A long overdue update

So much for blogging on a regular basis.

Having recently launched our public health infovis-specific blog (check it out here), I realized I was horribly remiss in updating my own blog. I will blame this largely on the fact that a) I went off to make science television for a bit and b) we’ve been in more of a data-gathering phase than a data-analyzing phase. That being said, there are a few things worth reporting on.

First, our preprint for TransPhylo: the Next Generation is up! You can find it on biorxiv as we await feedback on our initial journal submission. In this version, we’ve added the ability to account for unsampled cases within an outbreak, which is HUGELY useful because we can’t always identify and sequence every case, even for fairly tidy outbreaks like TB in a low-incidence setting like Canada. We’ve also made it possible to run the analysis as an outbreak is unfolding – no need to wait til it’s over. This is, obviously, rather useful.

Second, the last of our M. tuberculosis genomes from our big provincial sequencing project finally came through! The data came in fits and starts – the 276 I previously mentioned here came back in March, a good batch of them came in throughout May, and then the final plate, which maybe got lost in the couch cushions or something over at the sequencing centre, came in just two weeks ago. Our chief genome-pusher is currently on a post-wedding vacation; as soon as she’s back, we’ll get these out into a public repository, tagged with some useful metadata.

Everything else that’s on my plate at the moment is all small busy-work sorts of things as we wind down the summer. I’ve been rooting around in an unusual NTM genome sequence, playing with our first nanopore data, analysed a 140M point dataset (human genomic data, the horror!), and got a load of manuscripts from various projects I collaborate on out the door. And cat videos. Been watching a lot of cat videos.