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.

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