GSoCers Assemble! Announcing the InterMine GSOC 2017 students

Google Summer of Code is officially open as of 16:00 UTC today! This year InterMine will have five students coding over the summer, with five projects:


  • InterMineR will be getting better docs and hopefully submitted to R repos. Konstantinos Kyritsis will be working on this with the help of InterMine mentors Julie and Rachel.
  • Our Android App will get a younger sibling in the form of an iOS app, thanks to Nadia Yudina. I’ll be the primary mentor for this project.
  • We’ll finally have a proper registry of all the great InterMines out there, brought to you by Leonardo Kuffo with Daniela mentoring the project.
  • Samyadeep Basu will be looking at an ‘InterMine Similarity project’ – given a Gene (or other entity) from InterMine – are there any other interesting entities related to it in some way? Josh is the lead mentor on this project.
  • Yash Sharma will be working on creating Neo4j-InterMine API endpoints under Sam Hokin‘s mentorship.

We wish we could have accepted more of you. In total we had more than 40 students interested in GSoC 2017 with InterMine, resulting in around 30 finalised applications. Many of the applications were brilliant – far more than we could possibly have accepted. Deciding who to accept was really tough, and even if you didn’t get a place in GSoC with us you’re still entirely welcome to contribute to any of our projects if you had any ideas.

Suggestions for accepted students

Congratulations on being accepted. We’re really glad to have you on board. Please have a quick read through our GSoC guidelines to get started.

During the community bonding period, here are a few ideas for getting involved.

  • Find out more details that might pertain to your project (obviously) – investigate the API or work on bugs
  • Project management – in your project’s GitHub repo create milestones, tickets, project boards as appropriate.
  • Write an intro blog post about yourself & your planned work (to be posted here and/or a personal blog we could link to).
  • Come hang in the chat (below).

Non-GSoC InterMine community: you can play too!

We’ve created a couple of chat rooms at We’ll be encouraging our GSoC students to hang out in the #general channel, and you’re welcome to, as well. The students are from all around the world – come make them feel at home!

California Dreaming: InterMine Dev Conf 2017 Report – Day 1

2017’s developer conference has been and gone; time to pay my dues in a blog post or two.

Day 0: Welcome dinner, 29 March 2017

The Cambridge InterMine arrived at Walnut Creek without a hitch, and after a jetlagged attempt at a night’s sleep we sat down to a mega-grant-writing session in the hotel lobby, fuelled by several pots of coffee and plates of nachos.

By 7PM, people had begun to gather in the lobby to head to the inaugural conference dinner at the delicious Walnut Creek Yacht Club. We had to change the venue quite late on in the game, meaning we decided to wander down the street to collect some of the InterMiners who had ended up at the original venue (sorry!!). By the end of the meal, most of the UK contingent was dead on their feet – 10pm California time worked out to be 6am according to our body clocks, so when Joe offered to give several of us a lift back to the hotel, it was impossible to decline.


Day 1: Workshop Intro

The day started with intros from our PI, Gos, and our host, David Goodstein. 

Josh and I followed up by introducing BlueGenes, the UI we’ve been working on to replace InterMine’s older JSP-based UI. You can view Josh’s slide deck , try out a live demoor browse / check out the source on GitHub.

Next came one of my favourite parts: short talks from InterMiners.

Short community talks

Doppelgangers – Joel Richardson, MGI

Joel gave a great presentation about Doppelgangers in InterMine – that is, occasionally, depending on your data sets and config, you can end up with duplicate or strange / incomplete InterMine objects in your mine. He follows up with explanations of the root causes and mitigation methods – a great resource for any InterMiner who is working in data source integration! 

Genetic data in Mines – Sam Hokin, NCGR/LegFed

Next up was Sam’s talk about his various beany mines, including CowpeaMine, which has only genetics data, rather than the more typical InterMine genomic data. He’s also implemented several custom data visualisations on gene report pages – check out the slides or mines for more details.

JBrowse and Inter-mine communication – Vivek Krishnakumar, JCVI

Vivek focused on some great cross-InterMine collaborations (slides here), including the technical challenges integrating JBrowse into InterMine, as well as a method to link to other InterMines using synteny rather than InterMine’s typical homology approach.

InterMine at JGI – Joe Carlson, Phytozome, JGI

Joe has the privilege to run the biggest InterMine, covering (currently) 72 data sets on 69 organisms. Compared to most InterMines, this is massive! Unsurprisingly, this scale comes with a few hitches many of the other mines don’t encounter. Joe’s slides give a great overview of the problems you might encounter in a large-scale InterMine and their solutions.

Afternoon sessions

FAIR and the semantic web – Daniela & Justin

After a yummy lunch at a nearby cafe, Justin introduced the concept of FAIR, and discussed InterMine’s plans for a FAIRer future (slides). Discussion topics included:

  • How to make stable URIs (InterMine object IDs are transient and will change between builds)
  • Enhanced embedded metadata in webpages and query results (data provenance, licencing)
  • Better Findablility (the F in FAIR) by registering InterMine resources with external registries
  • RDF generation / SPARQL querying

This was followed up by Daniela’s introduction to RDF and SPARQL, which provided a great basic intro to the two concepts in an easily-understood manner. I really loved these slides, and I reckon they’d be a good introduction for anyone interested in learning more about what RDF and SPARQL are, whether or not you’re interested in InterMine .

Extending the InterMine Core Data Model – Sergio

Sergio ran the final session, “Extending the InterMine Core Data Model“. Shared models allow for easier cross-InterMine queries, as demoed in the GO tool prototype:

This discussion raised several interesting talking points:

  • Should model extensions be created via community RFC?
  • If so, who is involved? Developers, community members, curators, other?
  • Homologue or homolog? Who knew a simple “ue” could cause incompatibility problems? Most InterMine use the “ue” variation, with the exception of PhytoMine. An answer to this problem was presented in the “friendly mine” section of Vivek’s talk earlier in the day.

Another great output was Siddartha Basu’s gist on setting up InterMine – outlining some pain points and noting the good bits.

Most of us met up for dinner afterwards at Kevin’s Noodle House – highly recommended for meat eaters, less so for veggies.

A flurry of deadlines: Grants, GSoC, workshops, and more…

We blogged in February commenting that we had a lot of events over the March / April period. Here’s a re-cap:

  • Attending conferences: Amongst the team we attended Bioschemas, the Elixir all-hands, and the Cambridge Scientific Computation Day.
  • InterMine training: We delivered a training workshop about using InterMine at the EBI, part of their Introduction to Omics data integration week-long course.
    • This went well despite a server-room meltdown which conveniently timed itself for the morning of the same day (the training session was in the afternoon, so we thankfully had time to get the servers back up!).
    • In contrast to previous years, every single hand went up when we asked if the participants wrote code as part of their job. Next time, we will try to allow for a longer session on using InterMine web services, rather than the 15 minute slot we allocated this time!
  • Developer Workshop and Hackathon: 5 days in sunny California, spending time with InterMiners from around the world. Longer blog posts to follow, but in the meantime you can browse the agenda for links to slides from each session, or the storify summary of tweets.
  • Google Summer of Code: We’re participating in Google Summer of Code (GSoC) this year (previously) as a mentoring organisation. We had over 50 interested students and 30 distinct applications, many of which were simply brilliant. The deadline for students applying, naturally, was the day after the hackathon, making finding time to provide student feedback a challenge. Maybe there’s a reason to be grateful for jet-lag induced wakefulness at odd hours!
  • Grants: A tale of two grants… :
    • New application: We had a grant application deadline that was, once again, the day after the hackathon. Uh-oh! Feverish figure fixes, tentative typo tweaks and word-count winnowing was squeezed in at every opportunity.
    • Good news about an old application: Meanwhile, we got the news that we’d been fortunate enough to have our hard work pay off: a grant we’d applied for last year as part of the BBSRC BBR 2016 call was agreed to! Hint: the future of InterMine is looking very FAIR, possibly even SPARQLing. More details in a later post.

Events coming up soon:


Justin and Gos attended the BioSchemas kick-off meeting at Hinxton this week. As well as giving a short talk about InterMine (the slides are on FigShare), Justin managed to jot down a few thoughts about the event:

The aim of the Bioschemas schema is to come up with simple metadata that can be embedded in webpages (JSON-LD, RDFa, etc.) to make it easier to find data. For instance, suppose you wanted datasets that concerned the effect of a certain drug.  At the moment, if you search in Google for that drug name, you will find relevant datasets, but also possibly datasets that happen to use that drug as part of their protocol and more things besides.

But if you can embed a schema which names the subject of the dataset in a structured way (e.g. puts an ontology term URL in a dataset.subject field) then you can pull up more relevant data.

However, there is a strong concern with keeping such markup as light as possible so that people aren’t put off annotating their datasets.  Hence, a notional rule that there should only be 6 properties per class (e.g. just name, description, url, keywords, variableMeasured, for dataset).

As such, bioschemas won’t be replacing any of the existing ‘heavyweight’ schemas (DATS, DataCite’s model, OMICSdi model, our own InterMine data model), as it’s not meant to be used as an internal data model.

  • Bioschemas is about getting properties into (as supported by Google, Bing, Yahoo, etc.).  However, is a big bag of potential metadata with few constraints (no cardinality, for instance!).  It’s up to Bioschemas to come up with constraints for our purposes, especially on generic metadata such as DataSet and DataCatalog.
  • Bioschemas is also largely about general areas at the moment (datasets, data sources, etc.) though there is some specific work on protein annotations and samples.  But not, for instance, on genes and proteins at this stage (though presumably protein annotations would need some metadata for proteins….)
  • Things are at an early stage – the next year will (hopefully) see some Bioschemas definitions.  There is still debate about exactly what it can be used for beyond search.  For instance, we (InterMine) may be able to use them to improve our data integration process if all sources start embedding common metadata in their download files as well as on webpages.
  • Bioschemas is more than schema work. The initiative covers topics such as identifiers, citation, metrics and tools too (which will be relevant to us in the future).  We can get value from these other areas too – for instance there was discussion of a standard way of providing notification that a data source (uniprot, etc.) had updated, which would be very useful to us in building mines that automatically update.  There was also talk of having metadata that specifies when a data source changes its format – another thing that would be tremendously useful for us.
  • The presentations were interesting and the group friendly.  InterMine seemed to be well received.  The group doesn’t have a many actual data consumers and integrators, so I think that we can make a valuable contribution from that perspective.

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:

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: – or alternatively you could try familiarising yourself with the web interface for your preferred InterMine. You can find the full list of InterMines at, or try our experimental interface here:

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:
– Here’s a blog post about some of the cool things the community has done with InterMine resources:
– Our interactive web services docs:
– Our very in-the-works new ClojureScript UI. Demo: repo:
– Developer documentation:

Upcoming Events

March and April 2017 are looking to be quite exciting for the InterMine team. Here’s where to spot us over the next couple of months:

6-8 March 2017: BioSchemas kick-off meeting – If you’re there, look out for Gos and Justin!

8 March 2017: As part of the EBI’s Introduction to Omics Data Integration course, Rachel will be delivering a session on InterMine “Open tools for data integration – hands on example with InterMine

20 March 2017: Scientific Computation in the University of Cambridge Seminar Day – Daniela will be giving the talk “InterMine: Best Practices for Open Source Software

29 March 2017 – 2 April 2017: Our very own InterMine Dev Workshop and Hackathon. Registrations are still open at the moment (21 Feb 2017), but the early bird room rate will be expiring in early March, so try not to delay if you’re planning on coming!

24-27 April 2017: Josh will be attending the HUPO-PSI 2017 meetup in Beijing.

2016 holiday period


Quick FYI:

We’ll have several people out of the office – but not everyone – over the week before Christmas, starting from today (16 December). If you need to contact us, you may get a prompter response by emailing our lists (e.g. the dev list) which will reach all of us, rather than emailing individuals directly.

The annual InterMine office closure will be between 23rd December evening until 3rd January morning UK time. During this period no one will be in the office, and we may not be able to respond to emails, tweets, blogs, etc.

See you all in 2017!!