29th May 2017 – Rutger Vos, Naturalis Biodiversity Center

Rutger VosMy name is Rutger Vos, and I am computational evolutionary biologist at the natural history museum of the Netherlands, Naturalis. My educational background is in evolutionary biology, most especially in phylogenetics, i.e. the field of biology that concerns itself with researching the Tree of Life. For my PhD research, it became clear that I needed to handle amounts of tree and alignment data that were unmanageable to do ‘by hand’ on a normal computer, so I taught myself programming and how to use high-performance computing systems.
One thing led to another and I ended up doing my postdocs as a contributor to various infrastructures having to do with phylogenetics, most notably the CIPRES (http://www.phylo.org) project and TreeBASE (http://www.treebase.org) – but also projects having to do with data standards and data sharing in biology. ‘Open Science’, basically.
Meanwhile, the high-throughput DNA sequencing (NGS) revolution was starting to spit out more and more genomes, with which I started to play around. So much so that by the time Naturalis started looking for a bioinformatician to contribute to the NGS projects that were going on over there I could plausibly apply for a position.
At Naturalis I’ve become involved in a lot of different projects, all of which have bioinformatics or computational biology in common but are otherwise very broad-ranging. I’ve had the good fortune to be able to work with many of the kinds of data, information and knowledge that circulate in a natural history museum. For example, apart from DNA I’m also analyzing image data from our specimen digitization efforts, scanned texts, and species traits and distributions.
On Twitter (@rvosa) I let out my interest in ‘unnatural history’. It’s a totally vague term that I’ve adopted to look at and talk about the cultural ways in which we interact with nature. I mean things like art about nature; the way we, biologists, do science about nature; how we as a species are colliding with biodiversity because of our actions. By the way, I later found out there’s also a book called ‘Unnatural History’. I haven’t read it but it looks neat and it looks like it’s partly about the same topic.

13th March 2017 – Darwin Fu, Vanderbilt University

Darwin FuHello Biotweeps! I’m Darwin, a Chemistry PhD student in my final year (*knocks on wood* *prays to the ancient gods*) at Vanderbilt University. I spend my day writing programs for modelling how drug molecules interact with their targets. The goal is to improve our ability to use computers to predict which compounds will bind to a given disease target and the way they will bind. Better computational, or “dry lab”, experiments complement traditional “wet-lab” experiments, which can often be very time consuming.

I work in the lab of Dr. Jens Meiler (http://meilerlab.org) coding mostly for Rosetta (http://rosettacommons.org/), a software package for structural biology modeling. Rosetta is a collaborative project with 40+ research labs around the world actively developing methods for everything from designing catalytic sites of enzymes to predicting binding of HIV antibodies. You may have come across Rosetta in the form of Rosetta@Home, a citizen science distributed computing project, or through FoldIt, a computer game that converts unsolved protein structures into puzzles for players (see https://boinc.bakerlab.org/ and https://fold.it/portal/). You may have also heard about our recent exploration of comet 67P (just kidding, that is completely unrelated).

My research is focused on protein-small molecule docking and virtual screening for Computer-Aided Drug Design applications.  Depending on available collaborations, we work on systems ranging from G-Protein Coupled Receptors to Signal Transducer and Activator of Transcription proteins. Part of the job involves making computational tools more accessible to researchers who may be less well-versed in modelling. This usually means making tutorials, web servers, and graphical interfaces. I would love to continue along these lines after graduation and work in scientific software development. I am also interested in researching rare diseases and using modeling to repurpose “failed” compounds to structurally similar targets.

My undergraduate degree is in Chemical Engineering and Biochemistry from the University of California, San Diego. I had a choice between working on hands-on biomaterials research and molecular dynamics modeling of influenza infections. I chose the latter and went down a computational research path. I planned to do more biochemistry in grad school but a few weeks in the cold room and my terrible gel loading skills quickly changed that.

Besides research, I’m interested in science communication and citizen science, particularly for adult education. I also moonlight as a pub quizmaster and connoisseur of “weird” foods. My non-science dream job would be working in sports analytics. Feel free to talk sports, trivia, or odd eats with me (also scotch…yum).

Sadly, there won’t be as many relevant cute animal GIFs over the course of this week, but I promise there will be dancing protein animations instead. I hope to share my love of computer modelling and to learn more about computing applications in your fields. I am also in the process of starting a new outreach effort and would love some input. There may also be a little structure based contest with a nerdy prize. Stay tuned!

Reach me via Twitter (@EquationForLife) or check out the blog I’m restarting (https://equationforlife.wordpress.com/)