In the last post I showed you how to point to a file in windows and get the full path copied to your clipboard.  I wanted to come up with something similar for a Linux environment.  This is helpful on Vampire/ACCRE because you have to fully qualify the path to every file you use when you submit jobs with PBS scripts.

I wish I would have discovered this long ago.  Loading data into R or MySQL requires you to specify the full path to the file.  If you do this on a Windows machine there are two annoyances.  First, if you save something to your desktop the path to your desktop is really long.  Second, windows by default uses backslashes "\" in the file path, while R or other software requires forward slashes "/".

A quick announcement about a formatting fix here - you can now print posts from GGD a little more cleanly.  When you print it should no longer include the title and sidebar, so most posts should now only use a page or two.Getting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

Here are citations for the articles discussed at our most recent meeting (August 28). I have also appended a link to Nature Reviews: Genetics new series, Fundamental concepts in genetics, at the end. Our next meeting is scheduled for September 11.~JuliaGurwitz D, Fortier I, Lunshof JE, Knoppers BM. Research ethics: Children and population biobanks. Science . 2009 Aug 14; 325(5942):818-9 Hastings PJ, Lupski JR, Rosenberg SM, Ira G.

I tip my hat to Will for showing me this little command line trick. PLINK's output looks nice when you print it to the screen, but it can be a pain to load the output into excel or a MySQL database because all the fields are separated by a variable number of spaces. This little command line trick will convert a variable-space delimited PLINK output file to a comma delimited file.You need to be on a Linux/Unix machine to do this.

http://www.harvardscience.harvard.edu/blog/how-dachshund-lost-its-legsGetting Genetics Done by Stephen Turner is licensed under a Creative Commons Attribution (CC BY) License.

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.