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Practical Computing for Biologists

Steven H. D. Haddock and Casey W. Dunn

Publication Date - November 2010

ISBN: 9780878933914

564 pages
7.5 x 9 inches

In Stock

Shows how to use computing tools to work more powerfully and effectively


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; see Contents):

*Searching with regular expressions

*The Unix command line

*Python programming and debugging

*Creating and editing graphics


*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.


For Students

The Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.

For Instructors

The Instructor's Resource Library features all of the textbook's figures and tables, provided in ready-to-use PowerPoint presentations.

About the Author(s)

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. 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 (http://lifesci.ucsb.edu/~biolum/) and the Jellywatch.org citizen-science website (www.jellywatch.org).

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. 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, recognizing an outstanding young researcher in any field of science or engineering supported by NSF.


"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

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
    11. Merging Files
    12. Modules and Libraries
    13. Debugging Strategies

    Part IV: Combining Methods

    14. Selecting and Combining Tools
    15. Relational Databases
    16. Advanced Shell and Pipelines

    Part V: Graphics

    17. Graphical Concepts
    18. Working with Vector Art
    19. Working with Pixel Images

    Part VI: Advanced Topics

    20. Working on Remote Computers
    21. Installing Software
    22. Electronics: Interacting with the Physical World


Teaching Resources

For Students

The Companion Website includes downloads, community forums, tips and examples, and textbook errata and updates.

For Instructors

The Instructor's Resource Library features all of the textbook>'s figures and tables, provided in ready-to-use PowerPoint presentations.

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