Perl Programming for Biologists [Paperback]

D. Curtis Jamison (Author)

Book Description

Publication Date: July 14, 2003 | ISBN-10: 0471430595 | ISBN-13: 978-0471430599 | Edition: 1

Working on the assumption that the reader has no formal training in programming, Perl Programming for Biologists demonstrates how Perl is used to solve biological problems. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. The author incorporates numerous real-life examples throughout the text. Upon completing the book, readers are able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers' scripts to one's own purposes, and most important, writing reusableand maintainable scripts that spare the rote repetition of code.

Editorial Reviews

Review

"This well written book illustrates PERL with examples…Those with less or no programming skills should read this book before attempting the practice of bioinformatics ideas." (Journal of Statistical Computation & Simulation, January 2005)

"…the book is useful to biologists who already use languages like C+ or Visual Basic and want to learn Perl." (Biomolecular Engineering, November 2004)

“…written in a pleasant chatty style with obvious enthusiasm for the topic” (Robotica, Vol. 22, 2004)

“...unique and I highly recommend it as a first book on programming for biology-oriented professionals interested in  using perl...excellent for self-study...can also be a great resource as classroom material...” (Clinical Chemistry, Vol. 50, No. 2, 2004)

"...not be surprised to see [it] finding a space on the bookshelves in many biological laboratories in the near future." (Briefings in Bioinformatics, Vol 5(1), March 2004)

From the Back Cover

With a loose structure that allows for fast and easy coding, the Perl programming language is the most widely used scripting language in bioinformatics. Working on the assumption that the reader has never had any formal training in programming, and using examples geared toward real problems faced by biologists, Perl Programming for Biologists serves as an accessible, introductory reference for teaching Perl programming.

Curtis Jamison’s innovative text introduces basi c elements of computer science and software engineering in an abbreviated format, building toward a bioinformatics users’s guide for Perl. Each chapter opens with a set of learning objectives, provides numerous review questions and self-study exercises, and concludes with a bulleted summary of key points. Jamison incorporates numerous real-life examples throughout to illustrate how Perl is used to solve biological problems, offering valuable code fragments that the current practitioner can recycle into his or her own program. Divided into sections on basic, intermediate, and advanced-level Perl, the book includes chapters on:

• Variables and data types
• Arrays and hashes
• Control structures
• Subroutines
• String manipulation
• Object-oriented programming

Upon completing the book, readers will be able to quickly perform such tasks as correcting recurring errors in spreadsheets, scanning a Fasta sequence for every occurrence of an EcoRI site, adapting other writers’ scripts to one’s own purposes, and most important, writing reusable and maintainable scripts that will spare the rote repetition of code. Upper-level undergraduates, graduate students, biologists, and other life scientists will find Perl Programming for Biologists to be an essential resource.

Product Details

• Paperback: 208 pages
• Publisher: Wiley-Liss; 1 edition (July 14, 2003)
• Language: English
• ISBN-10: 0471430595
• ISBN-13: 978-0471430599
• Product Dimensions: 7 x 0.4 x 10 inches
• Shipping Weight: 13.6 ounces (View shipping rates and policies)
• Average Customer Review: 4.2 out of 5 stars  See all reviews (6 customer reviews)
• Amazon Best Sellers Rank: #1,465,396 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

8 of 8 people found the following review helpful:

3.0 out of 5 stars Not nearly as good as Learning/Intermediate Perl or Tisdall's books, June 17, 2006

By 

C. J. Fields (Champaign, IL USA) - See all my reviews

This review is from: Perl Programming for Biologists (Paperback)

Although James Tisdall's Perl books (Beginning/Mastering Perl for Bioinformatics) could be a little scattered, I found that they offered more for the biologist learning Perl than this one; you could almost buy both those books for the price of this one! This book seems structured more along the lines of the (superior) Learning Perl and Intermediate Perl by Schwartz et al, with a few biological references thrown in as examples. Some of the most important aspects of biological sequence analysis were glossed over fairly quickly if at all. I found it somewhat amazing that file format parsing, restriction enzyme analysis, sequence conversion, transcription-translation, program output parsing, and other fundamental topics were either covered very briefly in passing or not covered at all. Disappointing!

I believe one might find this book was a great read first time out (it is well written), but that once they progressed to other texts (Learning Perl, Intermediate Perl, Programming Perl), they would rarely, if ever, refer back to this one. That's not good for a $50 book. I can't see myself using it in the future when I have the Camel and Llama covering my back, along with Tisdall's texts. Basically a lot of sugar coating without much substance.

Oh, and there's a major mistake in the Object-Oriented Programming section, one which really breaks your programs. In short : -> != =>

My advice: spend your money on those texts and use your imagination on what Perl can accomplish for you as a biologist. If you are an advanced Perl programmer and biologist, at least check out Tisdall's books and wait for the long-rumored BioPerl book. I would give it 3 stars for the writing but the price doesn't justify it, sorry. The Amazon review system won't let me change the rating though, so you lucked out this time!

6 of 8 people found the following review helpful:

5.0 out of 5 stars Much better than Tisdall's book, March 26, 2006

By 

bmaverick (Europe) - See all my reviews

This review is from: Perl Programming for Biologists (Paperback)

I have taught Perl from Tisdall's "Beginning Perl fro Bioinformatics", and was frankly frustrated by the seemingly random order of presentation of topics. The students in the class felt the same. This book, however, does it right: it is a clear, pedagogic introduction to Perl programming with applications in bioinformatics. Highly recommended for biologists who never programmed before.

4.0 out of 5 stars Perl Bioinformatics Developer, October 29, 2009

By 

Rachel (NC) - See all my reviews

Amazon Verified Purchase

This review is from: Perl Programming for Biologists (Paperback)

Excellent book for the beginner programmer who is interested in Bioinformatics. However, an additional Perl reference book with examples is needed.