Joshua H.M. Sakai

Josh Sakai

Undergrad Institution: Willamette University
Internship Location: PNNL
Current Location: Madigan Army Medical Center - Department of Clinical Investigation
Current Job title: Data Science Core Bioinformatician

How did you find yourself at Oregon? What about the program attracted you?
I found the program through my undergrad mentor recommending that I go see a talk a UO rep was giving about the masters programs they had. Weirdly it was 1/2 physics people 1/2 bio and no hard com-sci people at the talk. I was immediately attracted to the program since I was just starting to self teach myself bash/shell scripting at the time for my thesis in metagenomics and knew I wanted to continue in this field. I had the background knowledge but had no formal training in programming so it sounded like a perfect fit.

What was the summer intensive like for you?
It was a lot of work but in comparison to undergrad it was much more fun. I got to focus on quickly filling my gaps in programming knowledge and it quickly galvanized my cohort. We did a lot of working together in small groups and I made a lot of good friends that way. Let me put it this way: if I didn't go to the weekend study sessions I wouldn't have made it, but I never felt like any one problem was depressingly unsolvable for me.

Where was your internship?
Pacific Northwest National Laboratory

What was your internship like? What were you responsible for? What was a typical day like?
I did a lot of things in my internship. Partially because I didn't have a dedicated place in the lab and it was in the middle of Covid-19 starting in earnest so I never worked on site. I was responsible primarily for algorithm development for parsing high and low resolution MS data, and kubernetes deployment development with some data analysis and visualization. A typical day was waking up 8-9 checking my weekly to do list, whatever notes I had made myself the previous day, and my email. Once I did that I usually worked on whatever file/script/branch/pipeline/deployment until my evening meetings. Lunch happened at some point.

Do you feel the program prepared you for the internship? In what ways?
Yep. I was taught the skills I needed to pick up a new data type I'd never worked with before. conduct complex statistical analysis, and pivot several times as my workload changed overtime. Most of what I did was never directly covered by the program but the base of knowledge was a good enough springboard to get me where I needed to get 4/5 times.

How did your internship prepare you for your current position/career path?
It made me flexible and gave me a lot of practice adapting to the needs of different projects and working with people who have diverse skill sets.

Do you have any advice to prospective students?
Go to the weekend sessions in the summer if you get in coding is like learning the romance languages. Your first is really hard but they tend to get easier, don't be discouraged make sure you're learning a language that is used in the field you want to be working in. Familiarize yourself the following. Leslie won't let you some of these but trust me. It's worth it
• Python : Numpy, Pandas, BioPython, Seaborn
• R : Bioconductor, ggplot (ggpubr), dplyr, tidyr, purrr
• please google it first though so as not to irritate them. Seriously if you can't find the answer in 10-15 minutes just go talk to them.