Out and about: where to find InterMiners over June and July 2017

We recently added a public google calendar you can subscribe to if you’re interested in knowing what we’re up to, or when public holidays might mean we’re out of the office. Here’s a quick lowdown on upcoming events:

20 June 2017: InterMine community dev call.

21 June 2017: Neo4j Life and Health sciences day in Berlin. Keep your eyes peeled for Daniela!

28 June 2017: Daniela will be presenting on our experiences with Neo4j at the London Neo4J GraphDB meetup.

4 and 18 July 2017: InterMine community dev calls.

22-23 July 2017: I’ll be presenting a poster at BOSC/ISMB about BlueGenes, with the fantastically witty title “Forever in BlueGenes: a next-generation genomic data interface powered by InterMine”. 👖


If you’re a GSoC student or mentor, there will also be the evaluation periods at the end of each month, but you’re doubtless well aware of those!

Further in the future, you may find us at SWAT4LS, ISWC, and further Bioschemas events. We’ll keep you posted!

Are you attending any fun events? Let us know!

If you’re going to be at an event this year where you’ll be telling others about your work with InterMine and might like some InterMine stickers or handouts – or perhaps you’d like to guest-blog about it or share your slides – please ping us.

 

 

 

InterMine community roundup: June 2017

Here are some of the exciting things that have been happening in the InterMine community recently:

Thanks to everyone who has contributed including students and their mentors. You guys are awesome!

excited Kermit via GIPHY

Have you done anything exciting with InterMine lately? email info [at] intermine [dot] org, tweet us at @intermineorg, or pop into chat.intermine.org to tell us about it… we’d love to feature you in a future round-up!

InterMine’s Python Client: Now with tutorials!

We’re excited to announce that our Python client is getting a new suite of tutorials / cookbook “recipes” to ease you into coding with InterMine.

The tutorials are in Jupyter notebook format (.ipynb), and you can preview or check out the tutorials on GitHub: https://github.com/intermine/intermine-ws-python-docs.

Right now tutorial 1 and tutorial 2 are online, and we’ll be adding more over the summer, with a target of around twelve tutorials. If you run through any of the tutorials and have feedback, we’d love to hear from you – info at intermine dot org, tweet us your thoughts, or open a ticket.

These tutorials are brought to you by Samarth, a fantastic community volunteer. Thanks Samarth!!

InterMine-Python tutorials
Screenshot of the first tutorial

Google Summer of Code: Coding period starts!

As of the 30th of May, the community bonding period is over and official coding starts for GSoC. The first evaluation period is between June 26 to June 30 (full timeline).

Preparing for the evaluation

We don’t have full details of the evaluation questions yet, but the Student Manual and Mentor Manual provide a decent overview – it’s likely to be a few short questions ensuring work and communication are occurring and are on-track.

Students: What you need to do:

Follow your workplan and communicate regularly with your mentor!  Evidence of work can include emails regarding progress, demos if possible, and GitHub commits / PRs. Read the Student Manual entry on evaluations. Remember you’ll need to complete an evaluation on your mentor, too.

Mentors: What you’ll need to do:

Make sure you’re communicating with your student regularly and you’re confident about their progress. If you are on vacation during the evaluation period (or immediately before), make clear plans now, and make sure your student knows what will be happening and who their backup mentor/evaluator is for this time period.

Please also read the Mentor Manual on evaluations, and consider arranging a face-to-face feedback session, since your student can’t see your evaluation details beyond a pass/fail status.

 

 

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:

gsoc-icon-192

  • 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 chat.intermine.org. 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.

20170329_221945

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: