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?'

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.

Identical Classifications In Science: Some advice for Jonathan Eisen

Jonathan Eisen — a colleague at the UC Davis Genome Center — has a quandary. He came up with a name for one of his projects but now needs to consider renaming it. The problem is that ICIS (Innovating Communication in Scholarship) sounds a bit like…well you all know what it sounds like. So Jon has appealed for suggestions on how to rename their project.

He should take comfort that he may not be the only one facing this dilemma. After all, the International Cooperative ITP Study Group (ICIS) has been an ongoing collaboration between hematologists since 1997. I wonder whether they are considering a name change? Maybe Jon could also ask the folk at the International Conference on Information Systems (ICIS) who have been meeting since 1980. Or they could talk to the people that came up with the Intelligent Coin Identification System (ICIS), or the The Intensive Care Infection Score (ICIS), or the Integrated Crate Interrogation System (ICIS), or the 20 year old International Crop Information System (ICIS), or the people who named this gene.

These are just some of the academic uses of ICIS that I could find from a couple of quick searches. I expect that there are more out there. This is a reflection on one of the most primal desires of all scientists…the need to come up with an acronym or initialism for their project. This urge is all too commonly associated with the additional need to make the name 'fun' (particularly a desire to name things after animals). Acronyms can also backfire for other reasons, such as when you don't fully appreciate how it might sound in other countries.

The shorter your acronym, the more likely that it has been used by other people before you (even within the same field). My suggestion would be to consider the shocking alternative of not using an acronym at all! After all, sometimes people can come up with new names that seem to catch on.