To GitHub or not to GitHub?


I wanted to write about open source for a while. Then I saw in several bioinformatics job postings an experience with open source software being listed among desired skills — something I never saw before. Then I bumped into an article in a paper version of Computerworld “Saying Yes to open source” and the following: Netflix is built on open source — since its so low priced service; Kaiser Permanente has been using GitHub since 2011.

Well, what is open source? Wikipedia says: “open source is a development model that promotes a) universal access via free license to a product’s design or blueprint, and b) universal redistribution of that design or blueprint, including subsequent improvements to it by anyone” and adds that Wikipedia is an example of applying open source outside the realm of computer software. Inside, the best example of an open source software would be Red Hut Enterprise Linux; while Unix, which I for example use on my MacBook, is not open source. RStudio is an open source IDE for R programming language. Eclipse, one of my favorite IDEs for whatever language, is also open source allowing to anyone to edit existing and to  write new plug-ins. A lot of commonly used bioinformatics software  is open source: Jmol and RasMol viewers, BioPython, BioJava, Bioconductor (and other R packages in CRAN), Galaxy — a workflow web-based system for analysis of genomics data and integration of data from UCSC Genome Browser and user data, and many other.

On another side of this free open source paradise is code hosting web repositories. And while many of them have been set up in the last 15 years, only the oldest, SourceForge (hosts more than 430,000 projects and has more than 3.7 million registered users, by Wikipedia), and the youngest, GitHub (hosting over 11.7 million repositories makes it the largest code host in the world), are the two everyone can name on-the-spot.

GitHub seems to be one to go with, for now. I first encountered GitHub last summer when my summer high school students refused to use SVN and sent me a link to GitHub. Now they have something to show up to the world :). We haven’t embraced GitHub at work yet, while are considering to use it for showing up the code (it is not free for private developments). While according to some posts it is worthwhile to pay and transition to GitHub for private developments as well.


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