KOkoeng·Oct 16, 2020
Sure! One thing I have to note though - the field is fundamentally different than software engineering. In software, it isn't unusual for someone to maintain a software package for a long time, and for other people to contribute. In biology, typically software projects are made by individuals (only supported through their graduate school) and are never contributed to by outsiders (most don't know how Git development and PRs work). There are lots of projects in the normal bio category, but probably aren't useful.
The 2 that come to mind that are a bit more organized and in development are SBOL (https://sbolstandard.org/) and Poly (https://github.com/TimothyStiles/poly, self plug).
SBOL is a project looking to make a better format for sharing DNA sequences. For context, the same format (GenBank format) has been used as the standard for shar
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ing biological sequences since 1982. As you can imagine, our understanding of DNA sequences has improved since that point, but we have no way to encode much of that information in a shareable format. So it doesn't get shared. That means a lot of genetic elements can't be computed (data is there, it isn't shared) so synthetic biologists just keep it floating in their heads to make experiments work. SBOL is a new format that has been running for about 10 years trying to change that - it is pretty much the definition of "design by committee", but their design is extremely thought out, and they have the community reach necessary to get acceptance. However, the tools just ain't there yet to use SBOL for widespread adoption. I do believe it'll get there though, but they don't have enough skilled programmers.
Poly, which is a project I've been involved, is aiming to make good CLI tools for biotech (in addition to a kickass Golang library). It's fairly early, but ran by an actual software engineer, and we're making pretty good progress on tooling, and a decent community of biologists. For example of some stuff we're working on right now for version 1.0.0 - universal identifiers for genetic sequences, JSON representations of GenBank files (for interop), codon optimization / DNA synthesis optimization, primer design, and plasmid cloning simulation. One of the exciting parts of the project is an algorithm I designed that is able to extremely efficiently index genetic sequences for search. The goal is to index ALL public genetic sequences and make them searchable through a simple API (Should get a 100-1000x speed up to what is currently available).
SBOL does calls every Wednesday with updates to their work, and Jacob Beal kinda runs the show (awesome guy). Poly has a gaming night every Friday, which is a good way to figure out if the community is right. We're trying to get more issues on Github, but that is a work in progress!