I'll start off with a caveat, I am an open-source advocate, a long standing committee member and current president of Linux Users of Victoria (http://luv.asn.au). My overall approach is that computer programs are scientific problems, and therefore there is an inherent tendency towards a better solution when the source code can be freely analysed, distributed and developed; release early, release often and with many eyes all bugs are shallow (to paraphrase Eric Raymond's famous essay 'The Cathedral and the Bazaar').

Armadillo is a C++ linear algebra library (matrix maths) that supports integer, floating point and complex numbers, as well as a subset of trigonometric and statistics functions.

The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. It features multiple dynamical cores, a 3-dimensional variational (3DVAR) data assimilation system, and a software architecture allowing for computational parallelism and system extensibility. WRF is suitable for a broad spectrum of applications across scales ranging from meters to thousands of kilometers.

The JQuery cycle is an extremely useful tool for building various slideshow effects. The following discusses its use on Drupal 6.x websites which, like all good websites, are running a *NIX operating system. All instructions on this page assume that you're operating as root/sudo on a Linux system and logged in as administrator on Drupal.

DeMon (Density of Montréal) "is a software package for density functional theory (DFT) calculations. It uses the linear combination of Gaussian-type orbital (LCGTO) approach for the self-consistent solution of the Kohn-Sham (KS) DFT equations. The calculation of the four-center electron repulsion integrals is avoided by introducing an auxiliary function basis for the variational fitting of the Coulomb potential."

Since the early 1990s the x86 line of CPUs has dominated the computer world. Although it has hardly entered popular consciousness that is all changing. A revolution is afoot, as significant as the change from mainframes to clustered or networked systems some twenty years ago. It is time to welcome our new GPU overlords who, in the November 2010 list of the world's supercomputers, have taken 1st, 3rd and 4th position.

The following is a "sufficiently paranoid" approach to upgrading Drupal core and modules. As always, when one is going down this path the first thing to do is put the site in offline mode from admin/settings/site-maintenance.

Then make a back-up of your site, existing modules and themes, and database.


cp -r drupal-site drupalsite-bak
mysqldump drupal6-site > drupal6-site.sql


Download the core modules, based on the suggested updates from admin/reports/updates. You might even want to turn this into a script;

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...