Twitter competition: win a signed copy of Bioinformatics Data Skills by Vince Buffalo

I have an extra copy of the fantastic Bioinformatics Data Skills book by Vince Buffalo (who you should all be following on twitter at @vsbuffalo). I've come up with a fun little competition to let someone have a chance of winning this signed copy.

All you have to do is write a tweet that includes the #ACGT hashtag (so I can track all of the answers), which provides the following information:

Name a useful bioinformatics data skill

The winner will be chosen randomly — hopefully by a powerful scripted solution that Vince will help me with — in two weeks time. I will post details of any interesting (or funny) suggestions that you come up with on this site. The full details are below.

Competition rules

  1. Tweets should name a 'useful bioinformatics data skill'
  2. Tweets must contain the hashtag #ACGT
  3. Last day to enter into the competition is 25th September (midnight PST)
  4. One winner will be chosen randomly
  5. Only one entrant per twitter account
  6. Retweets of tweets that use #ACGT hashtag will be excluded

Taking steps to write a new book about programming!

The old book

I am very excited to announce that I am involved in writing another book about progamming! The 2012 book that I wrote with Ian Korf — Unix and Perl to the Rescue!: A Field Guide for the Life Sciences (and Other Data-rich Pursuits) — was enjoyable to write, and seemed to be well received — (4.5 star average on and so we both wanted to do something else.

We wrote about Perl because it is the language that we had both used since the mid-1990s, and for a long while Perl was the language du jour for people working in bioinformatics. This has changed. The TIOBE software index uses search engine queries to track the popularity of all programming languages over time. In 2000, Perl was the 4th most popular language whereas Python ranked 24th. As of July 2015, Python has risen to 5th place, overtaking Perl which has dropped to 11th place. Not only is Python proving an extremely popular language, it is swiftly overtaking Perl in many areas involving the processing of biological data.

The new book

So we made a proposal to Cambridge University Press to write what we are provisionally calling Unix and Python to the Rescue! (this will no doubt be the start of a successful series which will culminate in Unix and Minecraft to the Rescue!). Happily, they have accepted our proposal and so we have recently started the process of writing the new book (hopefully due to be published in 2016).

We intend for this book to fulfill many of the same goals that we had for our earlier book:

  1. Contain basic material that introduces Unix & Python to someone who has never sat down at a terminal or written a line of code before.
  2. Include many advanced programming concepts in addition to the basics.
  3. Where possible, only introduce one new concept at a time.
  4. Write in a lively, engaging style in order to make the concepts fun!

For item #2, we envisage our book addressing topics such as NumPy, ScyPy, IPython Notebooks, and the pandas package, to name but a few!


The new co-author

For this new endeavor we have recruited the many talents of Michelle Gill (@modernscientist) who will bring her Python skills and all-round coding expertise to the project. Michelle is a scientist at the National Cancer Institute and has been using Python to analyze research data — and also using it for fun — for most of the last decade. You can find out more about Michelle, and see examples of her coding expertise on her excellent blog, themodernscientist. I asked her to say a few words about the new book:

"The purpose of this book is to equip scientists with the tools necessary to understand and analyze data in the way that directly suits their needs and can be reproduced in the future. With the ever increasing pace of research and volume of data generated, I am convinced the best way to accomplish this is by learning Python".

Michelle Gill


The new website

We previously had a website ( and twitter account (@unixandperl) to support the old book and related materials. However, it seems fitting that we need to 'expand the brand', and so we have an updated website that can now be found at (the old URL should still redirect here). This website continues to host information about the completely free Unix and Perl Primer for Biologists that we previously released, as well as the (also free) Command-line Linux Bootcamp that I recently added.

I expect that we will add some more posts to the new website in the coming months, and we will also continue to publish occasional items of relevance to the twitter account (also renamed to @rescuedbycode). Much of Python is new to me, and I hope to share some of my experiences from the point of view of someone who comes from a Perl background.

Okay, time for me to go and do some more research for the book.