Monday, January 30, 2006

A nice page on zsh.

Sunday, January 29, 2006

In the light of the Sun
there is no difference between day and night.
In the light of the Supreme Truth
there is no difference between Shiva and Shakti.


-Jnaneshwar (also known as Jnanadeva) From "Teachings of the Hindu Mystics," © 2001 by Andrew Harvey. Reprinted by arrangement with Shambhala Publications, Boston, www.shambhala.com.
Things for later:

EMBOSS syntax
ACD Guide for Soaplab
Learn to talk AWK
Journal of New Music Research

Saturday, January 28, 2006

Open Source/Free Software - Sound analysis links:

OSS Apps for sound and music.
Software for bioacoustics
linux-sound.org - DSP programs
Aglaophone - A system for real-time analysis and processing of sound
Audacity
LAFIRE - a new automated refinement program for macromolecular crystallography. I saw it in the new Acta. Cryst. D:

Acta Cryst. (2006). D62, 189-196 [ doi:10.1107/S0907444905038965 ]
LAFIRE: software for automating the refinement process of protein-structure analysis
M. Yao, Y. Zhou and I. Tanaka

Synopsis: A manual intervention-free automatic refinement software package (LAFIRE) has been developed for high-throughput protein-structure analysis. This program begins from an initial model that can be approximate, fragmentary or even only main-chain and performs a whole refinement process to provide a final model including water molecules.

Wednesday, January 25, 2006

O, My Luve is Like a Red Red Rose.



O, my luve is like a red, red rose,
That's newly sprung in June.
O, my luve is like a melodie,
That's sweetly play'd in tune.

As fair art thou, my bonie lass,
So deep in luve am I,
And I will luve thee still, my dear,
Till a' the seas gang dry.

Till a' the seas gang dry, my dear,
And the rocks melt wi the sun!
And I will luve thee still, my dear,
While the sands o life shall run.

And fare thee weel, my only luve!
And fare thee weel, a while!
And I will come again, my luve,
Tho it were ten thousand mile!
The imgCIF dictionary.

Tuesday, January 24, 2006

science 2.0
Chemical Mime types.

chemical/x-mmcif
mcif
MacroMolecular CIF
OpenMMS - A nice looking Java package for dealing with macromolecular data in Java, from our friends at the RCSB, PDB and SDSC.
The Java CLASSPATH. Classpath is one of the more confusing parts of Java, this is a good page to help to describe it. Basically, it tells Java where to look for Classes, kind of like how the PATH environment variable in UNIX tells the shell where to look for commands.

Monday, January 23, 2006

KIF - Knowledge Interchange Format. This looks like what the SUO is using to encode their ontologies in. I wonder how hard it would be to encode the mmCIF dictionary in KIF, or if it is possible.
An excellent Nature article on biological ontologies. They talk about the Standard Upper Ontology Working Group (SUO WG) of the IEEE and how biological ontologies are not using the same practices as other ontology makers. I'm going to look into how well the mmCIF ontology conforms to these ontology standards.

Sunday, January 22, 2006

"The world is transitory, the Name of God is the true reality. Everything in this world is destructible, transient, unlasting. So you must all repeat God's Name and sing kirtan and bhajans with devotion and concentration."
------Babaji, 1983

Wednesday, January 18, 2006

Wow, so cool, an open source version of EPMR (Evolutionary Protein Molecular Replacement) : openEPMR

Sunday, January 15, 2006

Friday, January 06, 2006



Sometimes, living on Mars can be quite pretty.



I love my input devices. I've had the Logitech Trackman Marble FX
mice for about 5 years now, and Microsoft Natural Keyboards for about
7 years. I just got the new Microsoft Natural Ergonomic 4000 to
replace a keyboard I had to leave in Holland, and the new one is
so sweet. Just beautiful. Input devices are important, and have
totally helped my RSI. I used to have it pretty bad, but a combination
of different devices, frequent breaks and yoga have made it better.
Still, for about a month I was using my Playstation Linux keyboard
as my main input device, and I started to feel some pain again. Back
to proper input devices for me.

Thursday, January 05, 2006

2Fo-Fc and Fo-Fc maps. Some links:

Solve manual
MAIN manual
TNT manual

Wednesday, January 04, 2006

Waste not fresh tears over old griefs. -- Euripides

Tuesday, January 03, 2006

Rule of Clarity: Clarity is better than cleverness.

Because maintenance is so important and so expensive, write programs as if the most important communication they do is not to the computer that executes them but to the human beings who will read and maintain the source code in the future (including yourself).

What a great article.
I like this one as well:

"When in doubt, use brute force."
Ken Thompson
"This is the Unix philosophy: Write programs that do one thing and do it well. Write programs to work together. Write programs to handle text streams, because that is a universal interface."

Doug McIlroy, the inventor of Unix pipes and one of the founders of the Unix tradition

From a great article Basics of the Unix Philosophy

Monday, January 02, 2006



I'm a zsh-lover!