Practical Computing for Biologists

ISBN : 9780878933914

Steven H. D. Haddock; Casey W. Dunn
538 Pages
229 x 191 mm
Pub date
Nov 2010
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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. Many of the techniques are relevant to molecular bioinformatics but the scope of the book is much broader, covering topics and techniques that are applicable to a range of scientific endeavours. Twenty-two chapters organized into six parts address the following topics (and more; see Contents): * 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 the main narrative focuses on Mac OS X, most of the concepts and examples apply to any operating system. 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.


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

About the author: 

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.

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