to have little or no prior programming experience. We then progress through more complex topics, such as the design and creation of relational databases for storing information and finally to the automation of sequence manipulation and sequence similarity searching using BioPerl modules. The ability to produce an analysis ‘pipeline’ is an excellent skill set for budding Bioinformaticians.

To help readers transfer between ‘manual intensive’ analyses (using paste & click WWW interfaces) and the more automated pipeline solutions, wherever possible, we describe how to accomplish the same task using both approaches, comparing and contrasting them.

As authors, we have made every effort to write the book in a light and engaging style injecting humour whenever possible. We have also included references to more detailed sources of information (especially for the algorithms of the tools used) and other on-line sources we use and trust. The associated website provides additional material for instructors/readers.


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Most Helpful Customer Reviews

Format: Paperback
Excellent book for learning Perl for bioinformatics. The introduction to Perl is not quite as good as in this one:Beginning Perl for Bioinformatics but it goes a bit further and introduces database and web programming and even some graphics with Perl.
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Most Helpful Customer Reviews on Amazon.com (beta)

Amazon.com: 2 reviews
Bioinformatics Biocomputing and Perl is a reasonable tutorial to Perl. 23 July 2009
By Heinz D. Falenski - Published on Amazon.com
Format: Paperback
I like this book as a tutorial. I am teaching myself Perl with this book. The chapter examples are good practice and the exercises at the end of the chapters are reasonable. I am about 1/4 through the book, and so far am enjoying the learning process.
6 of 10 people found the following review helpful
Worst bioinformatics book I have read 11 April 2005
By Robert M. Rutledge - Published on Amazon.com
Format: Paperback
I have been programming and working as a biologist for the past 6 years, but I have had only a small exposure to Perl. When I read this book description, I was excited since it indicated that Perl would be taught from the ground up and from the bioinformatics perspective. While the perspective is as advertised, this is still a terrible book. Unless you know something about Perl (and programming in general) before you begin, you will be lost. The authors organize some material well, but often relevant items are completely missing. They almost completely abandon Windows users when it would only take a few more sentences to address the difference between Unix and Windows. The end of chapter exercises are poorly thought out and do not provide sufficient practice for the novice. Frequently I found myself referring to "Beginning Perl for Bioinformatics" to make sense of the Moorhouse and Barry book.
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