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Can a programmer with zero knowledge of bioinformatics be of help too? Or do you need a bio background?

by akudha 6y ago

planet-and-halo 6y ago
I'd like to second this question. I'm very interested in bioinformatics as a field, but no background. Would be happy to devote some free time but I wouldn't want to be counterproductive.
- ViralBShah 6y ago
  The way to do this is to find non-domain specific tasks in these projects, and make useful contributions to the team - and slowly learning as you go along. Website, CI, benchmarking, helping out new users, pointing out unclear docs, writing a tutorial as you learn, etc. are all great ways to get involved.
  - planet-and-halo 6y ago
    Thanks a lot, these are great suggestions.
jakobnissen 6y ago
You don't need to have any particular skills except familiarity with Julia, but it's obviously an advantage to have a bio background - depending on what you're going to do. Usually, the best packages come about when people are motivated to creating something specific, for example if they think the status quo in some domain is not good enough. I'm sure we can dig up a handful of old, badly maintained projects that could use some love. Off the top of my head, it would be nice to have * Micro-optimized our smith-waterman algorithm. That's probably fairly easy to get started with if you're not a bio person * A number of our parsers have not been properly maintained. We use finite state automata https://github.com/BioJulia/Automa.jl https://github.com/BioJulia/Automa.jl to create parsers. That's for more advanced users * We need to consolidate our scattered sources of k-mer analysis code. Another developer is re-writing our k-mer iterator protocol, but we need a big toolbox for k-mer counting, minhashing, calculating k-mer spectra etc. That's also very computer-sciency and no so much biological Feel free to get in touch on the Julia Slack, or send me an email :)

Can a programmer with zero knowledge of bioinformatics be of help too? Or do you need a bio background?

by akudha 6y ago

Can a programmer with zero knowledge of bioinformatics be of help too? Or do you need a bio background?

I'd like to second this question. I'm very interested in bioinformatics as a field, but no background. Would be happy to devote some free time but I wouldn't want to be counterproductive.

ViralBShah 6y ago
The way to do this is to find non-domain specific tasks in these projects, and make useful contributions to the team - and slowly learning as you go along. Website, CI, benchmarking, helping out new users, pointing out unclear docs, writing a tutorial as you learn, etc. are all great ways to get involved.
- planet-and-halo 6y ago
  Thanks a lot, these are great suggestions.

jakobnissen 6y ago

You don't need to have any particular skills except familiarity with Julia, but it's obviously an advantage to have a bio background - depending on what you're going to do. Usually, the best packages come about when people are motivated to creating something specific, for example if they think the status quo in some domain is not good enough. I'm sure we can dig up a handful of old, badly maintained projects that could use some love. Off the top of my head, it would be nice to have * Micro-optimized our smith-waterman algorithm. That's probably fairly easy to get started with if you're not a bio person * A number of our parsers have not been properly maintained. We use finite state automata https://github.com/BioJulia/Automa.jl https://github.com/BioJulia/Automa.jl to create parsers. That's for more advanced users * We need to consolidate our scattered sources of k-mer analysis code. Another developer is re-writing our k-mer iterator protocol, but we need a big toolbox for k-mer counting, minhashing, calculating k-mer spectra etc. That's also very computer-sciency and no so much biological Feel free to get in touch on the Julia Slack, or send me an email :)