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<strong>Welcome.</strong>
 
<strong>Welcome.</strong>
  
Genomics is pretty awesome. These days, you can sequence entire transcriptomes, find all the binding sites of a specific transcription factor, determine every position of modified histones, and map 3D chromosomal conformation.
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Hi, I'm [http://mucociliary.org/index.php/About Ian Quigley]. I like biology and data science.  
  
  
As an experimental model, the African clawed frog ''Xenopus laevis'' is also pretty awesome. You can culture intact tissue, elicit cell fate changes in a snap, do live imaging, do biochemistry, and you can tag any protein you want and have it expressed in a living embryo in about a week.
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Right now, I do computer vision stuff at [http://www.recursionpharma.com/ 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.
  
  
However, it's been really hard to do both awesome things at once. Until now.
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Before this, I did functional and developmental genomics at the [http://www.salk.edu 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 [http://mucociliary.org/index.php/Downloads 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.
  
  
Here is a repository of genomics tools and methods optimized for use in  <i>X. laevis</i>. Please use them! While the [http://mucociliary.org/index.php/Downloads 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.
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The repository hosted here was partly inspired from discussions at the Xenopus Bioinformatics Course, run by the [http://www.xenbase.org/entry/ National Xenopus Resource], at [http://www.mbl.edu/ Woods Hole]. Lectures from that course can be found [http://daudin.icmb.utexas.edu/wiki/index.php/List_of_sessions here].
 
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This repository is run by [http://mucociliary.org/index.php/About Ian Quigley], a postdoc in [http://www.salk.edu/faculty/kintner.html Chris Kintner's] group at the [http://www.salk.edu/ Salk Institute]. It was partly inspired from discussions at the Xenopus Bioinformatics Course, run by the [http://www.xenbase.org/entry/ National Xenopus Resource], at [http://www.mbl.edu/ Woods Hole]. Lectures from that course can be found [http://daudin.icmb.utexas.edu/wiki/index.php/List_of_sessions here].
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Revision as of 02:07, 17 August 2016

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.