Working with Genomics Coming From a Pure Software Engineering Background
by Sebastian Ballesteros
A little bit about my background
While pursuing a Bachelor of Science in Software Engineering at McGill University, I joined the Canadian Centre for Computational Genomics as an intern in 2020. I started working at the C3G with no background whatsoever in the field of computational genomics. It wasn’t until I began engaging with the various tasks my new job entailed that I realized I was passionate about the domain. Starting with genomic variants going all the way to ethical genomics, I immersed myself in a field I didn’t know I could apply my software skills on.
Succeeding my internship, I went back to McGill to finish my last semester while still working part-time at the C3G. Due to my appeal to computational genomics, I took a class at McGill to further broaden my knowledge, which permitted me to learn the basics of computational biology methods that are in practice nowadays.
After graduation, I joined the team as a software developer as a part of the data team in the summer of 2021.
What projects have I been working on?
- Bento: The Bento portal is a platform for sharing and exploring –omics data. This was the first project I worked on as an intern and that opened the door to many new concepts and technologies. My main task was to enable visualization of genetic variants with the help of an existing library. While working part-time I carried out simple front-end tasks.
- D-path: This was the main project I undertook during my internship. D-PATH (Data Privacy Assessment Tool for Health) is a privacy assessment tool for the sharing of health-related data that aims to guide researchers, data hosts, and service providers such as cloud computing companies, in protecting the privacy and confidentiality of the human health-related datasets they process in a manner that is in agreement with the applicable legal, professional and ethical norms.
- FreezeMan: Now that I am currently working full-time, most of my time and effort goes to Freezeman, a sample tracking system that is slowly turning into a LIMS (Laboratory Information Management System).
The tools I am using
Most, if not all, of the applications I have participated in used React.js as its front-end and Django (Python) as its back-end. When I was working on D-Path and Bento I was developing tools tied mainly to the front-end. I had not touched Django at all until I dived into FreezeMan’s back-end, which was one of the main challenges I encountered.
The projection procedure starts by iteratively randomly splitting the dataset into 70% training and 30% test sets. For each iteration we:
Advice to developers seeking to pursue a future in computational genomics development
1. Start with the basics
When I began working at the C3G there were many concepts and definitions, especially those related to genomics and chemistry, that I did not understand. However, a short read or a quick video will get you started with what you need to know to get the job done.
2. Ask around
Most of the relevant information I needed for my tasks came from the people I worked with, the more I asked the more details and data they provided.
3. Explore on your own
Computational Genomics is a hot topic, there’s plenty of information and resources on the internet and research papers that can further help you expand your knowledge.
Published: December 21, 2021