The story of Computing Skills for Biologists

Stefano Allesina and I wrote the textbook Computing Skills for Biologists–A Toolbox, which was published by Princeton University Press in 2019. Here’s the story of why and how it came to exist.

Why did I want to write a book?

You can’t identify insight, because you have too much data? That’s how I often felt during my PhD and Postdoc. It was easy to produce tons of data, but generating insight required a broad computational toolbox. I had no formal training as a computational biologist but had to morphe into one in order to analyze my research data.

Acquiring computational skills to wrangle, analyze, visualize, and publish my data felt slow and inefficient. I didn’t wish this auto-didactic process on anyone.

At the time, Stefano Allesina, at the University of Chicago, was the first instructor to present a coherent course on the topic. I convinced him to turn his lecture notes into a book, as I wanted other students to have an easier time than myself acquiring computational skills.

Stefano does things properly so we didn’t simply turn his notes into a book (as I had assumed). We each took half of the 10 topics and started writing from scratch.

Why did we publish with Princeton University Press?

The book is funded by public money through an NSF grant (CAREER grant #1148867) so we wanted a not-for-profit publisher, who wouldn’t try to make money off of something that the public already paid for.

We settled with renowned Princeton University Press, which has lots of experience with similar titles. With our editor, Alison Kalett, we found a wonderful advocate who instantly understood our mission.

One drawback to producing a book “priced for graduate students” was missing out on color images. If we couldn’t have color images, we preferred to not have many images at all. No images in a chapter on data visualization? Weird, I know but we’d do it again. Now go buy the book, we’ve made it affordable for you!

How long did it take to write?

Stefano and I are both very dedicated to our projects. When our publisher gave us a contract that expected us to deliver a manuscript within three years, we laughed at that. Three years? We were sure that we could do it in under 1.5 years! Guess what. It took us three.

What did I do for the book?

I wonder if Stefano ever gets that question. So here it is: I initiated the book, wrote half of it and edited the other. I set up exercises, copy-edited twice, created large parts of the index, drafted the cover design, and designed and implemented the book’s website.

The book is like a child to me, and I am proud of it. If you haven’t done so, go buy it. If you get stuck somewhere while working through it, please write us an email. I (and Stefano, too) love to support you on your data journey.