Folding@Home; Longevity Team
mrfesta
22 Jun 2005
Proteins are biology's workhorses. 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. When proteins do not fold correctly there can be serious diseases, such as Alzheimer's,Huntington's, and Parkinson's disease. Folding@Home is a distributed computing project which studies protein folding to simulate folding for the first time, and to now direct researchers approach to examine folding related disease. Join the Longevity Team and help the medical community find cures.
More Information: Longevity Protein Folding@Home Team
Our current team STATS
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More Information: Longevity Protein Folding@Home Team
Our current team STATS
[thumb]
JonesGuy
22 Jun 2005
I understand that a whole bunch of work is being done. However, does anybody know if any actual benefit is being derived from this? Are there enough end-users to justify the work?
As well, I have some concerns that our theories on protein folding (and their natural states in vivo) aren't all up to snuff. But I'll leave that to the protein scientists to worry about. I'm just a bit nervous that we're accumulating a whole lot of false data.
As well, I have some concerns that our theories on protein folding (and their natural states in vivo) aren't all up to snuff. But I'll leave that to the protein scientists to worry about. I'm just a bit nervous that we're accumulating a whole lot of false data.
mrfesta
22 Jun 2005
Thats a good point. I'm no scientist 
On the stanford site they have the following section:
What have we done so far? We have had several successes. You can read about them on our Scienc Page,Results Section, or go directly to our Press and Papers page.
On the stanford site they have the following section:What have we done so far? We have had several successes. You can read about them on our Scienc Page,Results Section, or go directly to our Press and Papers page.
dnamechanic
22 Jun 2005
Hi QJones,
You have valid questions.
I have had similar concerns.
As Mrfesta points out; the Stanford site does have some interesting and supportive material.
------------------------------------------------------------
Theodore Roosevelt once said:
"It is not the critic who counts;
not the man who points out how the strong man stumbles,
or where the doer of deeds could have done them better....
... because there is no effort without error and shortcoming"
The credit belongs to the man who is actually in the arena,
...who at the worst, if he fails, at least fails while daring greatly,
...so that his place shall never be with those cold and timid souls
who know neither victory nor defeat."
-----------------------------------------------------------
This is a view that I like very much.
So, QJones, I do not think you are being critical, just concerned.
The critics of the Stanford Team are not making much progress.
The protein folding problem is complex, indeed.
The Stanford team, and the other groups that are tackling it, deserve our support.
You have valid questions.
I have had similar concerns.
As Mrfesta points out; the Stanford site does have some interesting and supportive material.
------------------------------------------------------------
Theodore Roosevelt once said:
"It is not the critic who counts;
not the man who points out how the strong man stumbles,
or where the doer of deeds could have done them better....
... because there is no effort without error and shortcoming"
The credit belongs to the man who is actually in the arena,
...who at the worst, if he fails, at least fails while daring greatly,
...so that his place shall never be with those cold and timid souls
who know neither victory nor defeat."
-----------------------------------------------------------
This is a view that I like very much.
So, QJones, I do not think you are being critical, just concerned.
The critics of the Stanford Team are not making much progress.
The protein folding problem is complex, indeed.
The Stanford team, and the other groups that are tackling it, deserve our support.
mrfesta
29 Jun 2005
Quick Update:
Membership: 55 members (28-31 are active)
Current rank: 617 out of 38,801 teams
Point Average: 2,500 points/per 24 hours
Membership: 55 members (28-31 are active)
Current rank: 617 out of 38,801 teams
Point Average: 2,500 points/per 24 hours
123456
30 Jun 2005
Just re-affirming; I am over at "World Community Grid". Lately this year all people except me in Imminst team stop computing; like they got kidnapped or something. So should I stop WCG software and use Folding@Home software? or are all of them the same? I already know that both are protein calculation programs.
mrfesta
30 Jun 2005
I checked out the World Community Grid site (was previously unfamilar with it).
I came across the following.
What is the difference between what Human Proteome Folding does and what Folding@home does?
There are large differences between the Human Proteome Folding Project and folding@home. Both projects are excellent but have very different objectives.
Folding@home aims to get at how a few proteins of KNOWN structure fold DYNAMICALLY. Folding@home is a project to further understanding of the folding process itself. Understanding why protein folding works (and why it doesn't) could have a significant impact in certain diseases like Alzheimer's and Huntington's Disease, which Folding@Home is actively studying.
The Human Proteome Folding Project will PREDICT the structures of large numbers of proteins of UNKNOWN-structure. The aim of this project is to get structures and functions for huge numbers of proteins so that biologists and biomedical researchers who run into these mystery proteins in their research can look to ISB's database for functional/mechanistic clues about their favorite mystery-proteins.
My vote is still for folding@home because the stats are easier to track
If you do join the folding@home team maybe use the username of: ImmInst (www.imminst.org)
I came across the following.
What is the difference between what Human Proteome Folding does and what Folding@home does?
There are large differences between the Human Proteome Folding Project and folding@home. Both projects are excellent but have very different objectives.
Folding@home aims to get at how a few proteins of KNOWN structure fold DYNAMICALLY. Folding@home is a project to further understanding of the folding process itself. Understanding why protein folding works (and why it doesn't) could have a significant impact in certain diseases like Alzheimer's and Huntington's Disease, which Folding@Home is actively studying.
The Human Proteome Folding Project will PREDICT the structures of large numbers of proteins of UNKNOWN-structure. The aim of this project is to get structures and functions for huge numbers of proteins so that biologists and biomedical researchers who run into these mystery proteins in their research can look to ISB's database for functional/mechanistic clues about their favorite mystery-proteins.
My vote is still for folding@home because the stats are easier to track
If you do join the folding@home team maybe use the username of: ImmInst (www.imminst.org)
jaydfox
30 Jun 2005
Good idea about using ImmInst as the username, it's like having a "sub-team". However, I'm already using my own username, so I'll just keep using that. But maybe new members, when they join, could use ImmInst.
John Schloendorn
30 Jun 2005
I would like to add to this discussion that it's also, and perhaps mainly, about the message that the existence of this team sends to the public, not just about particular research results.
jaydfox
30 Jun 2005
Well, we're close to breaking the top 600, and if we can sustain and perhaps grow our pace, we look set to overtake several hundred more teams in the next 12 months. Getting in the top 400 or 500 would be quite an accomplishment, and I suspect it comes with bragging rights.
And I suspect there are still a few dozen regulars here at ImmInst that have spare cycles they could be donating, which could accelerate the team into the 300's, maybe even the high 200's. We'd need a lot more hardware to break the 200 barrier though. But still, if another couple dozen members donated their CPU time, we could really move up the ranks. I just joined, and I'm not adding much, so I'm using the term "we" loosely here, but the team has already moved from the 800's to the low 600's in a few short weeks. Moving up into the top 500 shouldn't be all that far away, since I see that there are many teams in the 500-600 range that we'll overtake by the end of July.
And I suspect there are still a few dozen regulars here at ImmInst that have spare cycles they could be donating, which could accelerate the team into the 300's, maybe even the high 200's. We'd need a lot more hardware to break the 200 barrier though. But still, if another couple dozen members donated their CPU time, we could really move up the ranks. I just joined, and I'm not adding much, so I'm using the term "we" loosely here, but the team has already moved from the 800's to the low 600's in a few short weeks. Moving up into the top 500 shouldn't be all that far away, since I see that there are many teams in the 500-600 range that we'll overtake by the end of July.
jaydfox
30 Jun 2005
To give you an idea, The Longevity Meme is 239th overall for team average points per 24 hours. We could easily get that into the top 200 with just 6-8 more computers (recent models, that is). I'm averaging about 87 points per day, with an AMD 2200+ mobile processor. That's hardly high end; in fact I think that's about the same computing power you can get in a $200 desktop PC these days.
reason
30 Jun 2005
Note the breaking 500 gift post...
http://www.fightagin...ives/000513.php
Feel free to recruit amongst your associates
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
http://www.fightagin...ives/000513.php
Feel free to recruit amongst your associates
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
mrfesta
01 Jul 2005
To give you an idea, The Longevity Meme is 239th overall for team average points per 24 hours.
Hey jaydfox, where did you find that stat at?
Edit: Found it, didn't realize you could sort those results. We are 225th now
Edited by mrfesta, 01 July 2005 - 03:05 PM.
dnamechanic
03 Jul 2005
125 Biggest Questions for Science .....
...Science Magazine to celebrate the journal's 125th anniversary...
Thanks, Liveforever22, for posting the above in another thread:
http://www.imminst.o...9&t=7053&hl=&s=
Very interesting questions, all of them.
One question, in the Big-Question list, is quite relevant to this particular thread:
"Can we predict how proteins will fold?"
"Out of a near infinitude of possible ways to fold, a protein picks one in just tens of microseconds.
The same task takes 30 years of computer time."
This, is a telling question.
jaydfox
03 Jul 2005
Hmm, according to folding.extremeoverclocking.com, we're now the 599th top team, meaning we just broke the 600 barrier!
Of course, according to the Stanford website, we're number 604, and the Stanford stats are supposed to be more or less realtime. Hmm, give it a few hours, we should be back under the 600 barrier!
Of course, according to the Stanford website, we're number 604, and the Stanford stats are supposed to be more or less realtime. Hmm, give it a few hours, we should be back under the 600 barrier!
mrfesta
09 Jul 2005
Note the breaking 500 gift post...
http://www.fightagin...ives/000513.php
Feel free to recruit amongst your associates
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
at our current pace we should break that in roughly 36 days [thumb] Get ur friends that leave computers on overnight at work to join up and we can get there in half the time.
reason
09 Jul 2005
And if you're going to do that, you'll only have 18 days to let me know what sort of LM Team memorabilia you'd like to mark the occasion...
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
Karomesis
10 Jul 2005
has anyone done calculations to ascertain a guess at folding in a few years? Is there a progressive increase in the speed of folding along with moores law? Kind of like how the majority of the human genome was sequenced in its final year due to an increase in computational speed. With 50K$ what is the most powerful computer that can be purchased?
jaydfox
10 Jul 2005
Well, at this point in time, I think the folding it outpacing Moore's Law. However, that's only because the number of people running the folding is increasing, and their hardware is roughly increasing with Moore's Law, so the folding is staying ahead of Moore's Law by combining both increases.
As for what you can purchase for $50K, I think that what we should be concerned about is performance/price. You can get an AMD 2200+ for $200 or less, and you wouldn't need a monitor other than for setup. Just get a 16-port ethernet hub, some NAT software, an Internet connetion, and 16 cheap desktops, and just one monitor to hook up to one PC at a time to check in on ones that aren't working or need to be scanned for viruses or spyware or whatever. The whole setup should cost about $4K plus tax. Buying 16 PCs, you can probably get a bulk rate to get the price down even further, so you might be able to get this setup for $3K. Compare that to a high-end $3K system, which will definitely not have the same performance, and I'd be willing to bet not even half the performance.
For $50K, you can get literally hundreds of PCs, though at that point, you'd need a "real" WAN router, costing you a thousand bucks, within a factor of 3 (I haven't priced one in nearly two years, so I forget how much they cost), but you should be able to get a used one for fairly cheap.
Of course, all this presumes that you're spending all this money just to do folding. I prefer to let folding run in the background, so I can actually use my PC for games, programming, etc., some fraction of the time. I don't have a particular use for 16 PCs, let alone hundreds, so I wouldn't buy such as setup even if I had the money.
Once distributed folding participation peaks and starts declining, it'll follow more in line with Moore's Law. In other words, in about five to six years, it'll be going about 10 times faster, assuming a doubling every 18 to 20 months. In ten to twelve years, it'll be going 100 times faster. And that's just the distributed folding. Dedicated supercomputers can outpace Moore's Law through a variety of techniques, such as just using more processors, better software, etc. Just as the price to sequence a genome is falling much more rapidly than Moore's Law, the effectiveness of protein folding will also outpace Moore's Law, at least for the foreseeable couple decades. During that time, protein folding should not only get faster, but more accurate.
As for what you can purchase for $50K, I think that what we should be concerned about is performance/price. You can get an AMD 2200+ for $200 or less, and you wouldn't need a monitor other than for setup. Just get a 16-port ethernet hub, some NAT software, an Internet connetion, and 16 cheap desktops, and just one monitor to hook up to one PC at a time to check in on ones that aren't working or need to be scanned for viruses or spyware or whatever. The whole setup should cost about $4K plus tax. Buying 16 PCs, you can probably get a bulk rate to get the price down even further, so you might be able to get this setup for $3K. Compare that to a high-end $3K system, which will definitely not have the same performance, and I'd be willing to bet not even half the performance.
For $50K, you can get literally hundreds of PCs, though at that point, you'd need a "real" WAN router, costing you a thousand bucks, within a factor of 3 (I haven't priced one in nearly two years, so I forget how much they cost), but you should be able to get a used one for fairly cheap.
Of course, all this presumes that you're spending all this money just to do folding. I prefer to let folding run in the background, so I can actually use my PC for games, programming, etc., some fraction of the time. I don't have a particular use for 16 PCs, let alone hundreds, so I wouldn't buy such as setup even if I had the money.
Once distributed folding participation peaks and starts declining, it'll follow more in line with Moore's Law. In other words, in about five to six years, it'll be going about 10 times faster, assuming a doubling every 18 to 20 months. In ten to twelve years, it'll be going 100 times faster. And that's just the distributed folding. Dedicated supercomputers can outpace Moore's Law through a variety of techniques, such as just using more processors, better software, etc. Just as the price to sequence a genome is falling much more rapidly than Moore's Law, the effectiveness of protein folding will also outpace Moore's Law, at least for the foreseeable couple decades. During that time, protein folding should not only get faster, but more accurate.
Karomesis
10 Jul 2005
Will any breakthrough in quantum computing help to increase folding speed? I have heard it said that a multi-thousand q-bit quantum computer would be vastly more powerful than any concievable digital one.I am not a computer scientist so I can't even wager an educated guess. [cry]
jaydfox
10 Jul 2005
I can't say for sure about the quantum computer possibilities. From what I know of them, one of their strong suits is the ability to process multiple pieces of data at once, and then make a selection. For example, trying all 2^128 bit-combinations for a 128 bit AES password at once, and then selecting the one that decodes a file into something intelligible, or properly decodes a known file encrypted with the password.
However, I don't know if quantum computers can process so many parallel datasets and then give us the answer to all the calculations. Such would be required, methinks, for the folding problem to benefit. Perhaps someone more versed in quantum computing can shed light on this?
However, I don't know if quantum computers can process so many parallel datasets and then give us the answer to all the calculations. Such would be required, methinks, for the folding problem to benefit. Perhaps someone more versed in quantum computing can shed light on this?
mrfesta
31 Jul 2005
I've been slacking with this too :(
Update: Team is ranked 540, still about 28 days before we break the 500 mark.
Update: Team is ranked 540, still about 28 days before we break the 500 mark.
reason
28 Aug 2005
Ah, sneaked in; I was watching the past few days and it was sitting still at 503. Congratulations all round and many thanks to those who have helped us to the 500 mark. Ok, on with the program!
I'll post a note today/tomorrow. Everyone who was on the team prior to today (August 28th) and wants a momento of hitting 500 should send me e-mail with "Folding@Home 500" in the subject line giving me a) your mailing address b) your Folding@Home username.
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
I'll post a note today/tomorrow. Everyone who was on the team prior to today (August 28th) and wants a momento of hitting 500 should send me e-mail with "Folding@Home 500" in the subject line giving me a) your mailing address b) your Folding@Home username.
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
reason
04 Sep 2005
Ok, gifts packaged off to the four corners of the globe - the other side of the globe in a few cases. Those of you who haven't contacted me yet, any time is fine.
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
Reason
Founder, Longevity Meme
reason@longevitymeme.org
http://www.longevitymeme.org
JonesGuy
23 Nov 2005
Has anyone looked at IBM's new AIDS distributed computing project? I expect that will get 'overwhelming' mainstream support. Which is fine, absolutely.
I was looking at Dr. Pande's papers - it doesn't seem that they get referenced very often (though the team released a slew in 2005) ... I still don't know if the folding project is winning any type of cost/benefit analysis.
PS: I'm folding anyway!
I was looking at Dr. Pande's papers - it doesn't seem that they get referenced very often (though the team released a slew in 2005) ... I still don't know if the folding project is winning any type of cost/benefit analysis.
PS: I'm folding anyway!
caliban
23 Nov 2005
I found the folding app did not sync well with streaming content and takes up RAM at inopportune moments. After two attempts with different versions I now usually leave it off.
