Friday, December 30, 2005

Check out my new bookmarks on I'll be posting there more often now.

Thursday, December 29, 2005

Trying out the new google analytics. It's cool.
xanadu. So close and yet so far.
A nice article by Ted Nelson about ParaMode. Here's a small excerpt that is relevant to our cause:

But the history of Para mode does highlight three deep sources of power that, in one form or another, lie behind all successful new ideas --- and not just in the software realm. Those power sources are:

  1. a boundless extensibility --- the potential to modify, customize, and reconfigure something far beyond the original conception. People's minds have that. So do human languages and mathematical systems. So does software ... provided the initial developers don't get selfish and lock the doors to change.

  2. a solid foundation --- something to build upon that does at least part of the job well, something reliable yet elegant and ├Žsthetic. It's impossible to do everything ourselves; we must rely on the work of our ancestors.

  3. a culture of sharing --- so that several people, each with a piece of the jigsaw puzzle, can get together and come up with a solution. Sharing works well (or should) within a family, a small group, or a properly-run company. Ill-wrought "Intellectual Property Rights" laws, however, truncate the sharing process and give short-term profits to idea-squatters ... at the expense of long-term progress for all.

One of the first article about hypertext, from Vannenar Bush:
MEMEX - An early example of HTML

An exerpt that is particularily poignant:

The same dynamics of "concept editing" that occurred with TBL's Web and in the reaction to my own Memex project is actually fairly common in the software business. (I will, however, spare you by not documenting other obvious examples.) Typically, those who first work on an idea or concept will see that it has a very wide scope of application, however, they are almost always forced to focus on one or another specific, limited scopes in order to present their idea in a relevant fashion to potential adopters who have specific issues addressed by the innovation. Often, in the process of this focused positioning to convince early-adopters to accept an idea or process, much of the full richness of the vision is lost or put aside. The cost of acceptance is thus often the loss of very important, even essential, elements of the vision. Sometimes, the loss is permanent and only the original thinker knows what paths were not traveled... Sometimes, the loss is temporary as others eventually re-discover the lost facets or the original visionaries are able to eventually find a means to get others to understand more of the full vision. This re-discovery of the original vision's depth and breadth is hopefully what we see happening on the Web today as Blogging, Wikis and other read/write tools resurrect the original idea of the read/write Web.

Wednesday, December 28, 2005

Tuesday, December 27, 2005

A good lecture by Richard Hamming
"Until one is committed, there is hesitancy, the chance to draw back, always ineffectiveness. Concerning all acts of initiative and creation, there is one elementary truth the ignorance of which kills countless ideas and splendid plans: that the moment one definitely commits oneself, then Providence moves too. All sorts of things occur to help one that would never otherwise have occurred. A whole stream of events issues from the decision, raising in one's favor all manner of unforeseen incidents, meetings and material assistance which no man could have dreamed would have come his way. Whatever you can do or dream you can, begin it. Boldness has genius, power and magic in it. Begin it now."
~ Johann Wolfgang Von Goethe

Do what you Love.
Live where you Love.
Love where you Pray.

Monday, December 26, 2005

ZSH emacs emulation.
Neat Snowflake photos.

Wow, zsh rocks. Here are some zsh tips.

tcsh was sweet, it did lots of things, but really complicated command line things like this were just not quite unified enough to be really useful.
Great essay on procrastination by Paul Graham. A little excerpt here:

You can't look a big problem too directly in the eye. You have to approach it somewhat obliquely. But you have to adjust the angle just right: you have to be facing the big problem directly enough that you catch some of the excitement radiating from it, but not so much that it paralyzes you. You can tighten the angle once you get going, just as a sailboat can sail closer to the wind once it gets underway.

If you want to work on big things, you seem to have to trick yourself into doing it. You have to work on small things that could grow into big things, or work on successively larger things, or split the moral load with collaborators. It's not a sign of weakness to depend on such tricks. The very best work has been done this way.

When I talk to people who've managed to make themselves work on big things, I find that all blow off errands, and all feel guilty about it. I don't think they should feel guilty. There's more to do than anyone could. So someone doing the best work they can is inevitably going to leave a lot of errands undone. It seems a mistake to feel bad about that.

I think the way to "solve" the problem of procrastination is to let delight pull you instead of making a to-do list push you. Work on an ambitious project you really enjoy, and sail as close to the wind as you can, and you'll leave the right things undone.

Sunday, December 25, 2005

The goal of MR-CAFASP, is to evaluate the potential of fully automatic 3D protein structure prediction servers to provide valuable models during the structure determination process.

During previous LiveBench experiments it was discovered that at least in two cases, highly confident "in-silico" models significantly differed from the experimental structure. In both cases, the experimental structure was subsequently removed from the PDB, and in one case, the replacement entry contained corrected models very similar to the original "in-silico" prediction (see e.g. Bujnicki et al, "Fold-Recognition Detects an Error in the Protein Data Bank.", Bioinformatics, 18, 1391-1395, 2002 and Bujnicki et al. "Errors in the D.radiodurans large ribosomal subunit structure detected by protein fold-recognition and structure validation tools", FEBS letters, 525, 174-175, 2002 , and the crystallographers reply in the same issue). This lead to the question of whether in-silico models may be of help during the structure determination process - a very important issue for Structural Genomics.

This idea appeared in a previous CASP experiment, where predicted models were solicited for one target that could not be solved. In addition, D. Jones has also recently suggested that distant homology fold-recognition models may be used as Molecular Replacement phasing models (Jones, D. "Evaluating the potential of using fold-recognition models for molecular replacement.", Acta. Crys. D57, 1428-1434, 2001). D. Baker and colleagues have also described a method to generate structures using limited NMR data combined with in-silico procedures (Bowers, Strauss and Baker. J. Biomol. NMR, 18:311-318, 2000).
Fun with Firefox Chromes
Linux tips
anneal.inp - View
anneal.inp - Edit

Saturday, December 24, 2005
Seven Habits of Highly Effective Programmers
Lately, I've been a little restricted by the mighty tcsh, a shell which I've used for about 10 years. I have been thinking about moving to zsh for the last few years, and I think I will finally take the plunge.
Deploying Ruby on Rails - Not quite as simple when doing more complicated sites.
AJAX Activity Indicators.
Nice Crystallography HOWTO list

Friday, December 23, 2005

Structure prediction links:

BioInfoBank Institute
COILS - Prediction of Coiled Coil Regions in Proteins
REPRO - Protein Repeats Analysis
DSSP - a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB)
FFAS03 - Fold & Function Assignment System
Pfam - a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
HMMER - profile HMMs for protein sequence analysis
JUFO - This server offers a protein secondary structure prediction from its primary sequence only. An neural network was trained with an amino acid property profile and the position based scoring matrix of a blast run.
Protein-Protein BLAST - At the NCBI.
MAMMOTH - MAtching Molecular Models Obtained from THeory
Data formats for Robetta
BLAST - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
SAM-T99 - HMM-based Protein Sequence Analysis, SAM-T99
SAM - Sequence Alignment and Modeling System
TMHMM - Prediction of transmembrane helices in proteins
Data formats for Robetta

Thursday, December 22, 2005

Neat, a Linux A/D converter.
Gratitude For Your Life In General
Let's stop fixing and start savoring. The way you fix is through the
savor. We don't know of any way to fix your life or align yourself
or allow your Source or to achieve what you want. We don't know of
any way to do it other than savoring your way there. So as you make
a determination that you're going to be a big time savorer; a big
time complimenter and a hardly ever criticizer; a big time
appreciator and a hardly ever noticer of something wrong; and a big
time lover and a hardly ever hater; and a big time reacher for
thoughts that feel good. As you are reaching for these thoughts that
feel best, you are automatically finding your Path of Least
Resistance. And when you find your Path of Least Resistance, you are
connected to your source of clarity and abundance and physical
stamina and well-being.
Audio programming languages:


Wednesday, December 21, 2005

In the secret cave of the heart, two are seated
By life's fountain. The separate ego
Drinks of the sweet and bitter stuff,
Liking the sweet, disliking the bitter,
While the supreme Self drinks sweet and bitter
Neither liking this nor disliking that.
The ego gropes in darkness, while the Self
Lives in light. So declare the illumined sages
And the householders who worship
The sacred fire in the name of the Lord.

-Katha Upanishad Excerpted from The Upanishads, translated by Eknath Easwaran, copyright 1987. Reprinted with permission from Nilgiri Press, To order the book, please call 1-800-475-2369.
I searched through rebellion, drugs, diets, mysticism, religions,
intellectualism and much more,
only to begin to find that truth is basically simple - and feels good,
clean and right.

--Chick Corea
(jazz musician)

Tuesday, December 20, 2005

Monday, December 19, 2005

Links for you:

compchem software
biocore javadocs
PDB software list
An article about the future of interfaces
Writing makefiles
jgraph - a Java package for making graphs.
What are formants - The elements of phonemes.

In the vowels, F1 can vary from 300 Hz to 1000 Hz. The lower it is, the closer the tongue is to the roof of the mouth. The vowel /i:/ as in the word 'beet' has one of the lowest F1 values - about 300 Hz; in contrast, the vowel /A/ as in the word 'bought' (or 'Bob' in speakers who distinguish the vowels in the two words) has the highest F1 value - about 950 Hz. Pronounce these two vowels and try to determine how your tongue is configured for each.

F2 can vary from 850 Hz to 2500 Hz; the F2 value is proportional to the frontness or backness of the highest part of the tongue during the production of the vowel. In addition, lip rounding causes a lower F2 than with unrounded lips. For example, /i:/ as in the word 'beet' has an F2 of 2200 Hz, the highest F2 of any vowel. In the production of this vowel the tongue tip is quite far forward and the lips are unrounded. At the opposite extreme, /u/ as in the word 'boot' has an F2 of 850 Hz; in this vowel the tongue tip is very far back, and the lips are rounded.

F3 is also important is determining the phonemic quality of a given speech sound, and the higher formants such as F4 and F5 are thought to be significant in determining voice quality.
Theta waves

Have you listened to my Fall Navaratri 2005 podcasts yet?
An interesting
on how to setup a programmers linux environment by a guy who runs almost exactly my setup, with enlightenment, emacs and tcsh. My environment is a bit more hardcore than that, and mine is also very gentle and pretty, with pictures of cherry blossoms as a gentle background to a full screen gnome-terminal.

Java and Emacs from IBM.
jdee - Java Development Environment for Emacs
Richard Stallman video. A lecture in Australia, some interesting ideas about how to support yourself developing Free software.
Learn how to dance bhangra in seven days.
Firefox now supports E4X - ECMAScript for XML. Which is a programming language extension to ECMAScript/Javascript that makes it nicer to manipulate XML documents.

Sunday, December 18, 2005

A good article about speeding up your hard disk with hdparm
KAON2 - A tool for the semantic web.
OWL - The Web Ontology Language
OWL features
OWL guide
OWL ref
What is ontology - Great article which talks about the philosophical idea of ontology.
Ontology in computer science
OWL: Representing Information Using the Web Ontology Language
gene ontology format

Saturday, December 17, 2005

and blog
Wow, fantastic site by Tim Berners-Lee about design issues and web technology. We're getting closer to something really wild and powerful. Blogs and podcasts are part of that, but it's going to be much more. A way to empower many more people.

Those $100 laptops for every child, those are going to be the key, to have a world where kids can really contribute to the global dialogue, can really both listen and participate. Where we are going is going to take where we have been, all the philosophy, literature, all cultures and will synthesize it into something new. Where now we have a world of couch potatoes and a very few creative produces, we will have a world where everyone is creative, a musician, an artist, a writer, everyone will have their 15 years of fame, and in constantly changing groups.

Anthopologists study chimpanzees, but they should study Bonobos. In chimp society, they saw a mirror of the harsh kill or be killed world of the city, where rigidly enforced social and sexual roles force men to be the agressors, and women to be the ones looking for safety at all costs. In Bonobo society, problems are resolved by sex. I'm not saying that our problems in the future will be resolved just by sex, but by a sharing of ideas that will be even more potent than sex. We're moving there, or rather, this is a road that is now open to us.

We have a choice, follow the warmongers and the haters to a place where humans start de-volving, or transcend our biology and embrace our biology and become something new. The people of my generation, the Blue Children, just don't understand. The Indigo Children are starting to understand, but they are too angry. The Crystal Children have a chance at understanding and following this new road.

If you don't understand this. Try.

Friday, December 16, 2005

This is neat, some tools to monitor your disks:
That's neat, just a month before I visited Le Louvre, the
Mona Lisa (La Joconde) was moved to her new wall. A really
nice way of displaying this masterpiece.

However, I liked this one much more:

Thursday, December 15, 2005

I will require a mantaray.
google API guide
another one of the dutch clones. at least they are pretty clones.

neat, bendy.

(cute korean girls not included)

Tuesday, December 13, 2005

C++ is better.
Java is good. Python is bad. Simple.

java linux tips
netbeans IDE
eclipse IDE

Monday, December 12, 2005

xooglers - People who used to work at google.
To follow and demonstrate the path of Truth, Simplicity and Love is man's supreme duty and the highest Yoga. Diligent work is a quality of this path, for laziness is death on earth. Only by work can one claim victory over karma. All must strive to do their duty in the best possible way and not to wander from that duty. Service to humanity is the first duty. During these times, inhumanity and laziness have increased, so it is important that you work hard and not lose heart. Be brave, be industrious; work hard and have courage.

Babaji - September 30, 1982

Saturday, December 10, 2005

You know, after spending two years in Europe, I'm really not impressed with Europeans and their "civilization". At all. Just had to say that.

To any of you young crystal children living in Europe, there is a better place, a place where your talents and gifts will be respected and cherished, it's called the west coast of Canada. When you come, ask for sness.
x3d with xj3d.

Friday, December 09, 2005

Dogs can laugh
You and I...
we're older than the sun, wiser than the moon, and deeper than the depths of space. We've always been together, we'll always be together, and until thy Kingdom comes and we are known as One, nothing will ever change this. Whatever you can imagine, I can make happen. Whatever you want, I already have.. And for as long as you have thoughts to think, dreams to weave, and seeds to sow, NOTHING, for us, will be impossible.

What I'm trying to get at is, whatever you now want, I think we can handle it.

Your dreams are what I’ve dreamt for you.

--A Note from the Universe

Thursday, December 08, 2005

From The Schemish Snay
And up the tree climbled the Snay,
All dressed in snerfles and loam,
And with a sness slid down her dress;
He sent her squealching home.
cetaceans and seeing sound
Humpback whales at the neat Whalesong project.

The Glory


Wednesday, December 07, 2005

Why AJAX sucks. Hmm, don't know if I agree with it, but interesting. We need richer ways to navigate these hyperlinked structures, especially for where we are moving in molecular modelling and genomics.

Lemur - a multisurface control for music. neato.
Alchemists of Sound - A BBC video documentary.

Tuesday, December 06, 2005

Adding swapspace to Linux.
It is important for you smart crystal kids to try to talk to the dolphins. Here are some resources for you:

How to read a spectogram. This is more for human voices, but useful.
Bioacoustics of Marine Cetaceans
Spending time with the dolphins
DolphinEAR - Formerly DolphinPHONE. To talk to dolphins, you first must listen to them.
DolphinEAR sound samples
Cetaceans and seeing sounds
easy ajax for the masses with xajax
Some ssh tips. It looks like it has a good explanation of doing port forwarding with SSH, which is neat, but tricky.

Sunday, December 04, 2005

an introduction to sed
10 places you must use AJAX - sink, bathroom, etc. ok, ok, not that ajax.

Taj Mahal
project aardvark movie
The Transits of Venus
Acetic Acid
Black Pepper
I'm back in Canada!
Smart kids should have no problem figuring out the
relationship between the following links.

Meta states in nuclear isomers
Quantum Nucleonics
Selene the greek goddess.
SELENE the spacecraft to study the moon.
Javascript and 3D. A nice article, but the examples don't always work so well.
A couple links for the new Linux based synthesizer OASYS:
OASYS product page.
more XML database stuff.
DB2 xml with PHP

Thursday, November 24, 2005

fuser -n tcp port

Awesome command!

Friday, November 18, 2005

Friday, November 11, 2005

sweet. all of the h2g2 (Hitchhikers Guide to the Galaxy) BBC audio episodes in one place so cool!
Snorri == Good
Snorre == Bad

Thursday, November 10, 2005

wow flickrfs on linux. how cool is that?
Some fun links for you nice kids:

UNIX in Javascript - Oh, so cool!
AJAX - yummy Kool-Aid
Secrets of lightweight development.
Everything you wanted to know about T1 but were afraid to ask.
Step 1) Split Step 3) Profit!
largest virtual purchase yet

Tuesday, November 08, 2005

A little Haiku to express my
sadness at losing those
beautiful entries below
in their entirety.

those empty entries
ajax is responsible
mmm, yummy ajax.
more cihr - grant deadline mar1, application feb1.
cihr funding?

Friday, November 04, 2005

Tuesday, November 01, 2005

` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` `
The True Teacher has no students,
all is BEing and only silence speaks.
The Perfect Teacher has no teachings
because he know that you are free
already. So the True Teacher's non-
teaching is that there is no teacher, no
student, no teaching and that Nothing
has ever existed. This teaching must be
without words and must land in your heart.
If you try to understand it, it will only
land in your head.

- Papaji

` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` ` `

"The Truth Is"
Sri H.W.L. Poonja
Yudhishtara, 1995

Monday, October 31, 2005

Turing's Cat - an essay by George Dyson

Friday, October 28, 2005

Monday, October 24, 2005

That's hilarious! That totally random XSLT Universal Turing Machine link directly below turns out to be useful. It shows an example of TMML, or Turing Machine Markup Language that is a different way that I could do instructions for a machine: Describe it as a Turing machine (or a Cellular Automata) set of rules.
XSLT Universal Turing Machine.
bash-2.05a$ head -3 i
bash-2.05a$ sed -e 's/^/<img src=\"/' i | sed -e 's/$/\"</' > index.html
bash-2.05a$ head -3 index.html
<img src="HPIM0079.JPG">
<img src="HPIM0080.JPG">
<img src="HPIM0081.JPG">

Saturday, October 15, 2005

Thursday, October 13, 2005

Sunday, October 09, 2005

Friday, October 07, 2005

To find out which version of MacOSX you are running:



uname -a

Reports some information, but not as informative as sw_vers.
Some *fantastic* new paintings by my Mom, Fern Ness:

Serving XML
Compiling Koffice
Where I belong, the Flower Society.

Thursday, October 06, 2005

Tuesday, October 04, 2005

Monday, October 03, 2005

kde/qt flowcharting programs
right now, i am being shone on by the light of the eclipse.

Friday, September 30, 2005

ProShape - Neat looking molecular surface package.

Thursday, September 29, 2005

neat article on gpcrs - G-protein coupled receptors
how to get out of quicksand

Tuesday, September 27, 2005

uitwaaien. so cool.
Hey, check out the images on neato. google, you rock. and rawk.

Monday, September 26, 2005

Friday, September 23, 2005

Thursday, September 22, 2005

Monday, September 19, 2005

Friday, September 16, 2005

the football goal of the century.

The computer should be doing the hard work. That's what it's paid to
do, after all. The fact that it takes a little hard work from the
programmer to make the computer do hard work should not be a
consideration when the payoff is big.
--Larry Wall

I would only ammend "boring work" to hard work as well. sness.

Saturday, September 10, 2005