Luckily, the markdown syntax has recently been extended, in a project called MultiMarkdown, to include many of the aforementioned features. Multimarkdown essentially merges the markdown syntax with LaTeX which, if you haven't heard of it, is a rather inscrutable, but extremely powerful text formatting language.  It's popular in the CS and physics disciplines.  LaTeX produces beautiful documents, but it's easy to spend a week or more adjusting the formatting and reading the API trying to figure out some of the more complicated features.  Multimarkdown looks like it will do much of the more basic LaTeX formatting, but without the headache.

40 Essential Tools and Resources to Visualize Data | FlowingData.

The owner wanted a sum that far exceeded Mr. Heggestad’s budget — a colossal $600. “I was just out of law school, I had no money and no business buying it,” he said. But the owner was willing to take installments of $100 a month, and into Mr. Heggestad’s possession fell an incomparable scientific treasure.

The cabinet belonged to Alfred Russel Wallace, the English naturalist who conceived the idea of evolution through natural selection independently of Charles Darwin.

Wow!

Museum to Display Historic Cabinet That Belonged to Alfred Russel Wallace - NYTimes.com.

The impressive economy of this paper is that they targeted (using Agilent chips) less than 30Mb of the human genome, which is less than 1%. They also worked with very few samples; only about 30 cases of Miller Syndrome have been reported in the literature. While I've expressed some reservations about "exome sequencing", this paper does illustrate why it can be very cost effective and my objections (perhaps not made clear enough before) is more a worry about being too restricted to "exomes" and less about targeting.

More @ Omics! Omics!

via Targeted Sequencing Bags a Rare Disease.

source("http://bioconductor.org/biocLite.R")
biocLite("DEGseq")

Not so quick. When I ran this code R tells me it can't find the DEGseq library. A bit more poking around on the internets and I discover that there's an alternate download site:

source("http://bioinfo.au.tsinghua.edu.cn/software/degseq/DEGseqInstall.R")

But after installing some dependancies it also spits out a bunch of errors.  I compare the errors... Hmmm... Both installs appear to by dying on the tcl/tk install, but tcltk is a default R library.  I can see it right there in "/Library/Frameworks/R.framework/Resources/library".  Two hours later and after trying a bunch of crap I find this helpful website:

http://cran.r-project.org/bin/macosx/tools/

A quick and dirty install of the tcltk-8.5.5-x11.dmg and now "library(tcltk") works like a charm.  No errors.

I install DEGseq with the following set of commands:

source("http://bioconductor.org/biocLite.R")
biocLite("DEGseq")

Now, a day an a half later I can see if it's useful. Woo.

Citations:

L Wang, Z Feng, X Wang, X Wang, X Zhang. DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics (2009)

 
re.compile(',(?:\s*)|\s*')
 

Example Usage:

line = 'one, two three          four,           five'
pattern = re.compile(',(?:\s*)|\s*')
line.pattern(split)
>>> ['one', 'two', 'three', 'four', 'five']