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 😎.
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.
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.
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.
We’re in to the final stretch of the three month Google Summer of Code period, and results are coming through thick and fast.
On August the 17th at 5PM UK time (you can check when it is in your local timezone) we’ll be doing short presentations for each of the projects as part of our community call – around 5 minutes per project. Come join in and see the great work our students have been doing!
InterMine iOS app: Several members of the InterMine community signed up to provide beta testing while the app was under development. Nadia’s been doing some great work on this – users can now use keyword search across multiple InterMines, browse templates, lists, and create sets of “favourite” InterMine objects – perhaps building up a literature search for future use. It also loads its mine list straight from the registry! Expect it in the app store soon.
R: Konstantinos updated our InterMine R client library to include new features such as enrichment visualisation – expect a blog post about it soon! It’s under review in Bioconductor but you can use the library now directly from GitHub.
InterMine iOS app: Everyone who added their name to our iOS testing sign-up form should have gotten an email from GSoC student Nadia telling you to sign up to Hockey, the third-party application we’re using to distribute test builds. After you install Hockey and add your device ID, you’ll get an email notifying you when there’s a new test build available. You can submit any feedback via Hockey, or create a ticket in the repo. (github repo)
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!
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.
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.
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!
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.