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:
We have a brand new blog and so would like to take this opportunity to tell you our grand plans for 2016.
Currently InterMine is built with a series of ant commands, and dependencies are managed manually. This of course is not ideal, and we plan to use Gradle to replace Ant and manage our dependencies automatically. This change will make builds faster, easier and more efficient.
For those of you with InterMines of your own, this means that you will use different commands for building your databases and deploying your webapps. We’ll provide the new commands along with documentation, and aim to make the transition as easy as possible.
We currently use Lucene for our search index but plan to greatly expand our utilisation of this great library — making search on InterMine more robust, sensitive and powerful.
Some have already deployed their InterMine to the cloud. We intend to make this process much easier, probably by creating a custom InterMine buildpack which pre-configures a Docker container with all of InterMine’s dependencies.
New Data Sources
We are always adding new data sources and would like to hear your suggestions. On our list right now is:
And of course we will continue to update our current data source library as file formats and data change.
New User Interface
We’ve developed a new user interface which should be ready for beta testing in early 2016. It’ll exist alongside the current interface for some time, allowing you to feed back ideas, suggestions, and critiques in the new interface, whilst still being able to rely on the old one.
Here’s a sneak preview (subject to plenty of change, of course!):
To go along with our new interface, we’re going to be adding a lot of new tools for you to use. Our wish list so far (not in order of priority):
Advanced Search / Query builder / Guided search
Recommendation engine (which gene is like my gene?)
Complex Interaction viewer
more powerful region search
InterMine search tool
Text mining tool
JBrowse / other genome browsers
UniProt protein browser
We’d like to hear which tools are important to you. We also will improve the tools we currently have, making them easier to adapt to your data sets.
2017 and beyond
Genomes are being sequenced every day, technology is moving at an ever more rapid pace and everyone is facing a challenging funding environment. We don’t know quite what the world will look like in the next five years but we are working hard to be future proof. We’ve always had a deep commitment to openness, flexibility and collaboration, and feel that this will help us meet any future challenges.
Towards this end, we are running a pilot program to test out various graph databases and to explore the semantic web. We will keep you posted on our progress as always, and would like to hear your thoughts.
Thanks to our great community for all of their support over the years! We look forward to a really exciting year!