Forum:Open Source projects to contribute to

Question

[shane]

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.

Thanks

[richard.schneeman+no-recruiters]

I run an open source project designed to make contributing to open source easier: CodeTriage. It sends you issues in your inbox so you can help without getting overwhelmed.

Give it a try once you find some bioinformatics repos and let me know if you’ve got any feedback.

Answer 1

[Brad Chapman]

Shane;

Welcome to bioinformatics work. It would be easier to offer suggestions with an idea of your programming background and biological interests. As a starting point, the ADAM project has a nice contributing guide, great group of folks, and the issue tracker has 'Pick Me Up!' issues which are meant as starting places for interested contributors:

https://github.com/bigdatagenomics/adam

https://github.com/bigdatagenomics/adam/blob/master/CONTRIBUTING.md

https://github.com/bigdatagenomics/adam/issues

Hope this helps with getting started.

[shane]

Nice project, I like the idea of the pick me up tag. I've added in my experience to the original post too if that helps. Do you know of any projects as well put together as ADAM for contributors but in say Python?

[peter.amstutz]

Brad is being too humble here, his own project, bcbio-nextgen orchestrates bioinformatics tools in Python and has a few projects you might be able to help with.

Answer 2

[peter.amstutz]

Arvados is an open source data science platform that focuses on bioinformatics. There is also the Galaxy project.

[shane]

Just as a (very late) update. I've started getting my head around and contributing code to Galaxy. The developers are very friendly and there's a nice beginner tag on issues to pick up easy wins.

Thanks for the suggestion Peter.

Answer 3

[Ahill]

Shane - you might want to check out the tranSMART project. It's at an interesting stage right now. It's an ambitious project to develop a knowledge and data management platform for translational bioinformatics.