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22 Apr 2011
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£48.99
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9780878933914
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DescriptionReviewsContentsAuthors

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.


Description

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.


Reviews

'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

'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


Contents

Before You Begin
PART I: TEXT FILES
Getting Set Up
Regular Expressions: Powerful Search & Replace
Exploring the Flexibility of Regular Expressions
PART II: THE SHELL
Command-line Operations: The Shell
Handling Text in the Shell
Scripting with the Shell
PART III: PROGRAMMING
Components of Programming
Beginning Python Programming
Decisions and Loops
Reading and Writing Files
Merging Files
Modules and Libraries
Debugging Strategies
PART IV: COMBINING METHODS
Selecting and Combining Tools
Relational Databases
Advanced Shell and Pipelines
PART V: GRAPHICS
Graphical Concepts
Working with Vector Art
Working with Pixel Images
PART VI: ADVANCED TOPICS
Working on Remote Computers
Installing Software
Electronics: Interacting with the Physical World
APPENDICES
Working with other Operating Systems
Regular Expression Search Terms
Shell Commands
Python Quick Reference
Template Programs
Binary, Hex, and ASCII
SQL Commands
Index


Authors

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