Posts Tagged Simulation

Ancient computing – the Antikythera Mechanism

When diving deeper into the far end of the historic roots of bioinformatics, I came across the Antikythera mechanism. To me, it has all the hallmarks of what bioinformatics is about: taking in the available knowledge of the time, integrating all the data there is into a functional machine model that actually makes useful and verifiable predictions. And all of that already happened approximately 2100 years ago. Wow!

The timeline for BioInformatics I created however did not seem to accept a corresponding entry, although on dipity dates B.C. should work (since April 2011, they say) – but not for me (yet).

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Blueprint for the Brain

Science Bytes is a series of short videos, based on recently published studies from the Public Library of Science (PLoS), which highlight discoveries that are shaping our future.


Episode 1: Blueprint for the Brain from Science Bytes on Vimeo.

Meet two scientists who have begun to unlock the secrets of the brain’s architecture.

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(Digital) Life is for Sharing

Actually I know very few people who have NOT yet been infected by this contagious, addictive phenomenon. Obviously I am not referring to bird flu, swine fever or certain strains of E.coli but to “Angry Birds” here. Through unfortunate circumstances, I currently still am a (angry) customer of the piggy-pink Telekotz and am looking very much forward to the end of their tyranny contract with me. Now, after this clarification, I hope to have established the necessary critical context and am comfortable to bring the following ad to your valued attention: The idea and realisation of taking such a game, based on a relatively simple 2D physics simulation, into the “real world” is quite stunning.

“It’s time to end this struggle which has cost millions of innocent people their ability to concentrate in work!”
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Production Release: CUDA Toolkit 4.0 and Parallel Nsight 2.0

Parallel Nsight 2.0 Released

The latest development tools for CUDA (Compute Unified Device Architecture) GPU programming were just released by nVidia:

CUDA 4.0– Features include Unified Virtual Addressing (UVA), Thrust C++ Template Performance Primitives Libraries and GPUDirect 2.0 GPU peer-to-peer communication technology. Download at

Parallel Nsight 2.0– Features include full support for Microsoft Visual Studio 2010, CUDA 4.0, PTX/SASS Assembly Debugging, CUDA Debugger Attach to Process, CUDA Derived Metrics and Experiments, as well as graphics performance and stability enhancements.

A comprehensive Webinar Series is now open for registration. On their latest hardware developments checkout this post from last week.

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News from the parallel multiverse

Using all the processing power of of your computer while it is idly waiting for you is a great idea – especially when its used for advancing medicine and science. It’s become so simple, secure and fun – so here are some of the recent developments in the “parallel multiverse”:

Open-Source Software for Volunteer Computing und Grid Computing.

BOINC 6.12.26 released to public
The next version of BOINC is now ready for public use. Check the release notes and version history for details. (17 May 2011)
BoincTasks 1.00 released
Version 1.00 of BoincTasks (a Windows program for managing BOINC clients) has been released after 2 years of hard work and with the help of many volunteers. (19 May 2011)
BOINC Workshop
The 7th BOINC Workshop will be held 18-19 August 2011 in Hannover, Germany.

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Lively Molecules in a Crowded Cytoplasm

cytoplasm model at the end of a Brownian dynamics simulation performed with the ‘full’ energy model

Proteins are not static entities – since we live at about 300 degrees above absolute zero there is constant Brownian motion. However, looking at deposited X-Ray structures, one might get the impression that the structures are rigidly sitting in vacuum – nothing could be further from the truth! I like the analogy with early photography :

Photography, ca. 1893

because the photoplates were not that sensitive, long exposure times were necessary. Hence people had to hold very, very still for several minutes in order to get a decent picture. Photographers had special setups and chairs with neckbraces to keep the poor subject in place. This apparatus is the analogy to a protein crystal – it keeps the proteins in place, floppy and moving parts will not show up on the resulting electron-density maps.
The photographs of our great-grandfathers leave us with the impression that they were very stiff people, largely devoid of any humour. That’s probably not true, but how happy and lively would you look if you had to sit still for quite some time in your best outfit with your head squeezed onto some weird mechanical contraption? The same holds true for proteins. Read the rest of this entry »

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Playing with the building blocks of life

is wonderful – and you don’t need a Ph.D. to experience it and make a contribution. Even kids get to know how to make the molecule-thingy move within minutes, a simple down-to earth explanation of clashes, voids and rubberbands is sufficient – of course you have to avoid all the fancy terms from biophysics that usually impress (or shut up) the audience. To all those who take themselves too seriously as scientists, check out the story on the structure of a Monkey virus protein and their blog. The tool is available for all major platforms, and I can only recommend it. Great work! Cool for teaching and communicating the molecular basis of life. It’s still called “beta” but looks pretty stable to me. Maybe you can convince other nerds to spend some time on folding proteins rather than smashing trolls to smithereens in WoW- the fun factor is definitely there, and the science as well. Check out the video on nature “FoldIt: Biology for Gamers” which has a link to the full paper and the related News feature. An afterthought to the previous post on crowd-sourcing: Such massive online-games in science have the capacity not only to combine the CPU/GPU power of a vast number of machines, but also to integrate some of the most advanced pattern recognition algorithms on the planet: your brain.

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