A Software Engineer’s Experience at BCC 2020

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Edidiong Etuk (Eddie), an open-source lover and a software engineer from Nigeria, was supported to take part in Bioinformatics Open Source Conference 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.

TL;DR This post is about my experience at Bioinformatics Community Conference 2020.

Before attending the Bioinformatics Community Conference (BCC) 2020, I had zero experience with Bioinformatics. But, after the conference, I am more confident in my ability to tackle bioinformatics-related tasks, challenges and discussions. I enjoyed every moment of BCC2020 virtual conference, hung out with a lot of cool folks through the Remo conference platform, and got introduced to new concepts in bioinformatics through workshops, keynotes, short talks, poster sessions and community interactions. In this post, I am summarising my experiences and lessons learned from this conference.

BCC Pre-Conference Workshops

I registered for two workshops: Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis and I must say I found them easy to understand as a beginner. I had an idea of what Docker was but the tutors made working with Docker so easy. They also switched up and explained Descriptors (focus was on Workflow Description Language). It was a good introduction to Dockstore.

Next, I attended Reproducible Analysis in the Cloud with Dockstore and Terra, where I got introduced to Terra, Anvil, and learned more about Dockstore. The ability to access data, run analysis, and use the cloud all from Terra while fostering collaboration is what this training was about. All experiments I toyed with, worked and results could be seen easily and tracking bugs or experiment failure was seamless.

One regret I had during the workshops is the number of sessions I missed. All the sessions were so interesting that I wished I could attend all training and workshops. All the training materials and notes were made available, so I guess I’d have enough resources to start with when learning them on my own.

Main Conference

I attended the West sessions of the 3-day main conference as this favored my timezone. As a volunteer for BOSC, I spent a lot of my time in the BOSC building (yes a virtual building). There were several interesting talks during the conference about research and a variety of open-source tools which I can’t point to, but some of those I describe below.

Day 1

Day 1 started with a keynote from Lincoln Stein who showed us how Open-Source has improved the biomedical world.

The presentations were all short and precise and though some were very technical, I got a thing or two from them. The most memorable presentation was Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL).

It was very relatable and I applaud the creativity behind the presentation, bravo Michael!!

Poster sessions were cool and were held in a different virtual building from Galaxy and BOSC tracks. This was a good opportunity for me to see innovative work by the researchers in various bioinformatics communities. I also had a chance to chat with the representatives of the sponsors at the sponsor tables.

Day 2

On Day 2, Prashanth N Suravajhala gave the keynote on the importance of mentoring students. It was sad to hear that the building he was delivering his keynote from had some emergency situation during the presentation, but kudos to him for delivering an excellent keynote. 

Another memorable session was Building open source communities and empowering new contributors by Yo Yehudi. This talk was important as without Yo’s mentorship from Outreachy, I wouldn’t be here (Thanks Yo!). Although that session clashed with a Galaxy session, luckily the recordings were made available so I got to watch The cloud-native Galaxy: Galaxy on Kubernetes. I’m interested in everything Kubernetes so the session, of course, interested me.

Day 3

Day 3 hit closer to home due to my work at Popper, everything about workflow management seemed understandable. Although I gotta add, there are a lot of workflow engines out there for reproducibility in research.

It would make a lot of sense if they all came together to do a conference to ensure we’re all going in the same direction and not competing with each other. Of course, there were a lot of interesting posters which I got to check out.

Welcoming Community

Everyone at BCC 2020 was very welcoming, Birds of a Feather session at the virtual-bar was a great addition to the event. I had my drink with me, and of course, we all drank responsibly (lol!). I enjoyed switching tables and going to different floors on Remo where I got to interact with warm and friendly people during the conference.

The Bioinformatics community is the most welcoming out there! Special shout out to everyone who made me feel welcome, Michael R. Crusoe, Dave Clements, Emmy Tsang (who pronounced my name very well), Nomi Harris, and others! You were all fun to hang with and I hope next year I can meet y’all in person!

BCC exemplified diversity in tech and I loved it. BOSC Happy Hour West was thrilling as we had 18 people on the stage (please don’t try this on Remo! ?).

Next Steps

Due to my interest in Bioinformatics, I am working to dockerize DoBlastzChainNet and popperize it to make it reproducible. This is going great and I’ll appreciate any help.

Thanks to OBF for this amazing opportunity! Till next time!

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