Sunday, 28 September 2014

Making BaseSpace Apps in Bangalore

I'm speaking at the BaseSpace Apps developers conference in Bangalore tomorrow. It's my first App and my first time in India, so I'm pretty excited about the whole thing.

Earlier this year Matt Eldridge (Head of Bioinformatics) and I published a little paper on our sequencing QC tool: MGA. We've been using this for several years as a quick way to check sequencing yield and quality on the hundreds of lanes we're running each month. Matt has now almost completed development of a BaseSpace App version of the MGA tool so hopefully you'll be able to use it on your own samples in the very near future.


Right now the App is still only available to the developers as there are a couple of things to finish off. The genomes available on BaseSpace are not a complete set and we need several more to make the tool work as we think it should. There is some work here we need Illumina to do, but the BaseSpace development environment seems to be pretty good.

Illumina have used Docker as a method for easy App development. This is a tool Matt was made aware of by the Harvard Bioinformatics Core and the Galaxy team. Docker allows you to run applications on a desktop or server; that would otherwise be difficult to deploy without installing software and libraries that may affect other things running on these machines. Obviously this was built for the Cloud.

Matt completed this work (in addition to his day job - thanks Matt) in a pretty tight schedule after I received an invite to speak at the Bangalore meeting. I think it's only been about five weeks to get this far, and although the technical bits are way off my skills matrix, the BaseSpace App development using Docker seems to have been pretty excellent.

I'd certainly encourage you to look into this if you've got ideas for Apps. There is even the possibility of making a few quid by charging (although our App is intended to be free).

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