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UNIX and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits) Paperback – August 27, 2012


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Product Details

  • Paperback: 425 pages
  • Publisher: Cambridge University Press; 1 edition (August 27, 2012)
  • Language: English
  • ISBN-10: 0521169828
  • ISBN-13: 978-0521169820
  • Product Dimensions: 0.9 x 6.7 x 9.4 inches
  • Shipping Weight: 1.9 pounds (View shipping rates and policies)
  • Average Customer Review: 4.5 out of 5 stars  See all reviews (13 customer reviews)
  • Amazon Best Sellers Rank: #310,586 in Books (See Top 100 in Books)

Editorial Reviews

Review

"My chief regret about this book is that it wasn't available last year, when I was working with a group of life-science researchers. I could have persuaded them all to purchase a copy, thereby saving myself a great deal of the time I spent assisting with their data analysis tasks!"
G. K. Jenkins, Computing Reviews

"With their book on UNIX and Perl, scientists Bradnam and Korf have come to the aid of laboratory or field researchers floundering helplessly under overwhelming gigabytes of unstructured raw data. With a characteristic charming and chipper cheerfulness, the book quickly guides the readers through finding/installing a UNIX system of any variety... Highly recommended."
F.E.J. Linton, emeritus, Wesleyan University, Choice Magazine

"Unix and Perl to the Rescue! is a book I highly recommend for all those students, post-docs, and academics who are scared of programming but can benefit immensely from the power of Unix and scripting languages. It's time to come out of your shell."
Dr MD Sharma, Genetics Society News

"Bradnam and Korf provide an intuitive and enjoyable volume that shows how to make the terminal window useful to scientists looking to build automation into data queries using UNIX and Perl scripting.
With a thorough treatment of more than just the basics, this book fills a missing niche in the Perl and UNIX world with a focus on data processing. The authors have crafted a brilliant treatment of pattern searching with regular expressions to help the reader unleash some of the most powerful parts of the Perl programming language. For scientists looking to parse data files and extract the essential pieces this is a thorough and well explained complete with sprinkles of humor and biologically motivated examples."
Jason Stajich, University of California, Riverside

Book Description

Written in a fun, accessible style, this step-by-step guide teaches non-programmers the key aspects of Unix and Perl. No prior experience is required and new concepts are introduced using code examples for readers to try themselves. Essential reading for those who want to work more effectively with large data sets.

More About the Author

As a single cell zygote, Keith Bradnam was lucky enough to be endowed with a genome that was replete with genes for curiosity, geekiness, and the ability to make bad puns. However, it would take several rounds of cell division, some blastocyst differentiation, and a complicated delivery before he was able to show any of these abilities to the world at large.

After leaving school, Keith resisted pressure from his elder sibling to "get a job in a bank" and instead found his way to university in order to study ecology. It was here that he realized that he lacked the desire to become a career ecologist and so he transitioned from the sort of science that involved standing around on windy hillsides, to the sort of science that involved sitting down and working at a computer. Keith instantly took to the 'sitting down' part and after a period of several years, finally started making some headway on the 'working at a computer' part.

After several years of sitting down in front of several different computers Keith has since found himself in a position where he was able to write a book that aims to teach the non-programmer how to program ('Unix and Perl to the RESCUE'). He hopes that others will benefit from this text by becoming equally proficient at sitting down in front of computers.

Customer Reviews

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Although I haven't read it, but this book R in a Nutshell looks to be a great place to start.
Harkius
The authors' wry wit permeates every page and, miraculously, they are actually funny and use their humor to drive their teaching.
Jerry Saperstein
This book is a pretty good reference for both UNIX and Perl if you really just want the basics.
David Bradshaw

Most Helpful Customer Reviews

5 of 5 people found the following review helpful By Jerry Saperstein HALL OF FAMETOP 500 REVIEWERVINE VOICE on January 14, 2013
Format: Paperback Vine Customer Review of Free Product ( What's this? )
I normally take a dim view of authors of technical books who try to be humorists. On the whole, I think they fail, and there are a number of, for example, Photoshop book authors who I won't bother with because they think they're comedians - and they're not.

So here we have Keith Bradnam and Ira Korf expounding on two of the driest subjects known to humankind, Unix and Perl, and they actually are witty, engaging, entertaining and, best of all, educational. (Of course, if you are into Unix and Perl, you know they're really kind of exciting: but this book isn't written for us. It's for total beginners.)

This book does not pretend to be anything more than what the authors declare it to be: a basic (very basic, in fact) introduction to Unix and Perl for "the life sciences (and other data-rich pursuits)".

They say they will teach you what 20 Unix commands are and do - and that is precisely what they do. If you know Unix or Linux, you know they are very rich Operating Systems and have hundreds of functions and operators and thousands of variants. But the 20 Bradnam and Korf tutor the reader in are all you need to get going in Unix and Linux.

Everything is in bite-sized chunks which bear a faint resemblance to chapters. The authors' wry wit permeates every page and, miraculously, they are actually funny and use their humor to drive their teaching. Well done!

The Perl section will not please those who have already passed through the fires of learning Perl. There are almost as many books on Perl programming as there are about Napoleon - and this volume does not try to compete with the classics of the Perl language.
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2 of 2 people found the following review helpful By William Meisel on December 5, 2012
Format: Paperback Vine Customer Review of Free Product ( What's this? )
This book claims that it will introduce you to Unix and Perl in about 300 pages.

I know nothing about either, so I followed the book's directions, and they worked. I downloaded the recommended CYGWIN program

(NOTE: When you download CYGWIN, you have to include the "nano" editor and the "perl" programming language; these do not download automatically on the install, at least they didn't for me. Google how to do this; there are multiple explanations online.),

installed it, and, lo and behold, I was running a Unix environment. All of the commands worked the way the book said they would. I practiced creating files, renaming them, deleting them, etc.

Then, it was on to Perl programming. Perl is a forgiving programming language, and I did understand the commands I was learning via the programs I was told to write.

But, I do agree with the reviewer who said the book doesn't go as far as it claims it will. I thought I would be learning how to do some statistical programming in Perl, and that really doesn't happen.

But, I now know infinitely more than I did when I started. I am sort of amazed that the book contains enough well organized information to get you started off the bat. And, the authors have a dry sense of humor, particularly noticeable in their footnotes.

Verdict? Recommended for beginners who know nothing about Unix and Perl. Not recommended for people with prior knowledge.
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1 of 1 people found the following review helpful By nainalerom on June 20, 2013
Format: Paperback
I've tried and failed to teach myself programming a number of times; only with this book was I able to stick with it. Most of the books and resources I've tried had problems with pacing-- either they advanced too quickly or hand-held so much that I got bored. This book has the ideal amount of hand-holding so that I was able to progress sufficiently fast without much frustration. The wittiness also helped to keep me interested.
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1 of 1 people found the following review helpful By I Teach Typing on December 1, 2012
Format: Paperback Vine Customer Review of Free Product ( What's this? )
Because I spend 90% of my time at work doing biostatistics (SAS and R) on a windows box I got this hoping it would give me a good summary of how to use the Mac terminal. I am very happy with it. The writing is clear and to the point.

The book features dozens of little "chapters" (typically 2-3 pages each) that begin with an explanation of a task, then code is presented and then the code is explained. The chapters are largely self contained but you will want to work through all 100 pages on UNIX because the the later sections assume you have build a couple directories from earlier chapters. Don't panic about the number of pages because the writing makes them very easy to follow and work through. Most chapters have brief exercises to reinforce the topics. These are excellent.

All the commands you need to create, move, and run files are covered. Specifically: alias, cat, cd, chmod, cp, date, echo, file, history, less, ls, man, mkdir, mv, nano, rm, rmdir, source, touch, and which are all explained very well. With this set of tools you can manipulate your files but the authors do not explain how to find them! So, you will need to leave the console to find that work you did a couple weeks ago. Other that that weakness there is nothing wrong with the UNIX section. The authors introduce nano as a text editor, which is adequate for the book and they mention vim and Emacs as more full featured tools. Each editor needs a book of its own. So, it would have been great if the authors provided a recommended reading list for those.

The PERL section is long and nicely full featured. PERL offers a HUGE set of tools and this book covers the critical parts which you need to manipulate text files like a professional.
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