Where to find InterMiners: September-December 2017 edition

We’re busy as ever, and Gos is away at the #biohack2017 in Japan right now – you can spot him in a gold shirt sitting towards the back of the room here:

Other places to find InterMiners over the next few months include:

September:

12 September: FAIR in practice focus group – Research support professionals. Daniela will be at the British Library participating in this consultation. You may also be interested in the researchers focus group on the 13th. It looks like tickets are still available! (More)

21 September: **Cancelled**The usual community call is cancelled this week. We’ll be back as normal with updates in October, though!

25-27 September: Justin and Yo will be attending the Cambridge Bioinformatics Hackathon.

October:

2-3 October: You’ll be able to find Justin at the Bioschemas Elixir implementation meeting in Hinxton.

5 October: InterMine dev community call – back to our normally scheduled calls. Agenda.

13-15 October: Find Yo at the 2017 GSoC mentors summit in Sunnyvale, California

19 October: It’s another community developer call, yay! 

21-25 October: Justin will be representing us at ISWC in Vienna.

25 October: Better Science through Better Data in London – we’ll be sharing the story of InterMine in a lightning talk. Open data is awesome and InterMine couldn’t exist without it!

27 October: We’ll be delivering an InterMine training course in Cambridge, including an all-new API training section. Please spread the word about this one!

November:

November 1-2: You’ll be able to spot Justin at the Elixir UK all hands in Edinburgh.

December:

December 4-7: Get your Semantic Web on with Daniela at SWAT4LS in Rome!

Phew, that’s a lot!

 

 

 

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Blog: InterMine Cloud + ISATools: coming to a cloud near you

As many InterMiners may remember, due to some unlucky timing, we had a grant deadline that occurred during the InterMine Developer Workshop earlier this year, with seemingly countless group-work sessions like the one pictured here:

Thankfully, it looks like all our caffeine-fuelled hard work paid off the way we hoped: we are extremely excited to announce that the Wellcome Trust awarded us the grant! Here are a few highlights of what we plan to work on when the project starts in April next year:

Collaboration and metadata

This grant was written with Susanna-Assunta Sansone (Oxford e-Research Centre, University Of Oxford) to support a collaboration with the ISA-Tools group. ISA provides tools to structure metadata, covering the Investigation, Study and Assay of experiments; we will integrate the ISA format into InterMine and the ISA team will develop web-based tools to make metadata creation easier than ever.

Make your own InterMine with less sweat and toil

InterMines can be a challenge to set up right now unless you’re a developer. We’d like to do better. For simpler data formats, we’re hoping to create a UI-based wizard that allows you to drag and drop your files, select a few settings, and start a build – no need to touch a text editor. The more advanced / custom data formats will probably still require hands-on developer time.

InterMine in the cloud

If setting up your own InterMine becomes pleasantly easy, why not do it online? It’d be awesome if you could go to a website, click the “New InterMine” button, upload a few files (or paste their urls!), and end up with my-new-experiment.some-cloud.org for all your lab’s InterMine needs. Data will be merged with external supplementary data sources, and you’ll be able to analyse your data using visualisations (we’ll dedicate a chunk of time specifically to adding more datavis), our famous results tables, and familiar tools like gene set enrichment.

Enhanced import and export

We’d like to smooth out your way to sharing data with the community. Maybe you want to import data from Galaxy, or perhaps you want to export your InterMine as a virtual machine to be powered up and re-examined at a later date. Maybe you’d prefer to export data for publication as an ISA archive, bundled neatly with metadata, or maybe even generate the scaffold of a data paper automatically from your datasets. These are all things we’ll be working on with Susanna’s group.

Tell us what you think

As ever we are keen for input from the community and as we gear up for the next phase of development, now would be a particularly good time to hear from you! Tweet us, leave a comment, email the developer list, or pop by for a chat.

Google Analytics in BlueGenes: what should we track?

TL;DR: We’re implementing analytics tracking in BlueGenes. We can probably track anything you like, within reason. Leave a comment [comments now closed] or email us if you have anything you’d like to see! Must adhere our privacy policy.

Longer version:

InterMine’s JSP pages (the current, older UI) are set up with a couple of different types of tracking:

  1. Google Analytics, which currently anonymously records things like:
    1. Number of users and their locations
    2. Pages viewed
    3. With a bit of effort you can figure out what items were searched for by analysing query strings.
  2. InterMine home-brew internal analytics (to view in your own mine, log in as the super user and select the “usage” tab.) It tracks:
    1. Logins (anonymously)
    2. Keyword search terms
    3. Popular templates
    4. Count of custom queries executed
    5. List views by InterMine object type (but not list contents)
    6. Count of lists created, by type

So we have a couple of questions we’d love some feedback on, as we implement Google Analytics in BlueGenes:

  1. Do you use the current analytics? Which, or both?
  2. What would you *like* to record? Here’s a list of ideas

Things that are probably okay to track

  • Pageviews including counts and times – e.g. “17 views for /region-search on Monday the 13th at 10:pm”
  • Logins (anonymously)
  • Visitor location
  • Tools used (e.g. report page tools interacted with)
  • Popular templates
  • Mine used / switched to a different mine

Things we’re not sure about – what do you think?

  • Keyword search contents (anonymously). Pros: interesting analyses like this one. Cons: Could someone avoid InterMine out of fear someone would notice their gene is getting too much attention?
  • List contents (anon, as above).
  • What about mistyped identifier names in list upload?
  • Region search
  • Queries built in the query builder

I’m sure I’ve missed off quite a few things from both lists. We’d love to hear your input and feelings, both with regards to privacy and with ideas about useful trackable events and pages. Tweet us, comment on the web services tracking  github issue, email the dev group, or contact us some other way: http://intermine.readthedocs.io/en/latest/about/contact-us/

 

 

 

 

GSoC final month: testing, wrapping up, and live demos

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!

Here’s a quick summary of projects to date:

InterMine Registry: The registry is up and running! You can view all known instances of InterMine in the registry front end, or browse the API docs to learn more about programmatic access. Tip: like the logos you see? Add yours with these handy tips from Julie in an earlier post.

intermine-registry
Snapshot of the registry front-end UI.

Leonardo also wrote a great blog post about his work on the registry.

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.

Similarity Project: Samyadeep wrote up an in-depth technical project on the InterMine object similarity engine he’s been working on, using FlyMine sample data in Neo4J.

Neo4j: Yash will be demoing his InterMine Query <—>Cypher work on the call, or in the meantime, you can check out his blog posts on the subject.

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.

 

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