GitHub: How an Open Source Programming Tool With a Funny Name Could Help Revolutionize Medical Research

Most people I work with in medicine have never heard of GitHub .

For the unfamiliar, GitHub is an online repository, which is an essential tool used by computer programmers to store their programming code.  It has a number of virtues, including giving users the ability to track multiple versions of their code (sort of like remembering all the track changes you ever made to your word document).  This is an essential tool for programmers but its value goes beyond its function as a track changes repository, as it is a site that facilitates open source collaboration, given its “social” features, similar to social networks like Facebook or Twitter, in which you follow the content of others or others follow you.

The most amazing thing about GitHub is that many users post their code (their work, their blood, sweat, and tears) publicly on their GitHub profile.  Individuals will comment on others code, providing valuable input that the owner of the code can use to improve their work.  In addition,  can “fork” another person’s code repository, and work directly on the code in their own Github profile to make changes or improvements, sort of like a tag team collaboration. GitHub is the tool to help facilitate large-scale open source collaboration for the software/web programming world (such as that which lead to the Linux revolution).

By early 2012 there were apparently 1.2 million users hosting over 3.6 million repositories.  Now that’s collaboration to scale!

So again, you may ask, why should physicians or medical researchers care about GitHub?  Because it can have broader application beyond the software/web programming world, as shown by its use among non programmers, who are currently repurposing Github to advance collaborate in their own respective fields.  They are posting book projects and transcripts of talks on the site, to encourage conversation and collaboration. One user even published his personal DNA information to encourage development of open-source DNA analysis.  It has been suggested that Github could even be used by US citizens to “fork” the law so that they can propose their own amendments to their elected officials.

How might we use Github to democratize the world of medical research?

As researchers we do so many different activities that we perform in isolation, which forces us to “reinvent the wheel” constantly, from drafting of ethics board applications, to creation of research protocols, to the writing of snippets of statistical code or code for web programs.

We usually share this experience and knowledge in a piecemeal way to just a few individuals who we happen to see on a daily basis.  If we could share all of this information more openly and widely with the community, we could reduce work that is menial and duplicative, which would enable us to accelerate research in much more meaningful ways.  I recognize that not everything we do can be shared online because of health privacy laws (the Health Information Health Insurance Portability and Accountability Act (HIPAA)), but there is so much information that we can share, not only in academia but in industry as well, to facilitate large-scale collaboration towards a common purpose of making a difference in the lives of individuals suffering from disease.

So I have opened my own GitHub account, and I have posted my first project.  I have also created part one of a “how to” slideshow about github for non-programmers, who want to dive in to the open source movement.  I hope that this represents just the first of many resources and tools and ideas that I might share with the larger community to inspire open-source collaboration in our academic world.

PS. I want to give special thanks to Ben West for sharing with me his passion for open-source collaboration, introducing me to Eric Raymond’s book, the Cathedral and the Bazaar, and showing me the possibilities of Github.

Joyce Lee, MD is a pediatrician, diabetes specialist, and Associate Professor at the University of Michigan. She is currently on sabbatical at Stanford University through the Center for Health Policy. She blogs about design and healthcare at joycelee.tumblr.com, where this post originally appeared.

2 replies »

  1. In a way, you’re missing the point of GitHub. You characterize it as a place where “we could share all of this information more openly and widely with the community,” but you could do that with Git by itself.

    What GitHub brings to the table are the social features, which you note, but, really, that’s the core innovation: commentary on knowledge, at all of its levels (creating it; changing it; understanding its history; ancillary communications such as watercooler conversation; etc.).

    I’ve addressed it here: http://7fff.com/2012/07/14/the-most-important-social-network-github/

  2. I just discovered GitHub a few weeks ago listening to various technical podcast like The Talk Show. I never considered what you are suggesting here is a terrific use of this type of site. I think I’ll consider opening an account as well and use it to share my healthcare thoughts and project ideas. Thank you.