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Your research has generated gigabytes of data and now you need to analyse it. You hate using spreadsheets but it is all you know, so what else can you do? This book will transform how you work with large and complex data sets, teaching you powerful programming tools for slicing and dicing data to suit your needs. Written in a fun and accessible style, this step-by-step guide will inspire and inform non-programmers about the essential aspects of Unix and Perl. It shows how, with just a little programming knowledge, you can write programs that could save you hours, or even days. No prior experience is required and new concepts are introduced using numerous code examples that you can try out for yourself. Going beyond the basics, the authors touch upon many broader topics that will help those new to programming, including debugging and how to write in a good programming style.
- Sales Rank: #412919 in eBooks
- Published on: 2012-07-19
- Released on: 2013-08-20
- Format: Kindle eBook
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
About the Author
Keith Bradnam is a project scientist in the Genome Center at the University of California, Davis. He has extensive experience working with model organism databases and spent four years as a project leader at WormBase, helping to develop this important bioinformatics resource.
Ian Korf is an Associate Professor in Molecular and Cellular Biology at the University of California, Davis. His research seeks to understand structure and function in genomic DNA. He has developed new tools for gene prediction, co-authored the only book devoted to BLAST and helped in the development of BioPerl.
Most helpful customer reviews
6 of 6 people found the following review helpful.
Witty, wry, elegant and excellent
By Jerry Saperstein
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.
Rather it presumes the reader knows literally nothing about Perl and is motivated by the desire to escape enslavement by spreadsheet as they try to analyze mountains of data.
The authors set out to teach basic data analysis using Perl: they are not showing you how to parse a genome. They demonstrate the very basics of using Perl and make no secret that you are on your own in tackling larger projects.
This is a book for non-programmers, for neophytes, a stress-fee introduction into the scary world of programming. And it does the job well. The authors' wry wit goes along way into making Unix and Perl (or at least the very basics of the two) easily accessible. Mssrs. Bradnam and Korf have done an excellent job here.
Jerry
4 of 4 people found the following review helpful.
Good Up to a Point
By William M.
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.
1 of 1 people found the following review helpful.
Ideal for Mac users (and great for other flavors of UNIX)
By I Teach Typing
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.
In addition to the oversight on finding files the other weakness of the book is the lack of links on how to use other tools. These days knowledge of R and/or Python are a must. Detailed coverage of those are beyond the scope of the book but it would have been great to see long sections on integrating those tools or at least references on where to start. Despite the lack of external links I love this book for the quality of the writing and an excellent index.
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