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Practical Computing for Biologists, by Steven Haddock, Casey Dunn
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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.
- Sales Rank: #117775 in Books
- Brand: Brand: Sinauer Associates, Inc.
- Published on: 2010-11-05
- Original language: English
- Number of items: 1
- Dimensions: 9.00" h x 7.75" w x .75" l, 2.64 pounds
- Binding: Paperback
- 538 pages
- Used Book in Good Condition
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.
Most helpful customer reviews
13 of 13 people found the following review helpful.
Extremely Valuable
By A Reader
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.
3 of 3 people found the following review helpful.
Exceptional Resource
By Spruce
Update:
THIS BOOK MADE ME SHINE!
One of the exercises in the book involves using building a program using regular expressions to modify the format of lat/lon data into a .kml-readable format.
Guess what my employer asked me to do today?
Yup, manually reformat hundreds of lines of lat/lon data.
It took me 20 minutes instead of tedious hours, and I was paid for completion of the job, not the hours.
In science, it is all about efficiency and building a better mouse-trap. This book teaches you all the great shortcuts to stand out in a competitive field of study.
THANK YOU PCfB!!!!!
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. I've been reading books on python and bioinformatics, but they are often either too cryptic or too basic. Until I found PCfB, I couldn't find a book that got to the real meat of bioinformatics and biological data processing/management.
Review:
If you are pursuing higher education in science, buy this book. Seriously, put this book into your cart now.
Now that advanced computer skills are in great demand by employers in scientific disciplines, I really think a course involving this material should be mandatory in any undergraduate chemistry or biology department. But it isn't, so buy this book and catch up. This is the information they should have taught you in college.
PCfB is probably best for people who have a basic understanding of computers. The book is neither written for experts nor for novices and fits well at the college level. It provides sufficient detail and complex examples without interjecting excess esoteric programming theory.
The only downside is that the book is catered towards OSX/UNIX, but to be fair, the authors include how to run commands on windows and linux.
2 of 2 people found the following review helpful.
Exactly what I was looking for
By Zach
Fantastic book. Clear, accessible presentation that wastes no time honing in on the subset of computer skills guaranteed to deliver the most bang for the buck for the average biologist/ecologist. I was using this stuff literally the next day after I read it and have enjoyed major gains in productivity + decreases in frustration. I wish I'd read it the moment I stepped out of undergrad. It's worth mentioning that the focus is on data management/preparation, and not so much on analysis, for which the authors refer the user to R or Matlab. This book coupled with a good one on the stats program of your choice is all you'd need to get churning on your analysis.
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