40 Essential Tools and Resources to Visualize Data | FlowingData
This looks incredibly useful. I really need to sit down and learn Flash and Processing.
40 Essential Tools and Resources to Visualize Data | FlowingData.
Wallace’s Insect Collection Found!
Via the New York Times
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 $100 a month, and into Mr. Heggestad’s possession fell an incomparable scientific treasure.
The cabinet belonged to Alfred Russel Wallace, the English naturalist who conceived the idea of evolution through natural selection independently of Charles Darwin.
Wow!
Museum to Display Historic Cabinet That Belonged to Alfred Russel Wallace - NYTimes.com.
Blue Collar Bioinformatics
Just wanted to recommend Blue Collar Bioinformatics a slick blog with lots of useful bioinformatics scripts. Everything is written in python and the full working source is typically available on GIT.
F$@%ing R: Adventures with Tcltk in OSX
I've got a bunch of RNA-seq reads I need to analyze and for the the most part I've been writing my own code to do the analysis. However, a recent paper in BioInformatics (Wang et al. 2009) describes a new R package for the identification of differentially expressed genes in RNA-seq datasets. R is a pretty straightforward language with a built-in installation system so I should just have to type two lines of code...
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)
RegEx to id comma-space(s) or space(s) delimited text
I'm not all that great at RegEx, but I needed split a line of text on commas followed by spaces and/or by spaces (including tabs). 30 minutes later after swearing and sweating with iPython, I produced the following little expression. Who needs the CSV module?
re.compile(',(?:\s*)|\s*')
Example Usage:
Textmate Nexus Bundle
I wrote a very simple textmate bundle for working with nexus files.
Version 1 Functionality: folds NEXUS blocks, highlighting bayes block mcmc line and typing command-B will automatically calculate burnin at 25%, more to come as I think of it.... probably contains bugs
Download nexus bundle version 1. (03/05/09)
New measures of genetic differentiation
Lou Jost has pretty neat paper out describing new measures genetic diversity that accurately account for allelic differences. I've written some PYTHON scripts to parse genepop files, measure allele frequencies, and generate [some of] these measures of diversity. Enjoy.
http://www.ngcrawford.com/django/jost/
Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology,17(18), 4015 - 4026
Wordpress Update Issue (and fix)
Using the 'Automatic' update button I got the following error:
Fatal error: Cannot redeclare pclziputilpathreduction()...
To fix this I had to turn off the 'Wordpress Automatic Upgrade Plugin' that was formerly required for automatic updates. More details here.
Olivia Judson Likes Papers.app too!
Now Papers has been reviewed by the New York Times. Sweet.
For me, well, a few days after discovering Papers, I put 20 sacks of real paper into the recycling bin. At last, I’m back to knowing what I have and where it is.
Via the New York Times
