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Folding@Home Information

Stanford's goal: to understand protein folding, protein aggregation, and related diseases.



What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.

What does Folding@Home do? Folding@Home is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. Stanford uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. This has allowed us to simulate folding for the first time, and to now direct Stanford's approach to examine folding related disease.



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[H]ard|Folding News Articles
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  • News Articles: 142
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Databases, Stats, and Functions, oh my
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,415,625
Work Units: 6,103

Posted: Mon May 24, 2010 02:59 pm
This last month was spent on improving more of the site functions, the overall speed has increased and everything is appearing to load much faster now.

During this time Smokerngs brought to my attention that there was a glitch with the stats leftover from the stanford stats upgrade, the problem has been tracked and fixed, everything should once again be functioning as normal.
Support for GTX 4xx hardware
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,415,625
Work Units: 6,103

Posted: Fri Apr 23, 2010 06:37 pm
Stanford is now working on a GTX 4.x client

Quote:
We have been working behind the scenes to optimize the Folding@home GPU client for the new NVIDIA GTX 4xx hardware. So far, it's been going well with us hitting some strong performance numbers. We are internally testing this and hope to soon (weeks) release this for outside beta testing. Please note that GTX 4xx support will require a new client and also requires some changes to our cluster backend software.


New award for Stanford Folding@home research team member
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,415,625
Work Units: 6,103

Posted: Sun Mar 21, 2010 09:55 pm
Folding@home researcher Greg Bowman was awarded the 2010 Kuhn Paradigm Shift Award from the American Chemical Society (ACS) for his talk on two paradigm shifts resulting from Folding@home: 1) the new methods that Folding@home uses to simulate protein folding, misfolding, etc, and 2) the results themselves, which suggest a significant change in protein folding theory.
Nvidia GPU problems being worked on
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,415,625
Work Units: 6,103

Posted: Sat Feb 27, 2010 10:31 pm
Quote:
Further bug fixes to the v5 WS
Joe has been pounding on the v5 WS trying to shake it out from the recent disaster with problems returning NVIDIA GPU WUs. The upshot of all of this is that the v5 server code was pushed hard in many ways and several issues have now been found. Joe is testing them, but we're hopefully that beyond the initial good news we had a few days ago, that several additional issues may now be fixed.

It's too early too tell since we're still testing, but I'm optimistic. This only affects particular servers (vsp07b, vspg10a, vsp11a) and the vsp09a CS.

v5 Work server issues looking pretty good It is looking like the WS bug fixed has helped resolve the NV issue GPU work server issues. We are keeping a close eye on things, but it looks like the situation has been stable so far.


Full articlehere


Also there seems to be a shortage on small work units.

Quote:
Here's a heads up for donors running with clients configured for small WUs (v6 clients) or normal WUs (in pre-6 clients); note that this does not affect "big WU" client configs for v6 or earlier. It looks like we're running low on those over the weekend. I hope to have this resolved by Monday, but likely not tomorrow (Sunday). One workaround is to configure your client for medium-sized WUs:


Acceptable size of work assignment and work result packets (bigger units
may have large memory demands) -- 'small' is <5MB, 'normal' is <10MB, and
'big' is >10MB (small/normal/big) [normal]?


Full articlehere
Institute Of Cancer Research Selects Supercomputer
King_N
[H]ard|Folding Administrator


Posts: 87
Points: 2,415,625
Work Units: 6,103

Posted: Thu Jan 28, 2010 12:54 am
SGI (NASDAQ: SGI), a global leader in HPC and data centre solutions, today announced that The Institute of Cancer Research (ICR) has selected SGI Altix UV, based on Intel Xeon processors (codenamed Nehalem-EX), to support its future life-saving research. The ICR joins the growing list of globally significant high performance computing (HPC) facilities embracing Altix UV as the future of open, high performance, big-memory supercomputing. Altix UV will provide the ICR with a massively scalable shared memory system to process its growing data requirements, including hundreds of terabytes of data for biological networks, MRI imaging, mass-spectrometry, phenotyping, genetics and deep-sequencing information across thousands of CPUs.

Full Story Here
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