Manifesto

Getting into bioinformatics in 2023 is a weird time. We’re right on the cusp of a Biotech boom. There’s also a ton of legacy things that exist because bioinformaticians were an after thought for many years. As such, they were usually biologists who then picked up scripting and got just enough done to get by. That was all. I came into this scene at a time where tech was really having a boom and machine learning was starting to get hot and so I didn’t come in with all these preconceived notions and just learn from people on that. The internet was just enough starting to keep searching for something better. And over time I found those. I eventually stumbled into a community with nf-core that cares about things like containers and reproducibility. That’s awesome. The problem is, it’s a lot to take in with bioinformatics and a lot to learn to cover to be effective nowadays. So it’s like software engineering but then you also have the biology aspect as well to understand and then on top of that all the weird legacy stuff. So I started this site because I kept trying to explain the pathway that I took to learn all this in a quick way and I wanted it to be useful..

I started this site because I first tried to build a documentation site for my lab group. Then I made a site for my course. They both became outdated and neglected, because no one used them.

I think I just wasn’t dreaming big enough.

Some things I want to include like understanding containers, getting creative in an academic setting, and being scrappy with your compute dollars on those for free resources. Talk about our clone in that section. Let’s see. What other things does Edmund want to cover on that? I really want some backlinks. I don’t know if Starlight will support that. Let’s see. What else do you have? Well, okay. Cool idea. That was kind of less than I expected.

Some things I want to cover:

• Containers
• Being scrappy with compute costs
  • rclone
• History of bioinformatics¹

Footnotes

1. Like why we use so many weird file formats and why everything is a CLI tool and we don’t use like just use one programming to do everything. ↩