InterMine community roundup: June 2017

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

• InterMineR: GSoC student Konstantinos has been updating our R client, InterMineR, which is now ready for early testing and feedback. Download and install via dev tools!
• Similarity Project: Samyadeep’s GSoC work identifying similarities between objects in InterMine has produced an intriguing early graph: https://github.com/intermine/similarity/blob/master/intermine.pdf (also, who knew pdfs could be animated?)
• 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)
• InterMine Registry: Leonardo’s GSoC project has an early endpoint up that can be examined – check it out here: https://intermine-registry.herokuapp.com/registry/api-docs/ – how did we manage without a registry for so long? 😅  (github repo)
• Neo4j: GSoC student Yash Sharma has shared a nice blog post about structuring InterMine metadata in Neo4j. (InterMine neo4j github repo)
• Python cookbook: Like we mentioned in a previous post, Samarth has been creating a set of InterMine python tutorials. Tutorial 3 on filtering and constraints has just been published.
• Fly correlation webapp: Basheer set up this Fly correlation webapp which takes a Drosophila gene and retrieves a list of correlated genes based on gene properties. (github repo)

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!

Cool InterMine features roundup

I’ve said this before, but I’ll proudly say it again: one of the greatest things about being open source is the community. People are continually creative and resourceful with the tools we’ve built, and we love seeing all the different things you guys do with InterMine. Here’s a quick roundup of some of the things we’ve seen so far this year:

TargetMine’s Auxiliary Toolkit

TargetMine’s Auxiliary toolkit offers advanced analysis for networks and enrichment

TargetMine links out from report pages to provide external enrichment and interaction tools. Read more about it here, or  browse the tutorials: [Enrichment] [Interaction Network].

The Beany Mines:

The beany mines (Soy, Peanut, Legume, and Bean) recently added a shared motif search, as well as a couple of other great visualisations:

Legume @intermineorg updatehttps://t.co/SfiTGQjq94
New features: heat maps, genetic map displays & shared motifs pic.twitter.com/mIy01LZGV6

— Legume Federation (@LegumeFed) November 19, 2016

 

R and SOLR

Colin of HymenopteraMine and BovineMine did a great blog post about using our R client, InterMineR, and then continued to impress by making efforts to upgrade InterMine to use Solr.

MOLD

Ever wondered what Model Organism Linked Data might look like?  MOLD includes a queryable SPARQL endpoint and draws from multiple different InterMines to create a single dataset.

Tip: Make it generic

Generic tools are ones that aren’t hard-coded to a specific Mine or model. We’re always on the look out for new and exciting features, whether it’s a visualisation or a web service or a database tweak. If you think it’s good, you can email us to discuss it or simply create a pull request, and bask in glory forever after.

We’d love to see more!

This list is awesome (thanks everyone!!) but by no means conclusive. If you think we’ve missed something out, or you’re doing something new at the moment, drop us a line and we’ll add you to the next round up. We’d also love to hear from others who might be interested in guest-blogging an InterMine related feature.