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.

Updated version of my 'Genome assembly: then and now' talk is now available

This is a presentation that I have probably given five times now. Originally, the main focus of the talk was purely about the Assemblathon 2 paper, with some thoughts about how the field of genome assembly has changed since the days of Sanger-only sequencing.

Over time, I've increasingly downplayed the Assemblathon 2 content of the talk, and made way for updates relating to the latest developments in genome sequencing and assembly. To that end, I've decided to start adding version numbers to this talk to help make it easier to distinguish between different versions.

So here is version 1.2 of my talk, presented below with and without notes (my talks are very visual, so I have embedded notes to try to capture what I talk about for each slide). Don't be put off by the high slide count (many of these just reflect animated steps).

Without notes…

With notes (probably need to go full-screen to be able to clearly read these)…

Impactstory: Publications are an important part of research…but they’re not the only part

I'm a great fan of the Impactstory service that makes it easy to aggregate all of your research output in one place, and then see how people are engaging with your research. I like it so much, that I signed up to be an Impactstory Advisor.

Today I'm giving a talk at UC Davis about Impactstory, and so that everyone can see why I like this service so much, I've made a video version of my presentation. 

Visit the Impactstory website to find out more or follow them on twitter (@Impactstory). For an example of the types of things that Impactstory can track, have a look at my own Impactstory page (impactstory.org/KeithBradnam) .

Some slides from a recent talk about genome assembly (and thoughts on evolving slide decks)

Last week I presented a talk about genome assembly at a UC Davis Bioinformatics Core workshop. The first time that I gave this talk, it concentrated almost exclusively on the the results from our Assemblathon 2 paper. In the handful of times that I've subsequently given this talk, it has always evolved:

  1. More background to better explain some of the more common terminology in this field
  2. Less detail about the specifics of the Assemblathon 2 results
  3. New information relating to the latest developments in sequencing and assembly
  4. Added an 'intermission' so I can explain why I think Next-generation sequencing must die

Even if I didn't add any new content to my talk, and even if I was giving the same talk twice in the same week, I would still almost certainly change some aspect of my presentation. Here are some reasons for why I often end up changing things:

  1. Things which seemed like a good idea when planning and making slides, don't always work as well in front of an actual audience. Sometimes this might be unnecessary detail which slows things down, or it might be something which is no longer as relevant (or exciting) as when you first gave a talk on this topic.
  2. Inevitably there will be some parts of my talk which don't flow as well as others. Sometimes I will switch the order of sections, or drop sections altogether.
  3. If people ask me questions during the talk, then this is often because something is unclear. I try to make mental reminders about this, as it might mean that there is something I can better explain.
  4. Some visual elements will look great on my screen, and even on certain projectors, but then I will give a talk somewhere where a different projector makes a slide look horrible. Most common it will be when two colors end up looking far too similar. Always a good idea to change things so that they look clear on any projector.
  5. If I know that the audience for a talk may contain many people that don't speak English as their primary language, I might add more text content on key slides.
  6. A final reason for changing content is just to keep your talk fresh. It's possible that you become stale when you give the exact same talk over and over again. Changing the order of sections, or adding/removing content, means that you have to re-engage with your own material.

But hey, enough of my yakking…here are the slides. Note that I include two versions; the first version doesn't have any notes (harder to follow as I often prefer to talk around what's on my slides). The second version has notes added below each slide (these notes try to capture the gist of what I talk about on each slide). Also, don't be alarmed by the high slide count, each animation step appears as a separate slide (so that you can almost capture all of the animated fun of a real Keith Bradnam presentation).



What's in a name? Better vocabularies = better bioinformatics?

About 7:00 this morning I was somewhat relieved because my scheduled lab talk had been postponed (my boss was not around). But we were still having the lab meeting anyway.

About 8:00 this morning, I stumbled across this blog post by @biomickwatson on twitter. I really enjoyed the post and thought I would mention in in the lab meeting. Suddently though that prompted me to think about some other topics relating to Mick's blog post.

Before I knew it, I had made about 30 slides and ended up speaking for most of the lab meeting. I thought I'd add some notes and post the talk on SlideShare.

What's in a name? Better vocabularies = better bioinformatics?

from

Keith Bradnam

I get very frustrated by people who rely heavily on GO term analysis, without having a good understanding of what Gene Ontology terms are, or how they get assigned to database objects. There are too many published anayses which see an enrichment of a particular GO term as some reliable indicator that there is a difference in datasets X & Y. Do they ever check to see how these GO terms were assigned? No.

Slides from a talk on 'the art of good science writing'

I presented in our lab meeting today and used the occasion to talk about writing for science (as well as writing in general). I get to proof-read a lot of texts in the lab (scholarship applications, resumes, grad school applications, manuscript drafts etc.) and I have noticed some common issues that crop up a lot. This talk goes over some of these problem areas and offers some suggestions.

Thanks to the students for letting me share some of their writing.

Adding polish to presentations: 10 tips to make your talk shine

One of my greatest frustrations in life is sitting through bad presentations. Sadly, this is all too common in academia. We all know the signs:

  • Sparse, or nonexistent, background material
  • Too many slides full of bullet-point text (often read verbatim by the speaker)
  • Too many figures crammed on to a single slide
  • Speaker faces the screen while talking
  • Speaker has no passion, doesn’t seem to care much about their subject matter
  • No conclusion or summary to the talk, just data
  • Slides continuously vary in design, font choices etc.
  • Speaker overruns because they haven’t practiced

I could go on. I’ve been to so many talks where you can see audience members switch off after the first 5 minutes (and then usually reach for their smart phones to check their email). Bad talks become a waste of time for both the speaker and the audience. It doesn’t have to be this way. Indeed, it really shouldn’t be this way. You might be the greatest scientist the world has ever seen, but if you can’t communicate your research to others then there really is no point being in science. And by ‘communicate’ I mean making sure that people a) understand your talk and b) remember it.

Here are some slides (with notes) that list some relatively simple tips that I think could help many people who are new to giving presentations. These are tips that I have learned from many years of giving scientific talks in academia, but I think they could be useful to anybody who has to present their work to others.

10 tips for adding polish to presentations