About

About the Site

The site is a companion resource for the book Practical Computing for Biologists by Steven Haddock and Casey Dunn. Here you can download example files and other scripts, consult with other scientists, and give feedback on errors or suggest material for web instructions and for future editions.

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

PART IV: COMBINING METHODS 
14. Selecting and Combining Tools 
15. Data Organization and 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 

APPENDICES 
Appendix 1 - Working with other Operating Systems 
Appendix 2 - Regular Expression Search Terms 
Appendix 3 - bash Shell Commands   
Appendix 4 - Python Quick Reference 
Appendix 5 - Template Programs 
Appendix 6 - Binary, Hex, and ASCII 
Appendix 7 - SQL Commands
Index 

About the Authors

The authors followed parallel paths in their scientific careers, going from technical backgrounds into biological research. They developed their textbook to teach the skills they find to be most useful in their research.

STEVEN HADDOCK is a Research Scientist at the Monterey Bay Aquarium Research Institute and adjunct Associate Professor at U.C. Santa Cruz, studying bioluminescence and biodiversity of marine 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 and the Jellywatch.org citizen-science web site.

CASEY DUNN, an Assistant Professor at Brown University, does research that has a large computational component but always in conjunction with work in the field and lab. His first interests in computers stem from building electronics, and he further developed his computational skills working in Silicon Valley while an undergrad. As his datasets 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 web sites siphonophores.org and creaturecast.org.

Frequently Asked Questions

How long did the book take to write?
- It took about three years.

Where can I get the CourierPCfB font?
- From the downloads page.

Do you have a Facebook page?
- As a matter of fact, we do.

About the Bird

Ann P. Smith created the sculpture used on the cover of the book and this web site. Read more about our special PCfB bird. Explore Ann's other fantastical artwork at burrowburrow.com.