Folding@home

FLOPS

There has been much interest in our stats page (osstats) detailing different OS's and the FLOPS they produce:

http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats

We've been trying to come up with a way to standardize these numbers so that they can be more easily compared to each other.  That has resulted in a new FAQ:

http://folding.stanford.edu/English/FAQ-flops

We also plan on updating the osstats page to include both the Native FLOPS (which is on there now) and the more common x86 FLOPS, which allows for a more "apples to apples" comparison of FLOPS.  

Note that since x86 FLOPS are generally higher, this would increase our FLOPS estimate for FAH overall.  Our initial goal with our FLOP count was to try to be very conservative with FLOP counting on GPUs, but the motivation for x86 FLOPS is to try to be more consistent with other FLOP counting.

New paper #63: Accelerating Molecular Dynamic Simulation on Graphics Processing Units

We're happy to announce a new paper (#63 at http://folding.stanford.edu/English/Papers).  This paper describes the code behind the Folding@home GPU clients, detailing how they work, how we achieved such a significant speed up on GPUs, and other implementation details.  

For those curious about the technical details, I've pasted our technical abstract below:

ABSTRACT. We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. 

Also, this software is now available for general use (for scientific research outside of FAH).  Please go to  http://simtk.org/home/openmm for more details.

Folding@home passes the 5 petaflop mark

Based on our FLOP estimate (see http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats), Folding@home has passed the 5 petaflop mark recently.  To put it in context, traditional supercomputers have just broken the 1 petaflop mark, and even that level of performance is very challenging to aggregate.  The use of GPU's and Cell processors is has been key to this, and in fact the NVIDIA numbers alone have just passed 2 petaflops.

Thanks to all who have contributed and we look forward to the next major milestones to be crossed!

New paper #62: The predicted structure of the headpiece of the Huntingtin protein and its implications for Huntington's Disease

It's still early (since this paper was just accepted), but I wanted to give FAH donors a heads up on our work on Huntington's Disease aggregation, which is just about to come out in the Journal of Molecular Biology.  I'll comment on it more in a future post.

See our papers page for more details.

New FAH results on possible new Alzheimer's drug presented

This is very preliminary news, but something I'm very, very excited about, so I'll give some advance news.  On Tuesday, we presented our results regarding new possible drugs (small molecule leads) to fight Alzheimer's Disease at a recent meeting at Stanford.  This meeting was part of the NIH Roadmap Nanomedicine center (http://proteinfoldingcenter.org/) retreat and was supported by NIH grants to Folding@home.

It's very early (so we are not publicly talking about the details until this has passed peer review), but we are very excited that it looks like we may have multiple small molecules which appear to inhibit toxicity of Abeta, the protein which is the toxic element in Alzheimer's Disease.

This is exciting in many ways.  It's been a long road for FAH to get to this point, but we are starting to see the possibility of seeing these results published easily before our 10th birthday (October 2010).  Considering all the technology development that had to be done in the first five years, these results have come very quickly (in the last 3 years), which is exciting.  In particular, we are now looking to apply these methods to other protein misfolding diseases (we have pilot projects for Huntington's Disease underway).

Finally, I should stress that while we're very excited about this, it's still early and a lot can go wrong between where we are and having a drug that doctors can prescribe.  Over the holidays, we will be double checking the experimental data, crossing t's and dotting i's to make sure there is nothing missed before we think about submitting this for peer reviewed publication.  Also, there is still a long way from an interesting possible drug (where we are now) to something which has passed FDA clinical trials (where we'd love to be), and a lot can go wrong in clinical trials in particular.  

Thus, this is an important milestone for FAH and we are very grateful to all who have contributed.  Happy holidays to all!

Folding@home/PS3 wins "gold" award at the Good Design Award competition

We're happy to announce that the PS3 client for Folding@home has won a prestigious design award:

The PS3's Folding@home service has nabbed a prestigious Good Design Award, AKA "G-Mark." Since 1957, the Good Design Award has been instituted by the Japanese Ministry of International Trade and Industry to award outstanding design in industrial and consumer products.

Here are some more links.  First a news site discussing it

http://kotaku.com/5078119/foldinghome-wins-japanese-design-award

and the Sony Press Release

http://www.scei.co.jp/corporate/release/081106de.html

GPU2 open beta going well

The GPU2 code beta test is going well so far.  While there are some issues to deal with, it looks like this client is significantly easier to use than GPU1.  Also, we're excited since the science in GPU2 makes a big step forward.

There's been lots of suggestions (tweaks to the client, a visualizer, PPD change), and we've been compiling lists of requests and going over what makes sense.  Right now, I'd say that everything is on the table, but some suggestions are easier than others.  We'll prioritize on the easy & important additions first of course (and the hard & less important changes last).  Also, we're working on a visualizer that will give real time updates like the PS3, as well as a console version of the GPU2 client.  We may hit a show stopper, but that's on our roadmap.

We're excited about the turnout so far and are looking forward to doing exciting work together with this new technology.

Netxplorateur

Folding@home has been honored as a Netxplorateur in France (see http://www.netxplorateur.org/ for details).  This award has been given to FAH based on our work in developing a distributed computing network to address protein folding and misfolding related diseases.  We'll post more information as time goes on.

Thanksgiving

It's Thanksgiving Day in the US -- a holiday where we eat a lot food, play some football, and most importantly think about the previous year and everything we've been grateful for.  The FAH team at Stanford has lots to be thankful for over the last year, with the great turn out from FAH donors and new ports.  We're even more excited about 2008, as we have done a lot of work this year to set up some new surprises for 2008 (and it will likely be in 2008 that some of our achievements in 2007, like the PS3 and GPU clients, really shine).  Finally, we've had a strong year in terms of producing scientific results from FAH (check out our results page for details).

Anyway, from all of us on the FAH team, thanks to all the donors who make our work possible!

New results from Folding@home: paper #53

We have another new paper to come out in the Journal of Molecular Biology (paper #53 on our results web page).  This paper is on protein folding and is Dan Ensign's first paper as lead author.  It's also one of the first key results from the SMP client (I'm sure people feel like the SMP client has been out for quite a while, but this was actually a pretty fast turnaround, as analyzing the data, writing the paper, getting past peer review, and then getting published can easily take 12-24 months).

Dan wrote a nice non-technical summary of the paper which I'll include here:

This paper describes the first set of results generated using the SMP clients. The main advantage of using SMP for these sorts of calculations is that the amount of computation that one client can do is several times larger than the traditional clients. This means that our simulations can get many times longer that before; in fact, this has allowed us to generate several hundred folding trajectories of the fastest-folding protein known, the HP35-NleNle variant of the villin headpiece subdomain. In this paper, because our simulation time scales compare well to the 700-nanosecond experimental folding time of this protein, AND we've generated enough trajectories to get good statistics, we can shed some light on the experimental results. To summarize the result, the first helix of the protein was thought to be highly structured in the unfolded state of the protein; we've suggested that structure in this part of the molecule is not enough to lead to fast folding, and that longer time scales than the 700-ns mark may be present in this system.

Check out the movie: it shows some simulation we did for this work, although watching one trajectory is emphatically NOT statistically significant, which is the whole point of the paper!  The movie is from a DL.tv interview I did and the main part I want to draw people's attention to is the movie of the protein folding simulation -- that simulation was from the SMP client and from the data set discussed in this paper.