64-bit Linux Flash Player discontinued

It seems that at least temporarily the 64bit version of Flash Player will not be available for Linux. I found out when upgrading my system, where at some point I got the following error message:

[myPC:/home/leo] update-flashplugin-nonfree --install
ERROR: 64 bit player temporarily not supported
More information might be available at:
  http://wiki.debian.org/FlashPlayer

The solution is to install the 32bit version of it, as explained here at this forum (another option is to install gnash, but I haven't tried). The details are described on this post, specifically.

Debiansaurus

With all the buzz about these fancy new cell phones, I started missing my PDA. Actually I still have it here with me, a Sharp Zaurus that I bought in Japan around 2004 to use as a dictionary - this company was famous for having a good kanji recognition software. It also happens to run linux, I even got R to run on it (iPhone lovers don't need to envy me anymore). Since the software is a little bit outdated, I thought about upgrading the system, maybe to Debian - despite I would loose the nice "stroke recognition" app that is able to decipher the kanji you want to write in just a few touches.

But after seeing the lack of development for it (even the official ROM was last updated in 2005), I guess I'll just leave it as it is. I still can play with the tablet and listen to mp3 (although it doesn't seem to recognize newer SD cards...). Other places that may have relevant info on the Zaurus upgrade are here, here and here.

Communication package between R and Mesquite

Information just received from the R-sig-phylo mailing list:

We'd like to announce the beta release of packages for communication between Mesquite and R. Mesquite is a graphical application for phylogenetic and evolutionary analysis; R is a system for statistical computation primarily oriented around text-based programming. We have enabled communication in both directions:

• RMesquite enables R programs to make use of Mesquite, either as a graphical interface for editing trees and data, or to provide its broad array of phylogenetic calculations to R (http://rmesquite.r-forge.r-project.org).
• Mesquite.R enables Mesquite to make use of functions in R (http://mesquiteproject.org/packages/mesquite.R/MesquiteCallsR/MesquiteR.html). At the moment these include functions in the R packages ape and diversitree.

Only a handful of functions have been enabled in each direction; we seek your input as to what functions would be of most interest to R users and Mesquite users.

You may consider this as an experimental release for thrill-seekers. Please tell us if something doesn't seem to work or is confusing -- feedback is much appreciated. We hope to continue to strengthen the links between R and Mesquite.

Wayne Maddison, UBC
Hilmar Lapp, NESCent

Recent CUDA applications

Taking a look at Nvidia's CUDA zone I found some recent additions - besides important ones that I already knew like the Smith-Waterman and the phylogenetic likelihood algoritihms. Here is a list of these new programs and libraries that take advantage of GPUs:

1. Expectation Maximization algorithm for Gaussian Mixture Models
2. Multilevel algorithm for MDS (multidimensional scaling)
3. Multiclass classifier based on SVMs (support vector machines)
4. GPU computing in the R statistical environment (BLAS lowlevel routines and dist(), hclust(), cor(), and granger.test() functions)
5. Smith-Waterman algorithm for sequence database search
6. Quicksort library
7. Feature finding algorithm for mass spectrometry
8. Smith-Waterman algorithm for sequence alignment
9. MDR (multifactor dimensionality reduction) algorithm for detecting genetic epistatic interactions (white paper)
   

The last reference is just a two-page summary, and the 8th reference is behind a paywall - I couldn't access it myself - but the slides are available here.

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