Perl Programming for Biologists 1st Edition

by D. Curtis Jamison (Author)

6 customer reviews

ISBN-13: 978-0471430599

ISBN-10: 9780471430599

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Working on the assumption that the reader has no formal training inprogramming, Perl Programming for Biologists demonstrateshow Perl is used to solve biological problems. Each chapter openswith a set of learning objectives, provides numerous reviewquestions and self-study exercises, and concludes with a bulletedsummary of key points. The author incorporates numerous real-lifeexamples throughout the text. Upon completing the book, readers areable to quickly perform such tasks as correcting recurring errorsin spreadsheets, scanning a Fasta sequence for every occurrence ofan EcoRI site, adapting other writers' scripts to one's ownpurposes, and most important, writing reusable and maintainablescripts that spare the rote repetition of code.

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Editorial Reviews

Review

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

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

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

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

"...not be surprised to see [it] finding a space on thebookshelves 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, thePerl programming language is the most widely used scriptinglanguage in bioinformatics. Working on the assumption that thereader has never had any formal training in programming, and usingexamples geared toward real problems faced by biologists, PerlProgramming for Biologists serves as an accessible,introductory reference for teaching Perl programming.

Curtis Jamison’s innovative text introduces basi celements of computer science and software engineering in anabbreviated format, building toward a bioinformatics users’sguide for Perl. Each chapter opens with a set of learningobjectives, provides numerous review questions and self-studyexercises, and concludes with a bulleted summary of key points.Jamison incorporates numerous real-life examples throughout toillustrate how Perl is used to solve biological problems, offeringvaluable code fragments that the current practitioner can recycleinto his or her own program. Divided into sections on basic,intermediate, and advanced-level Perl, the book includes chapterson:

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

Upon completing the book, readers will be able to quicklyperform 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 thatwill spare the rote repetition of code. Upper-level undergraduates,graduate students, biologists, and other life scientists will findPerl Programming for Biologists to be an essentialresource.

See all Editorial Reviews

Product details

Paperback: 208 pages
Publisher: Wiley-Liss; 1 edition (July 14, 2003)
Language: English
ISBN-10: 9780471430599
ISBN-13: 978-0471430599
ASIN: 0471430595
Product Dimensions: 7 x 0.4 x 10 inches
Shipping Weight: 13.6 ounces (View shipping rates and policies)
Average Customer Review: 6 customer reviews
Amazon Best Sellers Rank: #2,089,547 in Books (See Top 100 in Books)
- #148 in Books > Computers & Technology > Programming > Languages & Tools > Perl
- #364 in Books > Textbooks > Medicine & Health Sciences > Medicine > Basic Sciences > Immunology
- #437 in Books > Computers & Technology > Computer Science > Bioinformatics

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Perl Bioinformatics Developer

October 29, 2009

Format: PaperbackVerified Purchase

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

Comment

Not nearly as good as Learning/Intermediate Perl or Tisdall's books

June 17, 2006

Format: 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!

8 people found this helpful

Comment

Intelligently written, but flawed

December 31, 2008

Format: Paperback

Jamison's narrative is well thought out; he is a good teacher, provided you are attentive enough to initialize the variables, arrays and hashes in the required order without him reminding you. But he also needs a good editor. It is a shame his book is marred with so many typos.

For instance, on p. 47, there are several typos. A couple are text typos, "when" instead of "we", which throw off the meaning of the text. More serious, however, is the statement after the print command, ""$gene is on both maps\n";", when the code above really refers to three hashes, which contain three map keys. Unexplained is the fact that the RH map refers to the mouse radiation hybrid map, maintained by the Broad Institute. Still, for all its faults, it's the only game in town for biologists who are just cutting their teeth on Perl.

It is essential to use a good Perl-friendly text editor/debugger with this book. Be savvy about using all the examples he mentions in passing, because the end-of-chapter exercises are inadequate to learning the language, and some of the programming challenges are mystifying. A major fault is that no answers are given.

Another thing to note: Jamison may be an excellent software engineer, but he is no biologist. At one point, he confuses transcription and translation. Rely on your own biological knowledge.

Comment

Much better than Tisdall's book

March 26, 2006

Format: 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.

6 people found this helpful

Comment

Perl for biologists

July 6, 2009

Format: Paperback

It is a followable step-by-step introduction for biologists in perl programming. It is pity that the solutions of exercises are missing from the book.

Comment

A customer

Highly Recommended

April 15, 2004

Format: Paperback

"...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)

One person found this helpful

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