Open source biology software projects

August 20, 2012 11:10 AM

What open source medicine/biology related software should I get involved with?

I have a good deal of programming experience (C/C++/Python), and am currently a student studying in the medicine/biology field, without any in depth experience in anything. I would be interested in volunteering with a relevant open source software project. This could be biology, medicine, biochemistry related, I'm not set on anything, but I know bioinformatics is likely to have something good.

I'm looking for something where they are interested in taking on volunteers and I could make a meaningful contribution. I think I would rather be involved with something more technical and related to the underlying science (rather than, say, a user interface), but as I mentioned I don't have much experience in the field so that would have to be a learning experience.

I have googled for things, but it's hard to see how active a project is.

posted by Raidallinen to computers & internet (3 answers total)

Raidallinen, here's a short guide to quickly skimming the publicly available information about an open source project to see how active it is and whether it's amenable to new volunteers.

I work on bringing new volunteers into Wikimedia technical projects, and you might be interested in helping bring the new Wikidata project to fruition (background on Wikidata). This is only indirectly related to the underlying science, but given how many scientists end up referring to Wikipedia, you'd definitely be helping out the field.

In medicine, OpenMRS and VistA seem like reasonable projects to check out.
posted by brainwane at 5:30 PM on August 20, 2012 [1 favorite]

How about BioPython?
posted by bergeycm at 12:47 AM on August 21, 2012 [1 favorite]

How about Bioconductor (wikipedia)? I'm not an expert, but I believe it is a variation of the open source R statistical computing environment, that includes a bunch of packages for analyzing bioinformatic data. It seems like an active project, and the development of very specific packages (libraries) would be very technical and very much related to the underlying science. I think the packages are generally developed with the R language itself, but can be programmed in C or FORTRAN as needed.

Many people really like R, so I recommend becoming familiar with it, even if you don't do the Bioconductor stuff. This is about the limit of my knowledge, but I hope this was helpful.
posted by mean square error at 9:53 AM on August 21, 2012