LSM2241 Lecture 2: A temporarily Org-mode-less lecture

My feedback from students after the first week of LSM2241 (Introductory Bioinformatics) was generally quite positive. Many commented on the well organized slides (where Org mode is my secret weapon) and provided useful suggestions. So when I sat down to make my new slides, I was pretty excited, but as it turns out I may have a tough adhering to some of their input.

The second week of LSM2241 is devoted to bioinformatics databases. There’s a high level of variability in student background: some students not have had any introduction to databases in general, so I have to cover that too. Compounding matters, this is also one of the lectures I didn’t give last term. I of course looked through slides from previous years for ideas, and also found presentations from other universities. Some clear themes emerged.

  • In previous years, lecturers had covered a lot of material in a short period
  • Screen shots, screen shots, screen shots. Wow, were there a lot of screen shots. This was true not just in previous years of LSM2241, but in other courses covering the topic.
  • It seems really easy to inadvertently include a number of out of date or inaccessible databases
  • It seemed helpful to use a few related queries to drive most of the examples across different databases.

While I wanted to start my slides from scratch, I got behind in my preparations, and eventually realized that my best bet was to use the previous years’ material as a starting point and (uggh) use PowerPoint. My revisions are pretty extensive, but the basic structure is quite similar, which leaves a huge number of slides, about three times what I’d like to target! Ironically, part of the feedback from lecture 1 was to speak more slowly. This may pose a challengeā€¦.

Next time: update R graphs and deal with screenshots

I did make a few plots for the lecture using R, and have started putting data into Google Docs for charts I’ll have to update in future years. This should make for clean Org babel R source code blocks, like

dblink <- "https://docs.google.com/spreadsheet/pub?key=0Amd94LRhVxVWdElNYVdHblVLRjZKR1lwaFFFZHVyWUE&single=true&gid=0&output=csv"
require(RCurl)
myCsv <- getURL(dblink)
dbs <- read.csv(textConnection(myCsv))
library(ggplot2)
names(dbs) <- c("Year","Databases")
dbs[[1]] <- as.factor(dbs[[1]])
p <- qplot(x=Year,y=Databases,data=dbs,geom="bar",fill="gray")
p + theme_bw() + opts(axis.text.x = theme_text(angle=90, hjust=1.2, size=16),
axis.title.x=theme_text(size=16),
axis.title.y=theme_text(size=16,angle=90),
axis.text.y = theme_text(size=16),
legend.position="none") +
ylab("Databases in NAR Database issue")

For screen shots, I’m looking at webkit2png. When it comes time to revise this lecture and put it into Org, I should be able to generate all the screen shots from Org babel codeĀ blocks. Why go through the trouble? For one thing, if I decide to change the example, I can regenerate the slide deck appropriately without manually cutting screen shots. If database interfaces change, I can see the results in the screen shots and revise just those sections. I only wish I had thought of it in time to make the slides that way this term.

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