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.

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

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.

How does the popularity of the UC Davis Genome Center vary with geographic location?

If I perform a Google search for the two words genome center, I see that the UC Davis Genome Center (henceforth UCDGC) is the top hit. But this is to be expected because Google has been personalizing search results for some time now, so this result is obviously tailored to me (if you didn't know, I work at the UCDGC).

If you are signed in to Google when you perform a search, the results will be heavily influenced by your search history and by what Google knows about you and your interests. Even if you sign out of Google, the search engine giant can track some information via cookies. Even if you disable cookies or use a private browsing mode, Google is still altering your search results because it knows your location (even if only approximately).

This explains why I will almost always see UCDGC as the top result when I search for 'genome center'. To get around this, I could use a search engine that doesn't track my activity, or I could use a private browsing mode in combination with a little-known feature of Google, that of changing your search location. It's possible to perform a search as if I was located in any major city or state in America.

So this allows me to see how often the UCDGC appears in the #1 position as I move around the country. I first performed a search for 'genome center' as if I was located in each state (e.g. set location to be 'Alabama', 'Alaska', 'Arkansas' etc.):

Ranking of UC Davis Genome Center among Google search results when searching for 'genome center' in each state

When you search for 'genome center', the UCDGC is the top search result in every state! One caveat to this approach is that it may not be all that meaningful to set your location to be an entire state. So I repeated the approach but this time I set my location to be the most populous city in each state:

Ranking of UC Davis Genome Center among Google search results when searching for 'genome center' in the most populous city of each state (as indicated by position of marker within each state). 

This shows that UCDGC is the #1 search result for cities in 36/50 states. The places where UCDGC is not #1 are all cities that have a notable genome center of their own (or are located close to one). A few notes relating to this:

1. The New York Genome Center dominates results not only in New York City (NY), but also in Newark (NJ), Bridgeport (CT), and Philadephia (PA)
2. The #1 result in Baltimore (MD) is for the Institute of Genome Sciences at the University of Maryland
3. St. Louis (MO) sees The Genome Institute at Washington University take the top spot
4. In the north west, a search from Seattle gives the Seattle Structural Genomics Center for Infectious Disease as the most popular result. But if you head to Spokane (Washington's 2nd city), then the UCDGC becomes the #1 result again
5. In Texas, the Department of Genomic Medicine at the Houston Methodist Research Institute, pushes UCDGC to 4th place. However, move to San Antonio or Dallas and the UCDGC regains first place
6. Chicago (IL) has the Institute for Genomics and Systems Biology at #1
7. In Minneapolis (MN) it is the University of Minnesota Genomics Center who is the top dog
8. The home of the King (Memphis, TN) is also home to the W. Harry Feinstone Center for Genomic Research which takes the #1 position. Once again, if you move to this state's second city (Nashville), the UCDGC regains the top spot in the search results.
9. Las Vegas, NV is home to the University of Nevada Las Vegas Genomics Core Facility. Moving to Nevada's second city (Henderson) puts UCDGC back on top.
10. In Salt Lake City (UT) you can find the Utah Genome Depot at the University of Utah dominating the rankings.
11. Finally, in Atlanta (GA), it is the Emory University Integrated Genomics Core which denies the UCDGC the #1 position

The UC Davis Genome Center is not only the top hit when you search for 'genome center' in various locations in the USA. If you use the Google location option to go truly global, you will see that we rank as the top search result for 'genome center' in London, Paris, Berlin, Moscow, Dehli, Seoul, Cairo, Buenos Aires, Bogota, Rio de Janeiro, Cape town, Kuala Lumpur, and Sydney!

While this could all be the result of UC Davis spending millions of dollars to adopt search engine optimization strategies to unduly influence our position in the search results, I prefer to believe that it reflects our reputation for world-class genomics research and training.