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.

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.

 

InterMine Registry

At the beginning of the development of this project, there was no place from where all the up-to-date InterMine instances information like name, url, description, versions, organism, colors, logo, could be retrieved at once. This lead to hard-coded information, and inefficient processes in order to get these data. Motivated by these problems, InterMine Registry idea was conceived. InterMine Registry is a place where all the up-to-date instances information is stored and can be consumed by applications like Blue Genes, iOS, InterMine R, the friendly mine tool or available to everyone who needs it.

The core of InterMine Registry is its RESTful API (http://registry.intermine.org/api-docs/). Running over Node.js integrated with MongoDB, it contains methods (endpoints) to administer the instances on the registry (add, update & delete) and search among them. Maintaining the registry up-to-date is critical. In order to achieve this goal, the Registry provides automatic updates of all the instances every 24 hours. In addition to this, all or one instances can be manually updated by using the API  synchronization methods. It should be noted that in order to administer instances, an authentication process must be done.

To complement the API, a fully responsive front-end web application is being developed (http://registry.intermine.org/), from which everyone can see all the InterMine instances and search among them. Instances are presented in a list and grid view, both of them having the same purpose but with different aspect. Moreover, a world view is presented, from which the users can see the InterMine instances location on a world map. In addition to this, authenticated users can administer the instances (add, update & delete) with a nice user interface.

This project is part of Google Summer of Code, still under development by me, Leonardo Kuffó, undergraduate student at ESPOL university (Guayaquil, Ecuador), under the mentoring of Daniela Butano. The source code of the application can be found at https://github.com/intermine/intermine-registry

 

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!