Have you participated in a hackathon? Are there any coming up that you are interested in? I’ve participated in a few and found them to be a good way to hone my skills, bounce ideas off of other scientists, and get acquainted with publicly available datasets - and sometimes they can even result in publications! They are often paired with a conference or can be run independently.
There was just a hackathon at GP2, with 32 in person participants and 16 virtual participants who worked on 8 projects, all within the Terra ecosystem:
- Single Gene Assessment (ABCB1)
- Single Gene Assessment (COMT)
- Screening GBA1 variants across ancestries with WGS data
- Pathogenic PD Variant Carriers
- Single Gene Assessment (DNAJC13)
- Haplotype Analysis (MAPT)
- scRNA-seq Analysis
- Runs of Homozygosity
The IPDGC/GP2 virtual hackathon in 2021 was published in Nature Parkinson’s Disease earlier this year.
Outside of the PD community, the NCBI hosts regular Codeathons (apparently the US government decided “hacking” has a negative connotation and they call these events Codeathons instead). The next one will be held virtually, February 26th - March 1st, and the topic is " Building Transparent ML/AI Solutions to Advance Biological Research".
There are many roles in these - you don’t necessarily need to code to participate. They are also create for sharing ideas.
Any thoughts on hackathons in general? Other ones coming up that people are interested in?
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Hi, Elizabeth!
Actually, I (along with @psaffie, I think!) attended both GP2 hackathons, the first one virtually and the second one in person.
In the first one, I basically had never coded before, yet it was a great experience. I was lucky enough to get paired with both experienced bioinformaticians and novices like myself. We got through and bonded over Terra errors. The biggest learning is that coding isn’t so terrifying, and using a lot of Google and having a little faith in yourself, you can get something done.
In the second one, I got to really understand the biological questions we were trying to answer and which tools were more suitable to approach them. We are still working on the outcomes of this edition, and I am very excited to share them when they are available!
I would love to participate in another Hackathon, and if someone is reading this and is afraid to apply to one, hear me out: do it! We all start being confused, bond over trauma, and then actually have a lot of fun.
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Great topic @ehutchins ! I actually participated in the IPDGC/GP2 virtual hackathon in 2021, where I teamed up with others on a visualization project for PD progression. Echoing previous posts, I also believe that coding skills aren’t the most crucial aspect. Everyone could find their role and contribute to the team. The experience was fun, and we learned a lot from each other. It was impressive how we managed to create a functional app despite the time constraints. Although we couldn’t polish the app to a publishable level, I think the main goal was achieved: gaining knowledge and making new friends. I’ve found it rewarding especially I picked the area which is not familiar to me but intriguing to me.
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I’ve never participated in a Hackathon, being most of a “rogue” researcher, until now hahaha. I intended to participate in future hackathons and seing such excellent comments in this topic motivates me more!
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This is great! @ehutchins (or others), do you have a calendar of hackathons for 2024? Is there some source you’re using to try and keep track of these year-over-year? Wondering if we might start incorporating that info somewhere on Discourse (perhaps a calendar widget?).
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The NCBI updates their list regularly.
Otherwise for me it’s word of mouth, or knowing that certain meetings might tend to have them as well - NextFlow for example always has two portions to their annual meeting (a meeting and a hackathon).
I love the idea of a calendar widget - can users submit hackathons that they know about and have them added to a calendar?
I think that is an interesting idea – definitely would need to lean on community-wide contributions if we wanted it to stay up-to-date/sufficiently comprehensive. @lmackenzie let’s chat about this and circle back!
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