Archive for July, 2011

A documentary on network-theory

As I met Marc Vidal personally, this is just about one-degree of separation for me 😉 – Enjoy!

(found via Barabasi lab, thanks to Henning Stehr for hints)

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My (first) PREZI-ous

In order to test how alternative ways of presentation work in real life, I’ve created the “backbone” of a lecture on the basics of structural alignment.
The current version of the prezi can be viewed at here/.

The plan is to combine this with a couple of intro-slides (keynote) plus using / demonstrating some “practical” aspects of alignment “life” with pymol and other software (cmview, processing sketches). I guess it’s choosing the right medium for the message, so I’ll include some “real” 3D models and use the black/white board as well – so the prezi gives the overall outline, but does not contain the entire lecture.

So far it has been a smooth and rewarding experience to use prezi, especially since it alows to gather all the concepts on one screen and subsequently put a logical path through it. This results in an interative process by adding / removing items and changing the path accordingly. It really helped because I could start by throwing in all the important concepts I wanted to talk about without a pre-conceived linear order. The ordering is an “emergent property” of the process. Any feedback is very much welcome!

Thanks to Bosco Ho for inspirations (the title is from him), see his post “Structural alignment done right”.

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Weekend Music Video

BERLIN CALLING – Sky & Sand (special Mix) by Paul & Fritz Kalkbrenner



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Speeding up molecular shape comparison

gpGPU acceleration is steadily contributing to progress in the computational LifeSciences, for example in rational DrugDesign. OpenEye scientific software announced a performance-increase of their molecular shape comparison ROCS by about 2-3 orders of magnitude (100x-1000x(!)) using GPUs. With this they won the “Best Show” award at the 2011 BioIT-World.

Now FastROCS processes 2 million conformations per second on a Quad Fermi box.

This enables all vs. all shape comparison across entire compound libraries. Below is an interview with Joe Corkery at the BioIT World, and they also have a couple of interesting posts on their blog.

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art is everything you get away with

Today is the hundredth anniversary of Marshall McLuhan, born July 21, 1911 in Edmonton, Alberta. A very interesting character and visionary, indeed, who coined several phrases in the sixties which are so familiar now. Sentences such as “The new electronic interdependence recreates the world in the image of a global village“, “art is everything you get away with” and “the medium is the message” – he is the guy who came up with it. With the rise of the internet and information society, his works, analysis and (stunningly accurate) predictions are increasingly gaining recognition. For example, he anticipated the conversion of TV and other forms of (electronic) communication. A classic case of a genius far ahead of his time, a heavily under-appreciated prophet in his own country?

Now Douglas Coupland (author of “GenerationX”, “Microserfs”) – who describes himself as a soulmate of McLuhan – has brought out this biography “Marshall McLuhan: You Know Nothing of My Work!” (see here for a review).

Something to go onto my wishlist …

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Nostalgia just isn’t what it used to be

As we are celebrating 20 years of the WorldWideWeb, a little bit of digital nostalgia is on the order:

Format: A Brief History of Data Storage

Format: A Brief History of Data Storage from Alan Warburton on Vimeo.

found via SchockWellenReiter
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cubus dilabor est

This beautiful 3D animation from a team of the Stuttgart Media University reminded me of Ceasars’ “alea iacta est“, but since the cube falls apart into smaller pieces here, the line above seemed more appropriate. The video is called “Cubism”, done by Nina Wellstein, Sascha Langer, Felix Schwarz, Mark Haberpursch and Sergej Feininger:

found on Glaserei

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