101 questions with a bioinformatician #14: Shaun Jackman

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Shaun Jackman is a PhD student working on various problems relating to genome assembly at the University of British Columbia. Specifically, Shaun works under the supervision of  İnanç Birol in the Bioinformatics Technology Lab at the BC Cancer Agency's Genome Sciences Centre in Vancouver. You may know him for his work in writing and directing the 1989 smash hit The Abyss, which was later developed into a popular genome assembler.

In addition to being a talented bioinformatician who has contributed to lots of useful software, he is also a very patient guy. I say this because he has been waiting for me to publish this interview for over 3 months (my sincere apologies for the delay, I will try to make this series a regular feature once again).

You can find out more about Shaun from his website or by following him on twitter (@sjackman). And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

I’m excited to see the increasing popularity of enabling reproducible research using tools such as R Markdown and iPython Notebook. After reading a paper, it should be straight forward to download the raw data, install the necessary software, reproduce the results and regenerate the figures. I’m really hoping that we get to that point.

I'm also happy to see more interaction between developers and users using revision control web sites, such as GitHub.


010. What's something that you *don't* enjoy about current  bioinformatics research?

Most genome sequence assembly tools are structured as a pipeline: for example, count the k-mers of a set of reads, construct a de Bruijn graph of those k-mers, remove k-mers caused by sequencing errors, identify heterozygous sequences and finally assemble contigs.

It should be possible to mix and match these individual components from different assemblers to create new assembly pipelines that are hybrids of existing tools. Not only could it create a better overall assembler, but it could identify which of the individual components of the various assemblers are strongest. It should be encouraged to improve on an individual component without having to reinvent an entire assembly pipeline.


011. If you could go back in time and visit yourself as an 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

Learn to use R and R Studio to visualize your data. I wasted a lot of time making ugly figures with inferior tools. Use Make to automate every analysis pipeline. No pipeline is too small or too large. A one-off analysis never is.


100. What's your all-time favorite piece of bioinformatics software, and why?

  • I use Make and R nearly every day.
  • I like Heng Li‘s tools because they stick to the principle of doing one thing well.
  • I’m fond of ABySS, for one because it was the first bioinformatics tool that I helped to develop, but primarily because it’s designed as a pipeline of reusable modular tools that use standard (when possible) file formats, all bound together by a Makefile.


101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality?

I’m an N, because it leaves all options open.