Slides from my exit seminar

This morning I gave my last presentation at UC Davis. My highly informal exit seminar was a great opportunity to reflect on some of the many projects I've been involved with over the last decade here at Davis. Thank you to all who came, and a special thanks to Ian Korf for his kind introduction.

I include the slides below, but note that some of these slides won't make much sense without the narration (and you also get to miss out on two embedded videos). There was some video recorded via the Periscope app, but I found out today that Periscope only keeps video around for 24 hours, so unfortunately if you didn't watch the video when you had the chance it is now lost.

2015-11-21 12.34: Updated to reflect that Periscope video content is no longer available.

Some short slide decks from a recent Bioinformatics Core workshop

Last week I helped teach at a workshop organized by the Bioinformatics Core facility of the UC Davis Genome Center. The workshop was on:

  • Using the Linux Command Line for Analysis of High Throughput Sequence Data

I like that the Bioinformatics Core makes all of their workshop documentation available for free, even if you didn't attend the workshop. So have a look at the docs if you want to learn about genome assembly, RNA-Seq, or learning the basics of the Unix command-line (these were just some of the topics covered).

Anyway, I tried making some fun slide decks to kick off some topics. They are included below.


This bioinformatics lesson is brought to you by the letter 'D'

'D' is for 'Default parameters', 'Danger', and 'Documentation


This bioinformatics lesson is brought to you by the letter 'T'

'T' is for 'Text editors', 'Time', and 'Tab-completion'


This bioinformatics lesson is brought to you by the letter 'W'

'W' is for 'Worfklows', 'What?', and 'Why?'

Slides: Thoughts on the feasibility of Assemblathon 3

The slides below represent the draft assembly version of the talk that Ian Korf will be giving today at the Genome 10K meeting. I.e. these are slides that I made for him to use as the basis of his talk. I expect his final version will differ somewhat.

After I made these slides I discovered that two of the species that I listed as potential candidates for Assemblathon 3 already have genome projects. The tuatara genome project is actually the subject of another talk at the Genome 10K meeting, and a colleague tells me that there is also a California condor genome project too.

Genome Assembly: the art of trying to make one BIG thing from millions of very small things

Here are the slides from a talk I gave this week at UC Davis (also embedded below). This talk was for a group of graduate students (from different backgrounds). 

Note, because I tend to make very visual slides which don't always work well in isolation (you need to hear my sparkling narrative!), I have taken time to duplicate many slides and embed notes to indicate approximately what I would have said to explain the slide.