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Folding@Home Reports Success
msheppard writes "This Article describes how the folding@home distributed computing project is reporting that they used the data processed on client machines to "predict the folding rate and trajectory of the average molecule." Too bad Seti@Home hasn't had a hit yet."
Did anyone else think this was yet another article about @Home going bankrupt?
Here.
MSNBC Article.
Folding@Home Home
For the real info though check out the Forums
Token link to how my team is doing.
PRIME1
http://www.kubuntu.org/
That's average protein molecule, you insensitive clod!
that the sister project genome@home was so monumentally badly mismanaged that it effectively merged with folding@home a distinct project. I lost complete faith in the Pande group at that point along with a lot of other genome crunchers and switched all my CPU's back to SETI...
I don't read your sig, why do you read mine?
Maybe next we can use our screensavers to do something cool like search the web for potential stories to post on slashdot.
Too bad Seti@Home hasn't had a hit yet.
Well, here's the thing: "we know molecules exist..."
If you like F@H, check out Distributed Folding.
Look, ma! I'm a karma whore
SETI@home has much nicer graphics, albeit, a much dumber purpose. I'll stick with folding@home, but I wish they would pretty the damn thing up a little--at least on the Mac OS X platform.
blarg.
I hadn't realized how many distributed (grid) computing programs were out there... Check out Google Directory's list of links to distributed computing pages/projects here... Distributed Chess sounds very interesting!
Sorry, brain no workie this morning.
go here instead
in saying that it's the first distributed computing success. Look at the success of the distributed.net project, they just recently cracked rc5-64, and have cracked several other ciphers before.
Okay, it's nice to see that distributed computing is finally becoming a useful tool. Nonetheless, I don't think there's anything particularly impressive about the biological results. The proteins they're folding are so small that most factors that affect the folding and conformation of the vast majority of proteins simply don't exist. When someone accurately predicts the structure of a normal globular protein at atomic resolution, I'll be impressed. When they can predict the structure of the F1F0 ATPase, then we can throw out crystallography- but it's not going to happen. (Ignoring for the moment that crystallography has it's own issues. . . at least it can show active sites and quaternary structure)
Don't get me wrong, the geek half of me thinks that what they're doing is very cool (and far more interesting/useful than Seti@Home). But I don't think it's very relevant to biology, and I doubt it'll ever replace traditional methods. Computers have almost unlimited potential as an aid to experimental structural biology, but in silico protein folding is still a pipe dream and a hand-waving exercise. The theory is really cool, the practical applications are nearly zero.
(Disclaimer: I don't have a PhD so I'm not very qualified in this field, but I do have a BS in biology and a fair amount of experience in programming and some knowledge of molecular simulation.)
Amen. If you are going to use your spare cpu cycles for something, apply them to a good cause. Besides if you study much on the SETI project, they look at a very limited range of data of the odds of finding anything interesting are exponentially worse than you'd even think. At least the various folding projects and the think project from intel and other medically related go towards good causes where every bit of data helps the cause.
This(postscript) is the the original paper on the hardness of String Folding problems.
If we get one Seti hit and we may be able to replace ALL of our current problems with new ones.
Earth: How do we cure cancer/every disease we know of?
ET: Use *this*, but now that you're living forever, you have to worry about massive overpopulation.
Earth: How do we get off this planet?
ET: Use *this*, but now you have to worry about war between your planets.
Earth: How do we achieve peace?
ET: Use *this*, but now you're bored outta your minds.
M@
Krispy Cream is people
Comment removed based on user account deletion
I tried to fold a molecule once, but I wasn't even able to fold a piece of paper eight times.
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I think what drives people to use these clients is simple. I have heard several "technically adept" (read: geek) friends state that they simply hate to see their computer sit idle.
They have paid for the hardware, paid for the bandwidth, paid for the electricity. It should be doing SOMETHING. Even if it is just displaying flying toasters.
By the time Folding@Home or Genome@Home actually produce data useful enough to lead to medical cures, your wristwatch will be powerful enough to fold proteins in seconds. Don't confuse a nifty theoretical exercise with experimental science. Neither the technology nor the methods are sophisticated enough for this to be of any help to people with cancer etc. I wish someone would come up with a project that actually produced useful biological data with distributed computing. BLAST@Home, maybe. Doesn't sound nearly as sexy as protein folding, I guess.
(You're still right about SETI, though. What a freakin' waste.)
I submitted this as a story, but it was rejected. Google has incorporated distributed computing into its toolbar as an option. The first supported project is Folding@Home, but they will add more projects in the future. Its optional, and currently has only been released to a few toolbar users. It will gradually be released to all users. Check it out at toolbar.google.com/dc/. Google is currently seventh in the team statistics...
*IF* SETI gets a hit, it will be more like:
Earth: Wow, a spike that may have possibly been generated by an intelligent life form millions of years ago...
ET: ???
"Ignorance more frequently begets confidence than does knowledge"
- Charles Darwin
Well, on a related topic has anyone thought of this explanation for why SETI has found no results :
Most current radios, based on decades old tech, broadcast a very orderly signal. It is confined to a narrow band range, only one transmitter is allowed per channel, the data being transmitted is uncompressed and so has many repeating orderly patterns.
To increase capacity future radios will do the opposite.. They will broadcast compressed data that seems completely random, they will use a large swath of spectrum, they will repeat parts of the same signal across a large portion of the spectrum using a "chipping" algorithm. Even farther in the future, so many radios at once may be talking on the same spectrum that to identify a particular sender in order to communicate you'll have to use multiple antennaes and know his location (you'll share spectrum based on location).
What is the end result of advanced communication gear that intelligent minds develop? What is the optimal result? To an outside observer the signal will seem like pure, almost totally random noise. Only to the electronics of a particular receiver that has the correct encryption and chipping key will it seem like anything else.
THAT's why we can't hear anything. Trillions of sentient beings could communicate using this method and we wouldn't hear a thing.
Hint: People can use their own spare CPU cycles on whatever they like
Sure they can. That's not in question. But the theory behind the distributed clients is to avoid wasting CPU cycles and to do something useful.
The point of the OP was that SETI@Home (and, frankly, RC5 crack searches) are osteniably no better than having the CPU cycles spinning anyway. Projects like Folding@Home, Genome@Home, and UD Cancer Research can provide a real, proveable benefit in both the short and long term. Mathematical projects like GIMPS and prime number searches do so as well, although my personal opinion is that they're not as valuable.
Use your CPU cycles however you like. Hell, don't run a distributed project at all if you don't want to. All that's being asked is to consider how to actually use the spare cycles effectively if you're going to join a distributed project.
I've read the Folding@Home FAQ looking for information about what they plan to do (from an IP standpoint) with the information they get. The "answers" they provide are pretty vague on the details.
Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's Chemistry Department), which is a non-profit institution dedicated to science research and education. We will not sell the data or make any money off of it.
Ok, they won't make any money off it, but who might? Who owns any patents? What actually is done with the data? And the non-profit bit tells me nothing. The Vanguard Group is a non-profit too, but that doesn't mean they aren't interested in money. (Vanguard is owned by the investors, hence non-profit, but not really) Just because it is a non-profit institution doesn't tell me much. Universities are non-profit but they make a ton of money off of IP. They can do whatever they want but before I commit my processor cycles to helping I'd like to know specifically what I'm helping.
The FAQ goes on to say:
Moreover, we will make the data available for others to use. In particular, the results from Folding@home will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles which analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site.
So the data is going to be available. How? What "levels"? To whom? For how much? Just saying it will be published in journals tells me little. What else will be done with it? Who stands to benefit from the data? (aside from the obvious)
Basically I want to know and am not impressed with their answers. I'd like some candor when it comes to something this important. With SETI@home, who really cares? That won't affect my life. Folding@home might.
Well, I kinda agree and I kinda disagree.
First, you can't expect to go from no success to complete success overnight. People have been trying to fold proteins for some time now and have basically failed because it is freakin' hard. The theory is in principle in place, a least to a first approximation, but the calculations are so intensive that they have basically beaten every comer. As an undergraduate I remember how everyone in the field thought getting bigger and better grants and buying bigger and bigger computers was the answer. Oh to be SGI in those days. They sum up the problem pretty well in the Nature paper, essentially a modern (desktop) computer would require a few decades to crunch through a single useful length simulation. Then you need to do it many times to get a useful answer (say 100-1000). Even supercomputers are going to balk at that kind of calculation. Moore's law what it is, we should then be able to get through an in silico simulation in a week on a single computer (when its this fast crystallography really will be dead) by, oh say 2040 at best. (somebody want to calculate that exactly, 10000yrs -> 0.02yrs is how many doubles). So yes, this hasn't gotten rid of x-ray crystallography just yet.
But this is still really cool. Complaints about interface and maintenance aside, this was a great system. It relied on four pretty bright insights.
First, that distributed computing is essentially the poor man's (cough, the academic's) super computer. Also, it automatically adapts itself to technological improvements. People will buy new computers from time to time and, hopefully, reload your software.
Second, that there was no reason other than no one had sufficiently brute forced the process that the existing methods shouldn't work. They use a bunch of 'cheating' techniques to make this managable during the screen saver timescale, such as a united atom model (I think that means they ignore aliphatic hydrogens) and implicit solvent (don't treat it as individual solvent molecules, just a uniform field). It was an open question as to whether this approach would work at all or if you had to go over to much more explicit methods to get it to work at all. It appears that this has kinda worked with the cheater methods in place.
Third, choice of a test case. Yes they chose something that was small. This isn't surprising. They wanted to be done sometime this decade, remember there is a graduate student as the primary author here. Small was necessary. However they also chose a FAST-FOLDING protein. That was clever. Basically, even with distributed computing, it is still hard to simulate a full microsecond of time. Thus they chose something that had some chance of completing its folding one the time scale that they could look at.
Fourth, they remembered their P-Chem. It is really hard to run these things to completion... so they didn't. You don't have to run the simulation until 99% of the molecules have completely folded, just until an appreciable number have folded and you can extrapolate the behavior from that. They ran a 20ns simulation (at the longest). The thing takes 7us for ~60% to fold. As a result only once in a great ong while did one of the simulations actually produce a folded protein. But by doing it ~10000 times they could figure out how that translated into the rate constant. That's clever.
That said, yes there is a long way to go on this, but its still a really clever paper. No we haven't cured cure cancer yet, but its still progress. And forget an in silico structure of the ATPase, that's largely understood already (check the RSCB/PDB there's a bunch). The real challenge will be getting a structure that size that hasn't been solved by other methods and convincing anyone else that you're right! Disclosure- I don't have PhD in this area yet, but I'm close.
Actually, we're in the experimental error. Keep in mind that folding time distributions are exponentially distributed (not Gaussian). This means that the std devs will be big just by their nature. 7.5 vs 6 are indistinguishable statistically.
We can only hope that the aliens can actually legally send signals and aren't emcumbered by "Patent 1,345,821,098,836: sending signals encoded in high frequency waves to unknown lifeforms over the aether", and that they think the unknown lifeform receivers have a shot of decoding the signal without getting hit by "IGADCA - Inter-Galactic Age Digital Copyright Act: violations of decrypting the radio encoding".
Hmm, maybe they have 8 arms and tentacles, and they'll just bite the lawyer's head off when they disagree with them.