Posted on 12/08/2008 12:10:04 PM PST by texas booster
... We present a novel computational approach for describing the formation of oligomeric assemblies at experimental concentrations and timescales. We propose an extension to the Markovian state model approach, where one includes low concentration oligomeric states analytically. This allows simulation on long timescales (seconds timescale) and at arbitrarily low concentrations (e.g., the micromolar concentrations found in experiments), while still using an all-atom model for protein and solvent.
As a proof of concept, we apply this methodology to the oligomerization of an Abeta peptide fragment (Abeta 21–43). Abeta oligomers are now widely recognized as the primary neurotoxic structures leading to Alzheimer's disease. Our computational methods predict that Abeta trimers form at micromolar concentrations in 10 ms, while tetramers form 1000 times more slowly. Moreover, the simulation results predict specific intermonomer contacts present in the oligomer ensemble as well as putative structures for small molecular weight oligomers. Based on our simulations and statistical models, we propose a novel mutation to stabilize the trimeric form of Abeta in an experimentally verifiable manner.
I am very happy to announce that a first key work from the Folding@home project on Alzheimer's Disease (AD) was just published.
Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach, by Nicholas W. Kelley, V. Vishal, Grant A. Krafft, and Vijay S. Pande. J. Chem. Phys. 129, 214707 (2008); DOI:10.1063/1.3010881
url: http://link.aip.org/link/?JCP/129/214707
Abeta misfolding and aggregation is believed to be the cause of Alzheimer's Disease. Simulations, like Folding@home, are a natural way to understand this process. However, there are several key challenges for simulating the key step -- oligomerization. This work represents a new way to simulate Abeta oligomerization, with a key advance of being able to simulate experimentally relevant timescales and concentrations, using a novel method. We use this new method and the power provided by Folding@home donors to simulate oligomerization in all-atom detail. This has lead to specific predictions about the process, which we are now testing experimentally.
In many ways, this paper is the "tip of the iceberg" for the Folding@home activities in AD, with a lot more interesting results to come, especially in terms of experimental tests of our predictions and interesting new possibilities for new drugs and AD therapeutics. So, while we're excited that this result is now past peer review, we're even more excited for what's coming down the pipeline, waiting peer review. We'll keep you posted as more results become public, hopefully with some even bigger announcements in 2009.
How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.
Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.
How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired user-name.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.
How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.
There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.
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Dr. Pande has published a new peer-reviewed article concerning the formation of certain peptides implicated in the development of Alzheimer's Disease.
While most of the article is lost to me in a fog from college biology past, it is great to see Folding complete a peer-reviewed article.
Net net - our work is making a difference with researchers across the world in finding a solid cure for Alzheimer’s Disease!
Pings out to the Folding@home team. Dr. Pande has published a new peer-reviewed article concerning the formation of certain peptides implicated in the development of Alzheimer’s Disease. While most of the article is lost to me in a fog from college biology past, it is great to see Folding complete a peer-reviewed article. Net net - our work is making a difference with researchers across the world in finding a solid cure for Alzheimer’s Disease!
*
It's been a while since I've posted on this topic, so I thought it would be a good time to talk about the long term vision for FAH. In the first few years, we have done a lot to build up methodology (novel distributed computing algorithms, tests of methods), especially in the last years working to bring GPU’s, PS3’s, and tightly coupled SMP calculations to a distributed computing platform.
While all of this has been going on, there has been a lot of work which would have a direct impact to disease and human health, and donors should see more results (i.e. papers) coming out in this direction soon. In particular, results on Alzheimer's Disease, Huntington's Disease, and some other surprises in the works (sorry, some details are best left until peer review is done).
In terms of a long term vision for the FAH software, our short term goals is to shore up the SMP client. Just as there was a big improvement from the GPU1 -> GPU2 client, we have been working steadily on an SMP2 client — a version which is much easier to use, requires less donor effort, and scales much better. This really is a combination of a modified client and (especially) new cores. This effort has been going on for about a year and it's far enough along that I'm starting to talk about it publicly.
In the previous post, I also mentioned about some of our work behind the scenes in revamping the back end of FAH, i.e. a whole new set of server codes. We have code for the workserver and collection servers, but in time we expect the full back end to be cleanly rewritten from scratch.
Longer term, with a more solid GPU2 and SMP2 clients done, we can then move on to other areas. Our goal is to be bleeding edge in the nature of our science, but get back to the simplicity and stability found in the classic client. We still have a ways to go, but I am excited that projects that were started some time ago are now looking like they will see the light of day.
Garde la Foi, mes amis! Nous nous sommes les sauveurs de la République! Maintenant et Toujours!
(Keep the Faith, my friends! We are the saviors of the Republic! Now and Forever!)
LonePalm, le Républicain du verre cassé (The Broken Glass Republican)
| Client statistics by OS |
| OS Type | Current TFLOPS* | Active CPUs | Total CPUs |
| Windows | 232 | 243460 | 2313203 |
| Mac OS X/PowerPC | 5 | 6661 | 122640 |
| Mac OS X/Intel | 27 | 8684 | 71188 |
| Linux | 44 | 25600 | 347156 |
| ATI GPU | 554 | 5036 | 17579 |
| NVIDIA GPU | 1797 | 16336 | 53812 |
| PLAYSTATION®3 | 1662 | 58922 | 694944 |
| Total | 4321 | 364699 | 3620522 |
| Total number of non-Anonymous donators = 1146358 | |
| Last updated at Mon, 08 Dec 2008 05:06:49 | |
| DB date 2008-12-08 05:00:01 | |
|
Active CPUS are defined as those which have returned WUs within 50 days. Active GPUs are defined as those which have returned WUs within 10 days (due to the shorter deadlines on GPU WUs). Active PS3's are defined as those which have returned WUs within 15 days. |
|
| *TFLOPS is the actual teraflops from the software cores, not the peak values from CPU/GPU/PS3 specs. Please see our main FAQ, PS3 FAQ, NVIDIA GPU FAQ, or ATI GPU FAQ for more details on specific platforms. |
BTTT
Congrats!
A special welcome to our newest folders:
jfelten
Mike12msu
walkerca
BerkeleyFarmsDairy
kdmasjj_stewart
Terpfen
laker_dad
Bella_bru
HeyDave
Thanks for joining the team!
I got a second PS3. Now all I need to do is convince my wife to get out of the DVD menus she leaves it on so it can get some folding done.
Here’s a “Thanks for the ping”...ping!
I got a PS3 and man, my production has SKYROCKETED. If anyone has a PS3, get that folding app on there. Whenever your PS3 just sits there, it racks up the units.
Woo-hoo! I finally made it into the top 200 on our team!
I know, no big deal but I only have one computer folding.
I was reading the website the other day, and was surprised to learn that the GPUs in video cards are even faster (simultaneous floating point operations) than the PS3.
Ping!
It sure is great to see these hard results coming out, like this. Thanks for walking point on it Tex.
In the daily hubbub, it’s easy to forget that I’ve got four CPUs plugging away as part of a technological marvel that works around the world, around the clock, to crack the mysteries of some of the most heinous diseases on Earth.
I recently passed 1500wu on my way to a quarter of a million points, and am still glad to be contributing; even a little bit.
Last night I visited a family I haven't seen for well over a year.
I gave them a nice computer and only asked that they run F@H. Been running for most of the time crunching away.
Even got the kids interested, at least until an aunt gave them a Wii for a birthday present.
OH, pnly 120 pieces of spyware, and it still completes a WU ever couple of days. Not too bad for an under-maintained system.
I just added an nVidia 8800GS to my home machine...Told the wife it was for the kids playing games. I’m knocking at your door on daily points. I should break 30,000 per week. Behind only a couple of folks (on our team).
Between new graphics cards and the PS3, anyone can rack up points quickly.
Thank you for helping out the cause!
Congratulations to Texas Booster, who will pass Three Million points today!
Thanks, for all that you do!
I hit #1 for the team...(for the past 24 hours...) at one point today. I’ve closed to just over 8,000,000 from the lead, and ~2,800,000 behind you. Watch out...here I come.
Folding systems at 20 paces?
I haven't been the #1 producer but a few times since the group started growing a few tears ago.
Passing me won't mean much, but if you pass lrenh or Klutz then you will have really accomplished something!
fyi...
Egon (just) and Pseudocode (recently) broke a million!
It looks like SazanEyes is folding with us and making a prodigious daily contribution! (2nd highest on the list today... Nice!)
http://folding.extremeoverclocking.com/team_summary.php?s=&t=36120
Anyone know SazanEyes’ FR name?
Hi guys, I fold as SazanEyes. I don’t post to FR much, but I wanted to give a boost to the team of Reagan. :-)
Actually, I’m also folding for another team right now, but I’ll probably switch all my hardware over to the FReeper team at the end of the month. This is what’s coming:
http://folding.extremeoverclocking.com/user_summary.php?s=&u=384443
Wow David, that’s pretty impressive!
Care to tell us a bit about the hardware you’re using?
And THANKS for folding, and thanks again for folding with us!
Right now I have two NVidia 8800 GS cards (overclocked) folding for FR. For the other team I’m using four 9800 GX2s, one 8800 GTS, and a PlayStation 3. It’s actually a pretty small setup. Most of the points come from the quad 9800 GX2 box, which was built specifically for F@H.
If anyone has a relatively modern graphics card (NVidia 8000 series or better, or recent ATI card), definitely install the GPU F@H client for it. It can do a ton of work.
I am amazed that you produce so much work from just a few systems. I keep about 40 systems running, but half of my points come from one NVidia 9600 card.
Could we call on you to assist others in getting GPUs working smoothly some weekend?
Yea, I would be interested. How do I check what graphics card I have?
Also, I just saw that I made the top 20 producers list. That's a first for me, I think.
Ever been invited to this?
http://www.majorgeeks.com/Belarc_Advisor_d1385.html
If you have an NVidia or an ATI graphics card we can proceed.
Yes. I had it on my older computer for a while. Had enough computer problems I gave up on reinstalling it.
Not sure if I’ll install it on this one, or not. Just got it back from overhaul and am a bit picky about clogging the works up with much of anything unnecessary.
I think it’s a great project.
Of course I doubt the oligarchy really WANTS Alzheimer’s patients healed etc.
Part of me thinks they’d take the findings and make it worse and more of a problem.
Thanks.
Congrats on your achievement.
Bump for later
How do I find out?
If you don’t want to install Belarc and are using Windows (2000/XP/Vista/7), try this:
1. Open the Start menu and right-click on the My Computer (or just Computer) item in the right column of the menu. (If you have a My Computer on your desktop, you can also right-click on that.)
2. In the pop-up menu, click on Manage.
3. When the Computer Management program opens, click on Device Manager.
4. You should see a tree view of all the parts in your computer. Look for the Display Adapters entry and expand it.
5. Let us know what it says your display adapter is called. For example, my desktop has “NVIDIA GeForce 8800 GTS” listed.
If it says NVIDIA 8xxx or 9xxx or GTX 2xx, or ATI 2xxx or 3xxx or 4xxx, then you can probably use your GPU to fold.
If you want to just try installing the software to see if it works, it’s available here:
http://folding.stanford.edu/English/DownloadWinOther
The GPU2 program has a standard Windows installer. You just download the install program, run it, click OK a few times, and everything is set up for you (just like the CPU version). If you want a detailed walkthrough to the install/setup process, look here:
http://www.hardforum.com/showthread.php?t=1339662
That page also explains how to run Folding@home on multiple graphics cards if you happen have more than one in your computer.
Right now I only have two PCs (with 10 GPUs) folding for the team. I stopped using one PC and the PS3 to try to save a little money on electricity, but my points per day have actually gone up thanks to the new work units.
I’d be glad to help others start GPU folding and offer some tips. For example, if you want to run F@H on your graphics card 24/7, then you probably want to adjust your card’s fan speed to make sure it stays cool. The most popular program to do this is RivaTuner:
http://majorgeeks.com/download737.html
BTW, I finally reached #20 on the team today in total points. I might be able to make #10 by the end of the month.
Keep in mind that I have been folding since 2001 or 2002 with CPUs, between 30 and 50 systems most of that time. Klutz has has over 400 CPUs running at once.
Here you come with 10 GPUs and a Playstation (!!) and will pass my points total in 3 months. Arrrgh.
I also saw that Stanford has looked at the whole FLOPS issues and decided to adjust FLOPs (but not points).
F@H is now running at 8.8 petaFLOPS. Insane.
I have nothing but respect for long-time folders that got their points the hard way. From what I’ve read, the reason GPUs are capable of such a high Points-Per-Day is not only that modern GPUs are quite powerful, but also because the GPU work units are different. The GPU work is considered more valuable by Stanford, so they bumped up the points to encourage people to do GPU folding. The same is true of the Playstation 3 work, but I believe they actually lowered the points for that work (they arbitrarily chose 1000 PPD) because otherwise the casual PS3 folders would crush everyone else. Even now I think most of the FLOPS come from PS3 users.
By the way, if anyone has a Facebook account, there’s an application that lets you track your points on your profile. I just joined and I’m the only team member right now:
http://apps.facebook.com/proteam/showteam.php?team_id=36120
Not to take away from general purpose CPUs. There are certain calculations that cannot be done by GPUs that tie the entire project together. Both are needed to advance science.
I also suspect that if Stanford could convince Sony to change the PS3 to that it ran F@H in the background 24/7 that Stanford would leap for joy. Imagine the FLOPs if 3,000,000 PS3's joined the project. Wow.
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Just joined the Facebook page.
I’d like to hear more about your system. In 6-7 days you have more points than my 3 years of folding.
self ping for home
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