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Correction to parameters to reproduce Fig. 3 from Sella and Ardell (2002)
Correction to parameters to reproduce Fig. 3 from Sella and Ardell (2002) To the world at large: We misreported the parameters needed to reproduce Figure 3 from Sella and Ardell (2002), “The impact of message mutation on the fitness of a genetic code.” The correct values are: phi = 0.32768 = (0.8 ** 5, not […]
Compiling Sean Eddy’s COVE suite on Mac OS X > 10.7
This blog post was about Compiling Sean Eddy’s COVE suite on Mac OS X > 10.7 For the basic problem and solution refer here: http://stackoverflow.com/questions/7376566/can-an-ansi-c-compliant-implementation-include-additional-functions-in-its-stand To fix the problem and compile the suite, add this in the COVE Makefile: MDEFS = -D_POSIX_C_SOURCE=200112L
UCSC Table Browser
Here’s something we all ought to put under our pillow: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030001 Programmatic queries of the UCSC genome browser will be highly useful!
org-mode for reproducible research
After overcoming the learning curve, I am very impressed with Emacs Org-mode as a tool for reproducible research. I started out wanting to document the statistical work I am doing for collaborators Michael Spivey, Stephanie Huette and Teenie Matlock here at U.C. Merced — a very exciting and interesting project on physical behavior during speech […]
Local install of davidardellorg_wordpress on Mac OS X 10.5.7
I thought I would make my very first ever blog post ever about how I installed a local version of davidardellorg_wordpress on my mac book pro with OS X 10.5.7. The steps to follow are: Install and configure mysql Turn on php in apache (optional) install phpmyadmin install davidardellorg_wordpress with various debugging and detective steps […]