Lev Lafayette

BEAST (Bayesian Evolutionary Analysis Sampling Trees ) "is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology".

The GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics simulation package that is very fast and has support for different force fields. It is notable for being used for protein folding at Folding@Home.

The Modules Package is a set of commands and information files that provides a simple command interface for modifying the environment. Each module in The Modules Package is a file containing the information needed to initialize the environment for a particular application (or any environment information). It's awesome, and installation is easy. But there is a bug...

Parallel NETCDF is an implementation of the Network Common Data Form which supports parallel I/O. An excellent summary of the advantages are described by Choudhary, Liao, Gao, and Li.

Installation is fairly trivial. Download the tarball from the site, extract, load some modules, configure for the appropriate site, make and make install, and create modules. For example;


wget http://ftp.mcs.anl.gov/pub/parallel-netcdf/parallel-netcdf-1.2.0.tar.bz2

Valgrind is an instrumentation framework for building dynamic analysis tools. Which is a fancy way of saying that it's a debugging suite that automatically detects many memory management and threading bugs, which is a very good thing. Valgrind can handle dynamically generated code, so long as none of the generated code is later overwritten by other generated code. It can also perform detailed profiling to help speed up your programs. It comes with extensive documentation.

MATLAB is a numerical computing environment allowing matrix manipulation, plotting of functions and data, implementation of algorithms, and high-level programming language. Typically it is run on desktop installs, which is quite problematic if one is doing a large computational problem.

It seemed a trivial request, and once you've realised a couple of minor issues it is; install the NCDF library, a common scientific data format, for R, the well-known statistics software.

There is a usual way to install a package in R. Simply load the program and run the install.packages function; but this didn't quite work.


R
>chooseCRANmirror()
>install.packages(c("ncdf"))

There have been two fairly significant forks in the Linux world in the past few weeks; one is a large number of the developers of Mandriva now concentrating on on that technology under the new title Mageia. As advocates of that this new Linux distribution state: People working on it just do not want to be dependent on the economic fluctuations and erratic, unexplained strategic moves of the company..

CGAL (Computational Geometry Algorithms Library) provides efficient and reliable geometric algorithms in the form of a C++ library data structures and algorithms for triangulations, Voronoi diagrams, polygons and polyhedra, arrangements of curves and their applications, mesh generation, geometry processing, subdivision and parameterization, as well as estimation of local differential properties, and approximation of ridges and umbilics, alpha shapes, convex hull algorithms, search structures , interpolation, shape analysis, fitting, and distances, and kine

Much has been made of the fact that France, the has banned the burqa, l'affaire du voile, with the exception of places of worship. Earlier in the year a law was passed that scarves covering the face were banned in schools and hospitals, as well as on public transport. Women, who violate this requirement will be fined €150 Euros and given a course of lectures on the basics of the secular foundations of the French Republic. Men, who force women to wear burqa, will face up to a year in prison.