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Practical Computing for Biologists [Paperback]

Steven Haddock , Casey Dunn
4.7 out of 5 stars  See all reviews (35 customer reviews)

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Book Description

November 5, 2010 0878933913 978-0878933914 First

Increasingly, scientists find themselves facing exponentially larger data sets and analyses without suitable tools to deal with them. Many biologists end up using spreadsheet programs for most of their data-processing tasks and spend hours clicking around or copying and pasting, and then repeating the process for other data files.

Practical Computing for Biologists shows you how to use many freely available computing tools to work more powerfully and effectively. The book was born out of the authors' own experience in developing tools for their research and helping other biologists with their computational problems. Although many of the techniques are relevant to molecular bioinformatics, the motivation for the book is much broader, focusing on topics and techniques that are applicable to a range of scientific endeavors. Twenty-two chapters organized into six parts address these topics and more:

  • Searching with regular expressions
  • The Unix command line
  • Python programming and debugging
  • Creating and editing graphics
  • Databases
  • Performing analyses on remote servers
  • Working with electronics

While most of the concepts and examples apply to any operating system, the main narrative focuses on Mac OS X. Where there are differences for Windows and Linux users, parallel instructions are provided in the margin and in an appendix. The book is designed to be used as a self-guided resource for researchers, a companion book in a course, or as a primary textbook. Practical Computing for Biologists will free you from the most frustrating and time-consuming aspects of data processing so you can focus on the pleasures of scientific inquiry.


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Editorial Reviews

Review

In this age of informatics and genomics, the ability to mine and manipulate data is an essential skill for graduate students in ecology and evolutionary biology. Practical Computing for Biologists provides a much-needed guide to using Unix and Python to assemble and analyze large data sets. I'm looking forward to using this book as a text to accompany our quantitative bootcamp for new graduate students. --Michael Alfaro, University of California, Los Angeles, USA


For a committed point-and-clicker like myself, Practical Computing for Biologists is a most valuable book. It offers just the right introduction for those less computer savvy biologists who would like to enhance and streamline their ability to handle, process, and analyze data. This book has already made me more confident in confronting the large amounts of data that face me in day-to-day research. --Ronald Jenner, The Natural History Museum, London, UK


The book covers a wide range of subjects that truly justifies the title of ‘practical computing.’ In addition to the usual programming-related topics, it also includes a thorough introduction to the programming environment, approaches to combining different programs together, a description of the basic text manipulation tools such as regular expressions, and even an introduction to dealing with digital art and images. As such the book is great value for the money, being at least three books in one. --Olga G. Troyanskaya, Cell


My copy of Practical Computing for Biologists arrived last week, and I've been very impressed. It is a well-written, well-paced guide to basic computing skills for scientists and engineers of all stripes (not just biologists). … And it's beautifully produced: full-color printing and great graphical design make this book a joy to read. If I ever do turn Software Carpentry into a book, I might skip the topics PCB covers and just tell people to go and buy it. --Greg Wilson, software-carpentry.org --Ronald Jenner, The Natural History Museum, London, UK


For a committed point-and-clicker like myself, Practical Computing for Biologists is a most valuable book. It offers just the right introduction for those less computer savvy biologists who would like to enhance and streamline their ability to handle, process, and analyze data. This book has already made me more confident in confronting the large amounts of data that face me in day-to-day research. --Ronald Jenner, The Natural History Museum, London, UK

About the Author

STEVEN HADDOCK is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at the University of California, Santa Cruz, USA, studying bioluminescence and biodiversity of gelatinous zooplankton. He came with a programming background to his graduate studies in Marine Biology, where he quickly realized the advantages that computing skills offered and felt compelled to help foster these abilities in others. He has developed many utilities and devices for research, including instruments to monitor bioluminescence from fireflies, a freezer monitoring system, a web-based conference registration database, and a PCR calculator for smartphones. In addition to teaching invertebrate zoology and writing a booklet to teach the technique of blue-water scuba diving, he has given tutorials in computing to students and administrators. His interest in education extends to his Bioluminescence Web Page (lifesci.ucsb.edu/~biolum/) and the Jellywatch.org citizen-science website (jellywatch.org).

CASEY DUNN, an Assistant Professor at Brown University, USA, does research that has a large computational component but always in conjunction with work in the field and lab. His first interest in computers stemmed from building electronics, and he further developed his computational skills working in Silicon Valley while an undergraduate. As his data sets grew larger and larger during grad school and his postdoc, he found himself reaching back to his computer background more often. In the course of his own research and helping other biologists with their computational challenges, he became concerned about the mismatch between training opportunities and the real day-to-day computational problems biologists face. In addition to teaching invertebrate biology, evolution, and development, his educational activities include the websites siphonophores.org and creaturecast.org. Dr. Dunn is the recipient of the National Science Foundation's 2011 Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by NSF.


Product Details

  • Paperback: 538 pages
  • Publisher: Sinauer Associates, Inc.; First edition (November 5, 2010)
  • Language: English
  • ISBN-10: 0878933913
  • ISBN-13: 978-0878933914
  • Product Dimensions: 9.1 x 7.6 x 1 inches
  • Shipping Weight: 2.5 pounds (View shipping rates and policies)
  • Average Customer Review: 4.7 out of 5 stars  See all reviews (35 customer reviews)
  • Amazon Best Sellers Rank: #74,785 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews
20 of 20 people found the following review helpful
5.0 out of 5 stars It's about time! January 19, 2011
By Ryan
Format:Paperback
More than any other book I've read, Practical Computing for Biologists delivers exactly what the title promises. I've tried several tutorials for both Python and R over the last few years, and even just the first 2 chapters of PCFB were more helpful than any of that (I'm now on chapter 9 and the book continues to please). I think it fills a huge need for biologists who want to be able to deal with data sets that are quickly growing in size, but who don't necessarily want to or have the time to become computer scientists themselves. I couldn't recommend this book more highly for any scientist who has experienced frustration dealing with large data sets (like high-throughput DNA sequences), or just wants to cut down time spent on repetitive computer tasks. I'm sure I'll be referencing it often, and for a long time.
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9 of 9 people found the following review helpful
5.0 out of 5 stars Extremely Valuable June 6, 2011
Format:Paperback|Verified Purchase
This is one of the most valuable and useful books that I have read in a very long time. This book is also extremely timely - given how reliant on computers the analysis of biological data is becoming. The authors clearly and concisely walk the reader through a broad range of extremely useful computational processes that will increase the efficiency of how any biologist stores, analyzes, and/or manipulates their data. Most of my colleagues know that they could be using their computers, and analyzing their data, more efficiently; but many do not know where to start, or are intimidated by the vast "computer programming" section of their local bookstore. This book acts as an excellent intermediate step - providing clear (and biologically relevant) examples of how a few key skills can immediately alter daily tasks. The authors then point the reader in the necessary direction for those who wish to learn more. Briefly, some topics that I found particularly helpful were: (1) the use of regular expressions to quickly modify text files (who hasn't suffered through manually doing this to convert the output from one program to the input of another?); (2) the fairly extensive introduction to Python programming and some of its uses; (3) the friendly introduction to MySQL (which can otherwise be very intimidating); and (4) the information on vector art. I also appreciate that the authors focused on Open Source programs; which makes all of the examples/programs available to anyone. I would highly recommend this book to all biologists - full stop. I also want to thank the authors for writing it - it has been a huge help to me, and couldn't have come at a better time.
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6 of 7 people found the following review helpful
5.0 out of 5 stars Great Book for beginner to low intermediate November 20, 2011
Format:Paperback|Verified Purchase
I am a PhD student at a major state university in the US. I was familiar with some high level command line programming, specifically R, but wanted to take the next step with my data analysis and computer skills. I found this book to be very helpful immediately. It provides many generalized solution for repetitive tasks that save an enormous amount of time. For example, it provides instruction on how to repeat an analysis on every file in a folder, rather than having to input and analyze every file separately. The book requires no prior knowledge; however, it is even easier to read, understand, and utilize if you are familiar with jargon and have some experience with computational computing. In conclusion, I would recommend this book to anyone looking to gain or increase computer skills.
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3 of 3 people found the following review helpful
5.0 out of 5 stars Biologists Need This Book May 17, 2011
Format:Paperback
I've needed this book for years, as a biologists who was trained in the recent era right before educators realized we need computing and bioinformatics courses. It is easy to follow by yourself and is brief enough to keep you moving a good pace without missing important tools. I highly recommend this to any biologists who wants to be able to feel comfortable using a terminal, save time searching and processing files and most importantly not have to wait for the computer person in your lab, or on your floor, or in the next building to do something trivial for you. Also, having control over your own processing means you actually know what was done and can make sure it doesn't affect the biological relevance negatively.
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2 of 2 people found the following review helpful
5.0 out of 5 stars Highly recommend this book to every biologist. June 16, 2011
By Myself
Format:Paperback|Verified Purchase
I am a graduate student in biology and frequently feel like the learning of new skills, that are extremely useful for my present and future work, requires the commitment to that learning for a longer time period than I actually have. If these skills are in another discipline, then the commitment has to be even stronger.
The main thing that should be changed about the book Practical Computing for Biologists is the title. A more suitable and informative title would be "Demystifying computing for biologists" or even "Demystifying computing for scientists". The authors clearly explain how to tackle problems that biologists in all career stages face frequently, and in doing so, introduce the fundamental concepts of computer science. By reading the book, the biologist learns that he/she can write a one line command in the terminal window (which take 30 seconds), that will save him/her hours of work. The scientist can also create a small program that will peruse archives of data (be it genomic data, ecological data, literary data) with a defined frequency to look for specific information. This way, a daily routine spent in front of a computer can be replaced by this program and time can be used in other tasks (in the case of biologists, bench work, paper writing, etc). And while writing and running these problems, the scientist gets familiarized with words and symbols such as bash, "shebang", sudo and { }.
The authors lead the reader through the intricacies of computer science without the readers knowledge, and without the need to purchase software, as the one required is mostly open source.
This book will not make you an expert in computer science, but you will certainly feel like you started understanding the field.
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Most Recent Customer Reviews
4.0 out of 5 stars Great intro book
Great book for ramping up your computational skills. It covers a lot of powerful tools in a very straightforward and easy to digest manner. Read more
Published 1 month ago by Rory Weston
4.0 out of 5 stars School book
Purchased this for someone else for use in a class. He said that it was a good book, so it sounds fine.
Published 1 month ago by Jill Hancock
4.0 out of 5 stars Well-written and useful
Touches on a wide array of subject matter. Useful for the biologists just looking to get into the programming game.
Published 2 months ago by A. Vahedi-faridi
5.0 out of 5 stars Great book!
Great for someone just beginning to learn programming. I am a molecular biologist and have gotten to the point where knowing how to program is almost becoming a requirement for... Read more
Published 3 months ago by Matthew Jenny
5.0 out of 5 stars great foundational reading
For anyone who needs to deal with command line programming for analyses, this is a great book. The linux & python sections were especially helpful.
Published 3 months ago by PhyloFish
4.0 out of 5 stars Not enough depth
This is a great introductory book, but what is has in introductory material, it lacks in depth. I would definitely recommend getting a supplementary book if you're interested in... Read more
Published 4 months ago by Polychaos
4.0 out of 5 stars Very good
I am using it for my Computational Biology class. This is the first time that I am computing... and this book is helping me a lot
Published 4 months ago by Veronica Barragan
5.0 out of 5 stars Great
Good starting point for those needing to do non-GUI stuff. Lots of useful tips and information on a wide variety of topics.
Published 4 months ago by Elizabeth Scott
5.0 out of 5 stars Exceptional Resource
My Background:
I am a biochemistry and molecular biology graduate who is learning BioPy and R to aid in my ability to process and understand large data sets. Read more
Published 6 months ago by Spruce
5.0 out of 5 stars Exactly what the title says
The book contains exactly what the title indicates. It is the perfect book for health science personel who wants or needs to handle big amounts of data and who wish to do more of... Read more
Published 6 months ago by Louise Thingholm
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