Submitted by lev_lafayette on Wed, 12/22/2010 - 05:38
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;
Submitted by lev_lafayette on Thu, 11/18/2010 - 03:51
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".
Submitted by lev_lafayette on Thu, 11/11/2010 - 00:32
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.
Submitted by lev_lafayette on Mon, 11/08/2010 - 23:26
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...
Submitted by lev_lafayette on Thu, 11/04/2010 - 04:35
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;
Submitted by lev_lafayette on Thu, 10/21/2010 - 23:49
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.
Submitted by lev_lafayette on Wed, 10/20/2010 - 04:10
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.
Submitted by lev_lafayette on Mon, 10/18/2010 - 05:27
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.
Submitted by lev_lafayette on Thu, 10/14/2010 - 13:03
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..
Submitted by lev_lafayette on Tue, 10/12/2010 - 10:13
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 kinetic