While not directly related to genetics, this is an excellent example of well-designed data representation. The New York Times reports the results of a survey of average time spent on various activities through the day by different groups of people. The graphic is essentially a stacked density plot with time (24 hours) on the X-axis.

Logan recently emailed me an article in the New York Times about single-molecule DNA sequencing and I realized I knew next to nothing about the new and emerging technology that will change the way we do association studies (that is, if we're still even trying to find genetic associations in the first place). The Wellcome Trust posted a news feature a few weeks back giving brief explanations and short videos on DNA sequencing, starting with the

The Systems Biology Graphical Notation (SBGN) project is an effort to standardize the graphical notation used in diagrams of pathways, biochemical processes, and cellular processes studied in systems biology.SBGN defines a comprehensive set of symbols with precise semantics, together with detailed syntactic rules defining their use and how diagrams are to be interpreted.

Hadley Wickham, creator of the previously mentioned R plotting system ggplot2 and author of a forthcoming book from Springer, is teaching a workshop in data visualization using R, ggplot2, and GGobi. Unfortunately this workshop conflicts with IGES and ASHG this year, but he mentioned the possibility of holding a workshop here at Vanderbilt if there is enough interest.

Here are citations for the articles discussed at our most recent meeting (July 31). Our next meeting is scheduled for August 14.~JuliaBogdanowicz W, Allen M, Branicki W, Lembring M, Gajewska M, Kupiec T. Genetic identification of putative remains of the famous astronomer Nicolaus Copernicus.

That's the title of a good article published yesterday in the New York Times about the emergence of statistics being in huge demand in the career market, becoming "the sexy job in the next 10 years" as Google's chief economist puts it. Now I just need to find one of these don't drink and derive t-shirts...For Today’s Graduate, Just One Word: StatisticsGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC

I've used this a little bit recently. Pubget indexes essentially everything that PubMed does, except you get the PDF you're looking for right away. Lots of other useful tools as well. I sent one email to the Pubget team and CC'd the biomedical library, and a few days later they've worked it out so PubGet recognizes Vanderbilt's subscriptions.

Here are citations for the articles discussed at our most recent meeting (July 17). Our next meeting is scheduled for July 31.~JuliaBianconi G, Pin P, Marsili M. Assessing the relevance of node features for network structure.

It took me a while to figure this out, so I thought I'd share. I have a dataframe with millions of observations in it, and I want to estimate a density distribution, which is a memory intensive process. Running my kde2d function on the full dataframe throws and error -- R tries to allocate a vector that is gigabytes in size. A reasonable alternative is to run the function on a smaller subset of the data.

This handy introduction comes from UCLA's Statistical Computing webbook on logistic regression. If you're familiar with linear regression but you've never used logistic regression before, this is a good place to start.

***Update Monday, November 09, 2009: The sma package is no longer available on CRAN.  See this updated post for making QQ-plots in R using ggplot2.*** Nearly everyone who has read a paper on a genome-wide association study should now be familiar with the QQ-plot.