Effective Python Development for Biologists: Tools and techniques for building biological programs

I came to this book interested in how Python was being used in biology. It turns out this book is highly practical detailing the steps for using Python in bioinformatics.The book starts assumed you are familiar with DNA related biology. I had to look up a few terms on Wikipedia, but I am glad the author assumed this knowledge still because it was not that hard to get up to speed.Examples always focus on the biological and the practical. Jones explains very clearly how to use Python, which libraries, and which tools to get most of Python in the biological workflow. Right away you will see the practicality of the examples such as reading and manipulating DNA sequences. Even though I am not a biologist myself it was still understandable and I wanted to research more.The beginning of the book shows you how to debug Python programs well. The topics were surprisingly wide ranging going from sharing code, to testing, and then some graphical tools explained towards the end.I liked that the author said which tools are good and which ones you may want to avoid. He was critical of the tools he did not like and praised the ones he did, helping to make it obvious what the best choice is in the biological workflow. At the end of the book he explained well why the command line is a preferred choice:"For most bioinformatics work, a command line interface is the best choice: it's most likely to fit in with other tools, it's amenable to automation, and you can document all the arguments used to run a program by simply copying and pasting the command line into a text file or an email."Overall this book in an excellent choice for learning about Python or biology related engineering.One small suggestion for future editions of this book is to include the code on GitHub. I would have liked to see the code online as well because typing the gene sequences manually was prone to error for me, although I liked that the examples were easy enough to type from the book too.

This book gathers extremely useful information that is otherwise sparsely distributed. Everything is explained clearly and accompanied by example files and code through the website. Highly recommend for novice bioinformaticians.