What’s The Answer? (beginner projects to pick up)

This week’s highlighted discussion tackles the topic of small projects for folks who are just beginning their training in bioinformatics, or possibly a career transition into a new area. It’s an issue that has come up a number of times, and this new idea for connecting students and projects is a good one, I think.

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

We’ve talked in the past about having some kind of mechanism to connect students or young coders who need projects with small tasks that need to be done. And just last week one of the searches to our blog brought this: small_projects_bioinfo

So when I saw the discussion at Biostars, I was interested.

Forum: Open Source projects to contribute to

I’m a Computer Scientist/experienced developer looking to get into the field, and contributing to Open Source seems to be one of the first suggestions people make for starting out in bioinformatics.

I was wondering if anyone had any recommendations for open source software projects worth contributing to, particularly ones that might have some low hanging fruit or are in real need of help. Is there any tools you folk are using right now that really needs feature X or are you a project maintainer that needs a dig out? The difficulty I’m having is that because I’m not working with these tools day to day, I don’t have the best view of the commonly used tools and their associated problems.

So if anyone has any suggestions I’m going to try fit in some OSS contributions with my own contracting jobs/spare time bio studying. My programming background is Java, Javascript, Python, PHP and I’m learning some R at the moment while I do some coursera specialisations. I’ve done quite a bit of systems admin if the work involved server-side clustering/distributed systems etc.



The answer with the idea for the “Pick me up!” tag struck me as a good system for this sort of thing. Maybe others could implement this kind of tag on their projects too, if they have suitable small tasks. So I thought I’d raise the awareness of that a little bit–in case someone comes to us on a search for “small academic projects in bioinformatics” again. I hope they find some. I still think it’s a need on both sides.