The CP2K project homepage

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
Find The CP2K project homepage at: http://cp2k.berlios.de/

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Posted in Theoretical and Computational | Leave a comment

Medium Large is back! Woo hoo!

Medium Large 617 clipping The fantastic web comic, Medium Large, drawn by Francesco Marciuliano, is back on the web after a long hiatus. At least the first strip, the introduction of Teenage Girl President, has reappeared. For the past six months, without ML, my days have been just a little less surreal.

While you are there, go read his Conversations With Dad blog. Guaranteed to make you spit coffee on your monitor at least once.

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A physics teacher begs for his subject back

I used to think that math and physics education in US secondary schools was worse than in any other industrialized country. Expectations and standards seem to have fallen so low that some of our best students are showing up at college without basic mathematical concepts (like the distributive property of multiplication over addition). Smart students can survive a weak education, but colleges are having to teach truly basic concepts and ways of thinking to students who should have seen some rigor in their secondary education.

It turns out that science teachers in the US are not alone in our concerns. Wellington Grey has written a very powerful open letter to the UK Department of Education titled “A physics teacher begs for his subject back.” It is an absolutely fantastic letter detailing the problems with the syllabus and exam for the physics General Certificate of Secondary Education (GCSE) [sort of equivalent to the GED in the US]. Although I haven’t seen the exam he’s talking about, I’ve skimmed over the Chemistry section of the syllabus specification that is the subject of many of his complaints. He is spot on. There’s precious little science in that specification, very little of the precision and exact use of language that science requires. Instead, there are a lot of politicized social concerns (which we may often agree with), but which, quite frankly, aren’t science.

Read his letter and make sure it gets a wide audience.

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Posted in education, Policy, Science | 3 Comments

ASCEND modelling environment

ASCEND is a flexible modelling environment for solving hard engineering and science problems. It offers: an object-oriented model description language for describing your system, an interactive user interface that allows you to solve your model and explore the effect of changing the model parameters, and a scripting environment that allows you to automate your more complex simulation problems.
Find ASCEND modelling environment at: http://ascend.cheme.cmu.edu/

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PhyloSort

A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
Find PhyloSort at: http://phylosort.sourceforge.net

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Avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.
Find Avogadro at: http://avogadro.cc/wiki/Main_Page

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Posted in Molecule Viewers and Editors | Leave a comment

PostGIS

PostGIS adds support for geographic objects to the PostgreSQL object-relational database. In effect, PostGIS "spatially enables" the PostgreSQL server, allowing it to be used as a backend spatial database for geographic information systems (GIS), much like ESRI’s SDE or Oracle’s Spatial extension.
Find PostGIS at: http://postgis.refractions.net/

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Posted in Earth Sciences | Leave a comment

Quantum GIS (QGIS)

Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) that runs on Linux, Unix, Mac OSX, and Windows. QGIS supports vector, raster, and database formats. QGIS is licensed under the GNU General Public License. QGIS lets you browse and create map data on your computer. It supports many common spatial data formats (e.g. ESRI ShapeFile, geotiff). QGIS supports plugins to do things like display tracks from your GPS. QGIS is Open Source software and its free of cost.
Find Quantum GIS (QGIS) at: http://www.qgis.org/

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Elmer

Elmer is an Open Source Finite Element Software for Multiphysical Problems. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).
Find Elmer at: http://www.csc.fi/english/pages/elmer

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SAGE

SAGE is free open source math software that supports research and teaching in algebra, geometry, number theory, cryptography, numerical computation, and related areas. Both the SAGE development model and the technology in SAGE itself is distinguished by an extremely strong emphasis on openness, community, cooperation, and collaboration: we are building the car, not reinventing the wheel. The overall goal of SAGE is to create a viable free open source alternative to Maple, Mathematica, Magma, and MATLAB.
Find SAGE at: http://sagemath.org/

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Posted in Mathematics | Leave a comment