The Google Summer of Code (GSoC) 2016 is drawing to a close so we thought it best to summarise our experience with GSoC from the mentors’ perspective. We originally came to GSoC through the Mozilla Science Lab. We’ve been having regular calls with Abby Cabunoc from Mozilla, who’s been kind to support openSNP‘s efforts in trying to make open science more accessible. Together we quickly identified a need for more volunteers and people working on the project. From there, we got to the Open Bioinformatics Foundation (OBF), which has been participating in GSoC for years. The OBF kindly agreed to take openSNP under its umbrella, all we needed to do is come up with a few projects, which didn’t take long with the help of Abby (thanks again!!).
We came up with 3 projects that we wanted to tackle for quite a while:
- Overhauling our frontend, which has been stuck in the non-responsive dark ages of Twitter Bootstrap basically since the start of openSNP in 2011. Something that’s been rather annoying to many of us over the years.
- Connecting the Phenotype and SNP information. We do have annotations for genetic variants that basically already tie these genetic variants to the phenotypic data we’re storing. But so far there’s no easy way to go from one to the other. Which limits the use of openSNP for many use cases.
- Getting more Quantified Self data from Fitness-Tracking devices into openSNP. We’ve been offering support for Fitbit for a while, but nothing for other devices. We wanted to change this and add some more support in general.
For project #1, the frontend work, we could win Mateus, who is largely teaching himself how to work with CSS, JS and all that weird stuff. He’s from Brazil but recently moved to Toronto. See his final blog post on what he achieved.
For project #2 (phenotype <-> SNP link) we could win Vivek who is an Biotechnology student at IIT Kharagpur (India). See his final blog post here.
For project #3 (more Quantified Self data) we could win Graham, who is an Computer-Science student at the University of Illinois. You can see his final blog post here.
We handled the communication by having a bi-weekly call with whoever had time to show up, which isn’t easy when you have one mentor in Germany, one in Australia, one student in the US, one in Canada, and one in India. It was rare that all students could make time for the call, but the majority of communication was still handled via openSNP’s gitter channel, or via email. Surprisingly, the gitter channel is also where students started to help each other if mentors were still asleep in their respective time-zones. Towards the end of GSoC we increased the frequency of group calls to make sure that all students had support with their deliverables (blog posts similar to this one, code excerpts, etc.). It’s a bit daunting for a first-time GSoC project to accept three students, but we’ve been lucky with three students who were all very well to work on their own, and who always stayed on our radars and checked in with us to share their progress. We’ve also been lucky to have Abby help us with making sure that the projects are well-defined.
Most of the students’ projects are not 100% finished but that’s not the end goal here, what we want is more people to join us on this journey of open science, not to give us finished products and then disappear. We’re confident that the students will keep on collaborating, as we believe that participating in such a small, easy-to-change open source project is a great source of programming experience for novel programmers. If all goes well, openSNP will probably participate as mentors again next year. We’re still unsure how many students we’ll take next year, we were probably very lucky this year. It will depend on how many actual problems we’ll have then. For starters, the gender ratio of people involved in openSNP is still predominantly male, and which open source project is ever truly finished?
If you’re now interested in joining openSNP you can find all of us hanging out in our Gitter channel at https://gitter.im/openSNP/snpr, where you’re most likely to find one of us being awake and ready for a chat. We also want to hold regular office hours via Google Hangouts once per month in the future, stay tuned for that.
Thanks to the OBF for making us part of this great experience and also to our three awesome students! Again, you can take a look at the final blog posts from the participating students here in order of the projects we proposed: