During my time as a bioinformatician at the UC Davis Genome Center and in the Dubcovsky and Ross-Ibarra labs, I found very few books taught the data skills I relied on most in my day-to-day bioinformatics work. Furthermore, texts didn’t emphasize scientific computing best practices alongside teaching technical skills. Bioinformatics Data Skills (published by O’Reilly Media in July 2015) is my book that seeks to fill this role.
Below are some quotes from reviews of Bioinformatics Data Skills. Other reviews are available at O’Reilly’s site (4.8/5 stars, 14 reviews), Goodreads (4.30/5 stars, 44 ratings), and Amazon (4.4 stars, 47 reviews). You can also read the review written by the terrific Molecular Ecologist blog. If you’d like to share your review, tweet it, and ping me at @vsbuffalo.
I wish this book was available two years ago when I first started my graduate studies - It literally could have saved me a year.
Superb book for those looking to develop bioinformatics skills. Covers loads of the supporting skills that are generally learnt through years of experience and aren’t obvious in other texts/courses.
Should be required reading for any PhD students or lab scientist working with data.
I have been programming in a UNIX environment for 26 years, and a leader in bioinformatics since I entered the field in 1998, and was surprised to find that I was able to learn useful tips and tricks in nearly every chapter.
Bioinformatics Data Skills is an
intermediate-level book, aimed at readers with some experience with a scripting
language like Python, and very basic Unix (e.g. the Unix filesystem hierarchy,
ls, etc.). Bioinformatics Data Skills
gives readers a solid Unix foundation in chapters 3 (“Remedial Unix Shell”), 7
(“Unix Data Tools”), and 12 (“Bioinformatics Shell Scripting”, “Writing
Pipelines”, and “Parallelizing Tasks”). Readers are also introduced to the R
language through learning exploratory data analysis (chapter 8).
Bioinformatics Data Skills has over 700 code examples for readers to follow along with. All supporting data and scripts (as well tips, anecdotes, and extended footnotes) are available in my book’s Github repository at http://github.com/vsbuffalo/bds-files/.