Published by Sinauer Associates, an imprint of Oxford University Press.
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.
- 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; and 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.
About the Author(s)
Steven H. D. Haddock, University of California, Santa Cruz, and Casey W. Dunn, Yale University
Steven H.D. Haddock is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at the University of California, Santa Cruz, studying bioluminescence and biodiversity of gelatinous zooplankton. He started programming in BASIC on an Apple ][ and began his undergraduate studies in engineering before deciding to change fields. He took this programming background with him 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.
Casey W. Dunn, a Professor at Yale University, 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.
Table of Contents
Before You Begin
Part I: Text Files
1:Getting Set Up
2:Regular Expressions: Powerful Search & Replace
3:Exploring the Flexibility of Regular Expressions
Part II: The Shell
4:Command-line Operations: The Shell
5:Handling Text in the Shell
6:Scripting with the Shell
Part III: Programming
7:Components of Programming
8:Beginning Python Programming
9:Decisions and Loops
10:Reading and Writing Files
12:Modules and Libraries
Part IV: Combining Methods
14:Selecting and Combining Tools
16:Advanced Shell and Pipelines
Part V: Graphics
18:Working with Vector Art
19:Working with Pixel Images
Part VI: Advanced Topics
20:Working on Remote Computers
22:Electronics: Interacting with the Physical World
"Practical Computing for Biologists is a clear guide to methods that unlock the power of the personal computer. Although the breadth of subjects covered is certainly an asset of this volume, what really makes the book stand out is how well the authors clearly describe each technique and its applicability to biological sciences. It is a great launching point for any necessary further investigation of computational techniques." - Matthew Aiello-Lammens, The Quarterly Review of Biology
"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). It is 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
"When considering my research and use of time, this book has been the most important book I've read in the last year, and perhaps the last decade. Striking a perfect balance by guiding you through tutorials and nudging your own self-exploration, the book has just enough guided direction to not annoy or overwhelm. It has helped (and is still helping) me to do what I was doing before, but more efficiently." - Cyme & Cystidium
The Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.
The Resource Library features all of the textbook's figures and tables, provided in ready-to-use PowerPoint presentations.