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Welcome.

Hi, I'm Ian Quigley. I like biology and data science.


Right now, I do computer vision stuff at Recursion Pharmaceuticals. We look at images of cells to figure out when they're sick and ask what drugs might fix them. When I say "we look at images", that means we measure ~1000 features per cell across many cells (we hit 1 trillion measurements in June 2016!) or we ditch measurements altogether and go straight to Deep Learning approaches. Turns out biological images have as much, or more, informational content as genomic approaches, but taking and processing pictures is a thousand times cheaper.


Before this, I did functional and developmental genomics at the Salk Institute, focusing on an old-school developmental model, the African clawed frog Xenopus laevis. Here, you can find a repository of genomics tools for working with X. laevis, from RNAseq to ChiPseq to HiC. Please use them! While the downloadable reference databases are for frog, the general approaches described here will work for most organisms, including obscure ones purchased from pet suppliers. Pet store genomics is wholly worth doing. Seriously.


The repository hosted here was partly inspired from discussions at the Xenopus Bioinformatics Course, run by the National Xenopus Resource, at Woods Hole. Lectures from that course can be found here.