Who are you, and what do you do?
I am Dr. Victor Hanson-Smith. I am a computational biologist. I lead a team of other computational scientists at Verge Genomics, a drug discovery startup company that is developing new treatments for neurodegeneration. We are currently working on ALS and Parkinson's Disease.
My passion is for untangling complex biological systems, and translating these discoveries to make a positive difference in the world.
I trained as a computer scientist, and I have spent most of my career embedded within molecular biology groups. During my PhD, I applied computer science to study genome evolution. I was fortunate to have some of the world's best mentors, who opened my eyes to the possibilities of science collaboration across diverse disciplines. My research led to interesting discoveries about how natural evolution creates complex biological machines. This work was inspired by a lifelong curiosity to understand bigger questions about the nature of reality. How does evolution work at a molecular level? What are the origins of life? As it turns out, my deep-dive into evolution equipped me with a specific set of skills that has translated well to tackle more immediate problems, such as curing Parkinson's Disease.
What hardware do you use?
My favorite hardware for team collaboration is a basic whiteboard. I love drawing pictures with other people as a way to better understand complex ideas, whether we're designing data structures or explaining biology concepts.
I currently use an iMac Retina 5K, 27-inch, Late 2015. When I travel, I use a 13-inch MacBook Pro from 2017. I work on an Uplift V2 standing desk. I like to stand all day, and sometimes I do little dances when I'm really in the zone.
My work---and my team's work---frequently involves computational analysis requiring supercomputing resources, which we accomplish using hardware on Amazon Web Services (AWS). We primarily use the trio of EC2 + S3 + RDS.
On my home desk, I have extra gadgets to improve the quality of remote communication with my team. I use a Logitech C922 Pro Stream webcam, and an Audio-Technica AT2020USB+ microphone. Sitting beside my iMac, I have an IPEVO VZ-R document camera. I like to share this camera during virtual team meetings; the camera points to a scratchpad on my desk, on which I sketch pictures to help explain complex ideas. It sort of mimics the experience of a whiteboard.
Beyond computers, much of our work involves data acquired from hardware specialized for molecular biology. For example, we use an Illumina HiSeq to measure which genes are turned on/off in human brain tissue.
And what software?
My desktop iMac runs OSX 10.14.6. Long ago, I held strong opinions about different OSX versions (for example, 10.6.8 was incredibly stable, but 10.7 broke too many things for the sake of innovation). These days I've stopped caring---as long as my Mac works.
I code in Sublime Text. I mostly write Python, R script, and shell scripts these days.
My software stack for computational biology analysis includes 100+ specialized tools and libraries---too many to list here. Some notable ones include STAR, Salmon, FastQC, Picard, BamTools, DESeq2, limma, and WGCNA.
I seem to always have a couple Terminal windows open, connected to Linux EC2 instances in our AWS cloud. My team and I frequently launch big multi-core jobs. In these situations, I like to run htop in Linux and monitor resource usage. A few other favorite Linux programs are grep, awk, and parallel.
My team and I maintain a Python Django web server, which provides a web-based user interface to our database. I currently use Postico 1.0.8 to interactively debug the SQL server.
I give a lot of presentations, and I am currently using Keynote v10.1.
I currently use Adobe Illustrator v25.3.1 to apply finishing touches to scientific visualizations, especially when it's intended for external audiences or a publication.
An important aspect of my job is staying abreast of peer-reviewed literature in the field. I use BibDesk to organize my library of papers.
I use Asana to help the team stay organized around project deadlines.
What would be your dream setup?
I love working in real-time with other people, and I specifically love dynamic pair programming. My dream setup would be a situation that would maximally facilitate working with my team members. It would probably include a huge array of monitors, lots of whiteboards, and a big shared work table. Also, a nice espresso machine.
On second thought, what I described is actually just our real office, which I haven't seen in over a year due to COVID protocols. I look forward to that changing soon, hopefully.