Google Summer of Code at InterMine

We’re pleased to announce that we’ll be participating in Google Summer of Code 2017 as a mentor organisation, under the umbrella of the Open Genome Informatics. Here’s the full ideas list for Open Genome Informatics Projects – InterMine projects are numbers 3 to 9.

Information for students:

About us:

InterMine is an open source biological data warehouse, based in the University of Cambridge. There are nearly thirty instances of public InterMines, covering a range of subjects from organisms like mice and rats, mines dedicated to plants such as the soybean, insects like the fruitfly or bees and wasps, and even mines dedicated to mitochondrial DNA and discovering drug targets.

We’re interested in mentoring students from a bioinformatics, computational biology, or computer science background.

You don’t have to be a biologist to work on InterMine related projects – many of the full time developers on the team didn’t come from a biology background – but biological knowledge is an advantage.

We use a range of languages in our projects, but most commonly you’ll see Java, PostgreSQL, Clojure/ClojureScript, and JavaScript. Each instance of InterMine has its own set of web services, and there are client libraries in five different languages, with a sixth in final stages of development.

Browse through our GitHub repos to see more of our projects: https://github.com/intermine

Getting started:

If you’re interested in applying for one of our projects, drop an email to the people named in the project description to introduce yourself, and explain which of the project(s) you’re interested in. There’s already been quite a lot of interest in the Similarity project from multiple students, so you might want to consider one of the other projects as a backup if you think you’d particularly like InterMine.

When you mail us, please make sure to include as many of the following as possible:

  • A CV / Resume. Tell us about yourself!
  • Links to GitHub, BitBucket, LinkedIn or similar.
  • Sample code. If you don’t have GitHub/Bitbucket etc. we’d still like to see what you can do. A class coding assignment or personal project you’re proud of is a great alternative.

A great way to familiarise yourself with the basics of building InterMine is to run through our tutorial: http://intermine.readthedocs.io/en/latest/get-started/tutorial/ – or alternatively you could try familiarising yourself with the web interface for your preferred InterMine. You can find the full list of InterMines at intermine.org, or try our experimental interface here: http://redgenes.apps.intermine.org/

We’ve also set up a few tickets on the core InterMine repo with the tag “Good first bug” if you’d like to get your hands dirty. Pop a note on the ticket and make a pull request when you think you’re ready. We have some guidelines for contributing that you should read before you make the pull request.

Finally, if you have any ideas or questions, please don’t hesitate to email us.

Useful links:

– Our twitter feed: https://twitter.com/intermineorg
– Here’s a blog post about some of the cool things the community has done with InterMine resources: https://intermineorg.wordpress.com/2016/11/22/cool-intermine-features-roundup/
– Our interactive web services docs: http://iodocs.apps.intermine.org/
– Our very in-the-works new ClojureScript UI. Demo: http://redgenes.apps.intermine.org/ repo: github.com/intermine/redgenes
– Developer documentation: http://intermine.readthedocs.io/en/latest/
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