101 questions with a bioinformatician #7: Holly Bik

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.

Holly Bik is currently a Postdoctoral Researcher in Jonathan Eisen’s lab at the UC Davis Genome Center…but not for much longer! Sadly (for us), Holly will soon be leaving Davis to take up a Faculty position in the School of Biosciences at the University of Birmingham, UK.

As a Birmingham Fellow in Bioinformatics, she will no longer be saying things such as "Dude, it's like totally, hella hot" (this is how we all talk in California), and will instead be referring to the weather in the correct British vernacular "I say, one finds this rain jolly bracing". As Curry Capital of Britain she will also be required (under Birmingham law) to dramatically increase her intake of onion bhajjis,  aloo gobi, and peshawari naans (something that sadly seem to have been outlawed in Northern California).

During her time at UC Davis, Holly has been working on PhyloSift, a software pipeline for the phylogenetic analysis of genomes and metagenomes. She has also been working on many other things. You can find out more about Holly by following her on twitter (@hollybik) or by visiting www.hollybik.com. And now, on to the 101 questions...



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

Given my biology background, my favorite aspect of any bioinformatics project is interacting with people from different disciplines (project personnel, and/or talking to people at meetings and on Twitter). I learn something new about computing, software, and/or hardware pretty much during every project.

I’m always astounded by how technology and computers have progressed since I got my first personal computer (way back in 1996), and how we’re now leveraging this computing power in conjunction with deep DNA sequencing technologies to address fundamental scientific questions. The power of bioinformatics is really incredible when you stop and think about it!


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

The lack of documentation for a lot of software packages, and to a lesser extent, encountering uninformative error messages when trying to run command line software that’s supposedly designed for researchers. Both can be a prohibitive barrier to testing out different tools that may actually be extremely useful and informative for your own research. I think there’s a reason that QIIME has become such a powerhouse package for microbiome research — biologists have access to a suite of tutorials, test datasets, and they can boot up the software easily as a Virtual Machine or Amazon Cloud instance.

However, the easiest tools to install and use are not necessarily the best to use for your particular research questions. I read so many software papers describing exciting new software (where the authors usually all come from computer science departments), but when I visit the website I find no useable instructions or run into insurmountable errors when trying to install or execute the code. As a biologist, no one ever sat down and taught me the nitty gritty about makefiles or compiling source code; people that publish software shouldn’t assume their users have a computer science degree. Most computational biologists will make a valiant effort to overcome such problems, but at some point you have to do a cost/benefit analysis of whether persevering is worth your time. I’m only going to spend two days trying to install your software if I think its really really worth it, but in most cases I’ll probably decide that it isn't (and so no citation for you).


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?

FILE MANAGEMENT. Read up on the best practices for data management, and start forcing yourself to develop good habits NOW. I guarantee that in 5 years' time you will not remember what data you saved in 'analyses.txt'.


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

I’m going to be shamelessly biased: my favorite software ever is Phinch, a data visualization framework that I’ve been developing in collaboration with Pitch Interactive — a data visualization studio in Berkeley, CA. We’re using solid software engineering and design principles to build exploratory, interactive visualization tools for scientists. And because the visualizations are built in 3D, the user interface is absolutely gorgeous! Who says you can’t create art when doing bioinformatics research?



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 a gap (. or -), because I’m mysterious and don’t like to be classified!