Google Summer of Code: Let the enquiries commence!

Last month we applied for InterMine to join Google Summer of Code (GSoC) as a mentor organisation, and we’re pleased to report that we have officially been accepted!

Students: Interested in working with us for GSoC?

Our GSoC site has a project ideas list and the student application guidance, which hopefully will answer most of your questions.

Want to learn more?

  • You can also read our GSoC blog posts from last year to learn more about how things went.
  • If you still have questions:
    • If the question is project-specific: email both listed mentors of the given project.
    • If the question is about GSoC in general, see the student manual.
    • We’ll be running a GSoC question and answer video call session where students can learn more about the specific projects. Updates about the exact date and time will go out on this blog, our mailing lists, and twitter.

We’ll look forward to hearing from you!



‘Twas the week before Christmas… [aka InterMine availability over the holiday period]

… and all through the lab, not an organism was stirring, not even a… crab?*

Emails and support: Just a quick blog reminder that the office will be pretty empty from around now until the second of January, so don’t be surprised if we take a while to reply to messages. Some of us may be in the office or working from home, but it’s pretty patchy over the holiday season, and I don’t think any of us will be answering emails between the 23rd and 26th of December, nor on the first of January.

Developer calls: There is no developer call this week (normally it would be scheduled for Thursday the 21st). I’m not sure at this point, but the call on the 4th of January may (or may not) be cancelled as well.

Be good, have fun, and we’ll see you next year!

*I can only apologise for the terrible rhyme. Apparently nothing rhymes with “Cambridge” except “drainage” (and even then it’s somewhat weak), so I tried “uni” and that only rhymed with “loony” and “goonie”. Finding rhymes for the word “office” was no better.

Looking ahead: InterMine+Google Summer of Code 2018. Could you be a mentor?

2017 is coming to an end, and I have to say it’s been a fabulous one! I’ll probably post a “cool things InterMine did this year” round-up in a week or two – but in the meantime, here’s my final Google Summer of Code blog for you all!  We’ll cover the InterMine swag just sent out across the globe, as well as plans for next year – and how you can help out.

Thank-you gifts for mentors and students

Last week, we posted care packages to all our GSoC mentors and summer students, in the form of t-shirts, stickers, and pens. The postal-service-wrinkled shirt shown above is the women’s fit shirt printed on black; unisex shirts are a slightly lighter grey colour. If you filled out the swag survey when it was sent to you, your gift should be with you soon! Tweet us your images of the items in use for extra InterMine Cool Points 😎.

GSoC 2018 – call for project ideas and mentors!

Early 2017, we put together an ideas list for GSoC projects – InterMine’s projects are numbers 3 to 9. If you want to get more of an idea what it’s like to apply, (or be a mentor), read our application guidance from last year.

Do you have a nifty idea, or an InterMine itch you’d like to scratch?

Please share it with us! Add it to our 2018 Google Summer of Code ideas list, or if you need to sound things out and discuss them a little bit, comment on the GitHub issue, or email the dev list. You can even propose several ideas, if you like! Please add all ideas by the end of 14th of December (end of this week).

Would you like to try mentoring?

Fancy a chance to earn some nifty exclusive swag like pictured above? Add your name as a possible mentor to an existing idea (or your own new idea). You can always drop us a line if you want to discuss things first. We like projects to have more than one mentor if possible.

Maybe you’re a student thinking of GSoC?

Awesome! If you have your own InterMine project idea (whether it’s brand new or you’ve already started it), or if one of the ideas on our ideas list lights your fire, it’s not too early to start talking with potential mentors about it. The application guidance we mentioned above would be a good read, too.



Community Outreach: What we’re up to & how you can participate

A large part of working in open source and science is sharing what you do with others – it’s not just about code and papers. We have quite a bit going on and coming up that we’d like to share and get your ideas about.

Community outreach calls

We’ll experimentally be trialling a community outreach call on December 7th at 5PM GMT. This happens at the same time as our normal developer call usually would, but we’re specifically focusing on community members and ways to communicate and help them out. It will not have a focus on technical issues or code.

Developers are still entirely welcome to come along, but please encourage your curators, enthusiastic users, and outreach people to come along too! Agenda

Open outreach repo on GitHub

We’ve created a GitHub repository dedicated to outreach-related topics. The idea is to take discussions out to the open about what we’re doing so others can chime in and/or re-use or work. Examples include:

Science Festival – March 2018

We’ll be participating in the Cambridge Science Festival, teaching about better data enabling better science. The basic idea is teach this through gameplay with puzzles, rewarded with candy and stickers. Do you have kids who might be willing to playtest our ideas? Let us know!

Webinars and tutorials

We’ve done workshops in person, we did a developer workshop: we’d like to try something online this time! What formats interest you / your users the most?

  • A series of short 5-minute-ish webinars covering various topics
  • A longer training session, covering querying InterMine via website and/or API? Perl, Python or R?
  • Other? Share your feelings in a comment, contact us, or add to the GitHub issue
  • Maybe you’d like to volunteer to run one!

Google Summer of Code

Do you have an idea for a fun InterMine project that would only take a couple of months? Or maybe you would like to mentor a project over the summer? We had a great time during GSoC this year, and we’re planning to apply to do it again next year. Interested? More info on GitHub.

Rachel’s world tour of the UK

As part of the upcoming ISA-InterMine cloud grant, Rachel will be visiting bioinformatics cores and labs to try and solicit use-cases from people who are working with biological data right at the front. Want to help our or invite us to your lab? Get in touch.

Guest blogging

Come tell our followers about the awesome thing InterMine thing you just did. A conference? a talk? a new features or exciting dataset in your mine? We’d love to be the platform for your voice!



Talks and Workshops: Sharing our materials for re-use

Would you like to grab some ready-made slides or InterMine training workshop materials? We’ve rounded up of some recent things that have been going on. Feel free to remix materials for your own talks and outreach efforts. If you do use them, we’d love to see the result!


You should have permissions to make a copy; if not, please contact us / tweet us / pop by chat to poke us with a stick.

3-min lightning talk at GSoC Mentor Summit: Citable version on FigshareGoogle Drive (editable) version

Better Science Through Better Data: Citable version on Figshare | Google Drive (editable) version | Featured image above was live-scribed during  the talk. Licence is CC-BY from Springer Nature, and the image is available from

Blank InterMine-branded slides: Get ’em here.


BlueGenes Poster: This poster was presented at BOSC 2017Citeable version on F1000Inkscape editable version –  (download Inkscape here:

InterMine Poster for Elixir UK All Hands 2017: PDF version | Inkscape editable version 

Workshop learning materials

We run an InterMine training workshop every term, covering the basics of using the webapp, as well as discussing how to draw data from the API. If you’re near Cambridge, keep your eyes open on the blog or twitter feed, as we’ll always announce them well in advance.

Workshop training materials in PDF: Workshop Exercises – handouts with answers | Workshop slides – note that these exercises were all correct with data from HumanMine in October 2017. Numbers of results may change if we add or update new data sources in the future, but the majority of the materials should still be generally correct apart from the results counts. 

You can download the original OpenOffice files as well if you’d like to adapt the materials for your own workshops, or feel free to contact us if you’d like to coordinate some training with us.

Side note: We’re also delivering a half-day workshop training session as part of the EBI’s 4-day Introduction to Multiomics Data Integration course – applications are open now until 01 December 2017.


Data, Scientific (2017): Better Science through Better Data 2017 (#scidata17) scribe images. figshare.

Retrieved: 15:48, Nov 06, 2017 (GMT)

InterMine 2017 Fall Workshop – Biological Data Analysis using InterMine

University of Cambridge is hosting an InterMine workshop 27 October 2017.

The course is aimed at bench biologists and bioinformaticians who need to analyse their own data against large biological datasets, or who need to search against several biological datasets to gain knowledge of a gene/gene set, biological process or function. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available.

The workshop is composed of two parts:

Part 1 (2.5 – 3 hours) will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. No previous experience is necessary for this part of the workshop.

The following features of the InterMine web interface will be covered:

  • Search interfaces and advanced query builder
  • Automated analysis of sets, e.g gene sets, including enrichment statistics
  • Analysis workflows
  • Tools for cross-organism analysis between InterMine databases.
  • Web services

Part 2 (1 hour) will focus on the InterMine API and introduce running InterMine searches through Python and Perl scripts. While complete beginners are welcome, some basic knowledge of Perl, and/or Python would be an advantage. The InterMineR package will also be introduced. Those not interested in this part of the workshop are welcome to leave or there will be a more advanced exercise using the web interface available as an alternative.

See here for details:



InterMine 2.0 – Summer update

InterMine 2.0 is a large, disruptive release scheduled for this autumn, before the Xmas holidays.

There are lots of exciting features, but they will require InterMine maintainers to update their mines. Usually devs are able to update their mines with a simple git pull request. In this case, they’ll have to take specific actions to make sure their software is up to date.

Model changes

Several changes and additions to the core InterMine data model were discussed and approved by the community. See here for specific details on the new core data model.

This means that it’s likely that an InterMine 2.0 webapp will require a database built by InterMine 2.0 code.

Blue Genes

InterMine 2.0 will come with detailed instructions on how to deploy the new InterMine user interface.

Come to the next InterMine community call to see a demo of the latest features!


We’ve got a new software build system in the works. This will change the commands you use to build a data source and deploy your webapp. See a previous blog post for details.

Closer to the time, we’ll release detailed instructions on how to update your build system to work with the new tools. And as always the InterMine team will be on hand to answer any questions or issues on the community calls and the dev list and chat.

We hope to make the transition as easy as possible!

Software Dependencies

All software dependencies will need to be on the latest version.

  • Java 8
  • Tomcat 8.5.x
  • Postgres 9.4+

API Changes

We are making some non-backwards compatible changes to our API.

/user/queries will be moved to /queries

These three end points have a parameter called xml which holds the XML query. We are going to rename this parameter to be query (as we now accept JSON queries!) to match the syntax of all the other end points.

/user/queries (POST)

If this update is going to cause you any trouble at all, please let us know ASAP!


If you have any questions or concerns about any of these changes, please contact us or come along to the community calls.