Tag: News

🎉 BlueGenes 1.0.0 release 🎉

We are super excited to announce that BlueGenes 1.0.0 has been officially released!

BlueGenes is a new user interface to InterMine utilising its extensive web services combined with a modern web application stack, to provide a more interactive experience for exploring and analysing your data. In contrast with the previous interface, BlueGenes is separate from the InterMine server, increasing the ease of further development to both.

The new interface provides the same feature set you’re already familiar with, wrapped in a new design offering an enhanced user experience. In addition, it allows you to quickly change the InterMine server you’re connected to, to any other instance in your organisation or that is available through the InterMine Registry. While the old webapp acted as a front-end to a single InterMine, BlueGenes can be configured to serve multiple InterMine servers.

A new Tool API for adding custom visualisations and analyses tools to your InterMine has also been introduced. This allows you to create your own tiny JavaScript apps (or adapt the ones we have developed for HumanMine and FlyMine) for your InterMine data, which BlueGenes will display for list analysis, query results and/or report pages, depending on what you specify it supports.

While this is the first major release, we still have lots more coming. Some admin tasks, notably creating templates, is not available in BlueGenes yet so you will have to access the legacy webapp for this. The web services have yet to be separated from the legacy webapp, so it will continue to be available for a while (if you wish to wait with switching to BlueGenes, we recommend using the latest InterMine 4.x release instead).

This new release requires InterMine 5.0.0. To upgrade to InterMine 5.0.0 please read the upgrade instructions carefully.

InterMine 5.0.0 release

This releases contains new web services to support BlueGenes’s new features, in particular:

  • Login using OAuth2 (e.g. Google, Elixir)
  • Upgrading lists
  • Generate external links
  • Submit feedback
  • Reset password

This release includes the Frictionless Data Package specifications implemented by Nikhil Vats. Please see the documentation here for more details.

All the InterMine artifacts have been published on the Maven Central repo instead of Bintray’s JCenter due to the recent jcenter/bintray shutdown announcement.

For more details about this release, please see the release notes.

Documentation

The user documentation has been adapted to the new interface by Hanan (Outreachy intern) and is available here.

The InterMine Server documentation (aka dev documentation) has been revised by Mardhiyah (Outreachy intern) and is available here.

FlyMine and HumanMine

FlyMine has been updated to use BlueGenes. If you use Firefox, you might experience an issue due to the browser cache, in that case you need to delete the cache. The legacy user interfaces is still available here.

HumanMine will be updated soon.

Thanks to …

… all our users/contributors for their support, feedback and help. Thanks to Joshua Heimbach and Yo Yehudi for their great and essential past contributions to this project. Thanks to our excellent interns who have directly contributed to BlueGenes; Akshat for the 2019 GSoC project Javascript Data Visualisations, Sakshi Srivastava for the 2020 Outreachy mid-year project Javascript Data Visualisations, Roshni Prajapati for the 2020 Outreachy mid-year project Improve UI & UX of BlueGenes, and Hanan Younes for the 2020 Outreachy end of year project Create InterMine user training docs.

Contact us

If you have any questions or concerns about any of these changes, please do not hesitate to contact us.

Data integration and Machine Learning for drug target validation

Hi!

In this blog post I would like to give a brief overview of what I’m currently working on.

Knowledge Transfer Partnership: what & why?

First, in order to give context to this post, last year InterMine at University of Cambridge and STORM Therapeutics, a spin-out of University of Cambridge working on small modulating RNA enzymes for the treatment of cancer, were awarded a Knowledge Transfer Partnership (KTP) from the UK Government (read this post for more information). With this award, the objective is to help STORM Therapeutics advance their efforts in cancer research, and contribute to their ultimate goal of drug target validation.

As part of the KTP Award, a KTP Associate needs to be appointed by both the knowledge base (University of Cambridge) and the company (STORM). The role of the KTP Associate is to act as the KTP Project Manager and is in charge of the successful delivery of the project. For this project, I was appointed as the KTP Associate, with a Research Software Engineer / Research Associate role at the University of Cambridge, for the total duration of the project: 3 years.

Machine learning and a new mine: StormMine

Now that you know what the KTP project is about, and who is delivering it, let’s move on to more interesting matters. In order to successfully delivering this project, the idea is to use the InterMine data warehouse to build a knowledge base for the company, STORM, that enables their scientist to have all the relevant data for their research in a single, integrated, place. For this reason, several new data sources will be integrated into a STORM’s deployment of the InterMine data warehouse (StormMine, from now on), and appropiate data visualizations will be added.

Then, once the data is integrated, we can think towards analysing the data to gather insights that may help the company goals, such as applying statistical and Machine Learning methods to gather information from the data, as well as building computational intelligence models. This leads the way towards what I’ve been working on since my start in February, and will continue until July 2019.

In general terms, I’m currently focused on building Machine Learning models that are able to learn how to differentiate between known drug targets and non-targets from available biological data. This part of work is going to be used as my Master’s Thesis, which I hopefully will deliver in July! Moreover, with this analysis, we will be able to answer three extremely relevant questions for STORM, and which are the questions leading the current work on the project. These questions are

  1. Which are the most promising target genes for a cancer type?
  2. Which features are most informative in predicting novel targets?
  3. Given a gene, for which cancer types is it most relevant?

If you are interested in learning more about this work, stay tuned for next posts, and don’t hesitate contacting me, either by email (ar989@cam.ac.uk) or connect with me in LinkedIn (click here)!

 

InterMine 3.0 – Solr search

InterMine 3.0 is now available and features a brand new search powered by Solr.

Default search configuration will work well, but Solr allows for endless configuration for your specific needs.

Now the first search after deployment is instant, you can inspect the search index directly (via http://localhost:8983/solr/) and there’s a facet web service (via /service/facet-list and /service/facets?q=gene). Certain bugs, e.g. searching for the gene “OR”, are also now fixed.

New Configuration Option – optimize

There is a new keyword search configuration setting: index.optimize. If set to `true`, reorganises the index so chunks are placed together in storage which might improve the search time. (Similar to defragmentation of a hard disk.) See the configuration docs for more details.

Docs

Installing Solr

Configuring the keyword search

InterMine 3.0 upgrade instructions | release notes

A big thank you to our clever and hard-working 2018 Google Summer of Code student Arunan Sugunakumar — who did the bulk of the work as part of his summer project. Great job!

New Blog!

We’ve decided to streamline our blogging experience a little bit. Rather than maintaining several separate but mostly similar blogs for HumanMine, FlyMine, and InterMine, this blog will act as a combined stream.

Don’t worry – this doesn’t mean you’ll be forced to view irrelevant updates if you’re only interested in one of the sub categories. WordPress is great about filtering via tag or category. Here are a few quick links:

InterMine-specific updates: https://intermineorg.wordpress.com/category/intermine/

FlyMine-specific updates: https://intermineorg.wordpress.com/category/flymine/

HumanMine-specific updates: https://intermineorg.wordpress.com/category/humanmine/ (It’s empty now, but coming soon!)