Computing as a Biologist

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I have never considered myself to be computer savvy; however as I began dealing with larger datasets and more complex analyses, I quickly realized that knowing something about computers was essential—both to automate tasks and make my research reproducible. I believe it is essential for all biologists to feel comfortable computing. As someone who learns well from books, I would highly recommend the following books to build up your computing skills. I realize I do not have a book that deals with R specifically. If anyone has any good suggestions of tutorials or books that give a good introduction to R please let me know!

1. Practical Computing for Biologists. (2011). By Steven H.D. Haddock and Casey W. Dunn. Published by Sinauer Associates, Inc. 

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This book was really my first introduction to all things computing and I still use it constantly as a reference. It is a great introduction to regular expressions, the Unix shell command line, python, and basic programming concepts (e.g. for loops, if statements, etc.).  Additionally on the book's associated website (http://practicalcomputing.org/) scripts and datasets are available for download which can be used to follow the examples presented in the book.

 

2. Bioinformatics Data Skills: Reproducible and robust research with open source tools. (2015). By Vince Buffalo. Published by O'Reilly Media Inc. 

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I was recommended this book and found it extremely useful. One of the greatest benefits of this book is that it stresses the importance of and provides suggestions for managing your data and staying organized—which is essential for reproducible research. The book also covers  how to handle sequence data and the various file formats you may come across. Additionally the book provides a nice introduction to Git, and provides nice refreshers of the Unix shell and R.

 

3. Practical Programing: An introduction to computer science using python 3 (2nd Ed.). (2013). by PAul Gries, Jennifer Campbell, & Jason Montojo. Published by The Programatic Programmers, LLC. 

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This book is not specifically for biologists, but it is probably one of the best introductions to python I have come across.  I had a much better conceptual grasp on object oriented programming , modules, classes and methods after finishing the book which before I struggled to understand clearly.  

The organization of the book is different from most introductory python books. For example the second chapter, instead of being about strings, lists, and dictionaries as is typical in most python learning books, is all about functions. Lists are not introduced until chapter 8, after which modules, classes, methods, and object oriented programming have already been discussed in detail. 

And because the authors are Canadian, there are fun Canadian jokes that made me laugh as I made my way through the book!