A Book Like This: The Digital Cell

It’s real! I recently received a physical copy of my book, The Digital Cell: Cell Biology as a Data Science.

It is published by Cold Spring Harbor Laboratory Press and is available here. The official release date is 1st December 2019.

As I’ve described before, “The Digital Cell” a handbook to doing cell, developmental and molecular biology in the 21st Century; integrating computational and quantitative approaches.

The response to the book has been fantastic so far. Since people have asked me the same few questions, I’ve assembled a quick explainer/FAQ below.

What is in the book?

The chapters are:

• Digital cell philosophy
• Dealing with data
• Imaging data
• Imaging processing and analysis
• Statistics
• Coding
• Putting it together

It covers electronic lab notebooks (ELNs), reproducibility, statistics, programming, Fiji/ImageJ, R, some command line-fu, version control and a bit of dataviz.

Who is it aimed at?

Anyone who is doing cell, developmental or molecular biology. Probably the ideal reader is a graduate student starting their project. But anyone who doesn’t currently do any computer programming or feels their stats knowledge is a bit weak will benefit. The emphasis is on imaging data, but the principles apply across cell, developmental and molecular biology.

It’s an entry level text. It is not aimed at expert programmers. The idea is to convert all cell biologists to become digital cell biologists.

Is it just a collection of posts from quantixed?

No.

Essentially all the content is new. The preface and one part of the statistics section have origins on quantixed.

You wrote a book? You must be mad?

Maybe. Yes, it took a lot of time and effort (see below), but I think it was worth it.

As academics, we tend to write papers that are read by a small number of highly specialised people. With very rare exceptions, even our highest impact papers are only read by a subset of people in the field. When thinking about embarking on this book project, I realised that this book would be my chance to make an impact on the way that cell biologists do their research; having a further reach than any paper I would write.

What’s that on the cover?

The image was donated by my colleague Anne Straube. Her lab works on the organisation of the cytoskeleton and this image shows microtubule growth in a cell over time. The background code is an R script that I wrote together with my student James.

If I buy the hard copy, do I have to rekey all the code examples?

No. The code is available here to save you rekeying it.

Did it take a long time? Where did you find the time?

Yes. Richard Sever, who had the idea for the book called me on 24th June 2016, to discuss it. The date is etched in the mind of all UK academics as the disastrous day after the EU Referendum. We discussed it again at the ASCB Meeting in December and then agreed a contract early in 2017. I had a deadline to complete the book which slipped by, but I got there in the end.

Finding time was difficult. Anyone who has taken on a project like this says the same thing. Richard did offer for me to visit the USA to write it in a concentrated spell. I foolishly turned this down, believing that I could fit the writing around everything else. Without going into too much detail, there was a Pareto principle to the writing. I probably wrote 80% of the content in 20% of the time – just doing bits here and there. The remainder was difficult and I had to work exclusively on it to get the project finished.

Would you do it again?

This book? Yes. Would I write another book? Maybe…

I learned a lot about what it takes to do a big project like this. My slowness was partly due to poor planning and partly due to the content which was mostly generated fresh. I think it would be easier to convert a course I was teaching into book format, i.e. where a lot of the material was already prepared.

—

The post title was taken from “A Book Like This” by Angus & Julia Stone from their album of the same name. Because, well, “Paperback Writer” by The Beatles is too obvious and anyway, The Digital Cell is only available in hardback.