How Is Rosetta Different Than Folding@home?

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Profile rbpeake

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Message 490 - Posted: 25 Sep 2005, 20:48:10 UTC

I have been a participant in the Stanford University project, Folding@home, for a number of years.

http://www.stanford.edu/group/pandegroup/folding/

The Rosetta discussion of "parachuting" into energy minima sounds somewhat like this discussion of Folding@home simulation methods, found here:

http://users.adelphia.net/~al444/clone.html

But I am not sure if the two projects are similar or not?
Regards,
Bob P.
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Message 510 - Posted: 26 Sep 2005, 4:03:48 UTC

The Rosetta@home project goals are very different from those of Folding@home. The goal of Folding@home, I believe, is to determine how long proteins take to fold, given the sequence of the protein and knowledge of its three dimensional structure. The goal of Rosetta@home is to predict the three dimensional structure from the amino acid sequence. As explained in the Daily Telegraph article and the press releases, Rosetta has been the best method for structure prediction for quite some time (WIRED magazine had a nice article as well: http://www.wired.com/wired/archive/9.07/blue.html?pg=1).

Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David
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Message 515 - Posted: 26 Sep 2005, 4:47:57 UTC

The fundamental difference between Folding@home and other projects like Predictor@home, Distributed Folding and this very Rosetta@home is that method used by Folding@home not good enough to participate in fair method comparation context - CASP. And it never been good enough. In fact, there was few structure prediction made by Vijay project, but results was way far from perfect. They clam something like [quote" we are trying to understand ... *how* proteins reach the final shape" end of quote]. But that understanding apparently not good enough to be compared with other methods.
In fact, what really attracts me to this project, is that it looks like David Baker's group is one of the best one in a blind structure prediction.

TestPilot, AKA Administrator
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Message 519 - Posted: 26 Sep 2005, 5:27:57 UTC - in response to Message 510.  

Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?



There's actually two parts to this and one is attracting new participants and the other is keeping the existing participants. So far Rosetta is doing a fantastic job at attracting new people as well as what is needed to keep them.

First, I've found that much regarding obtaining new participants is word of mouth through the various team sites. Team sites will probably always be the largest pool of possible participants for Rosetta.

I hate putting it this way but you also benefit when another project has major issues such as Predictor being off-line for planned server upgrades so there's a week plus a few days of nothing coming out of their project. Another example was when Seti was having problem after problem for several months, many projects benefited from the Seti crunchers taking on new projects or spending more time with existing projects they already had.

Second and probably more important is to keep the participants you have. Most projects do well at this particular point at the beginning but eventually begin to falter. The faltering point is in one important area and that's communications with the participants. Over time in some projects, the participants are eventually left to guess as to what's happening when there are problems as communications has become a rare thing. When questions aren't answered by the project staff and participants try to help each other when it comes to certain project related things, it sometimes becomes the blind leading the blind and causing more problems. Keeping a consistant level of communications with the participants is the most effective method for retaining the participants you have.

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Message 521 - Posted: 26 Sep 2005, 5:44:34 UTC - in response to Message 510.  
Last modified: 26 Sep 2005, 5:44:57 UTC

Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?


Hmmm... perhaps sending news releases announcing the project to the networks? FOX News, CNN, MSNBC, etc?


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Message 545 - Posted: 26 Sep 2005, 18:39:24 UTC - in response to Message 510.  

The Rosetta@home project goals are very different from those of Folding@home. The goal of Folding@home, I believe, is to determine how long proteins take to fold, given the sequence of the protein and knowledge of its three dimensional structure. The goal of Rosetta@home is to predict the three dimensional structure from the amino acid sequence. As explained in the Daily Telegraph article and the press releases, Rosetta has been the best method for structure prediction for quite some time (WIRED magazine had a nice article as well: http://www.wired.com/wired/archive/9.07/blue.html?pg=1).


Thank you for your answer! I asked the same question on the Folding@home forum, and Vijay Pande, the lead project scientist, replied with:

"yes, their goals are fairly different than FAH. They both involve proteins, but Rosetta is interested in predicting structures, whereas FAH is interested in predicting whole folding pathways. The people behind Rosetta are great, so I have hope they will do something nice with Rosetta@home."

Which certainly is a nice response as well!

Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David


I agree that a press release is a good idea. Newspapers like the Tuesday New York Times might pick it up, and once word of mouth gets around, these dc projects seem to gather a critical mass. Also perhaps you can get in a word with your professional journal publications by saying something like "we wish to thank the thousands of contributors at Rosetta@home without whose donations of computer processing time this project would not be possible" might help to get the word out as well.

You present a well-managed and well-run ("buttoned up") project on this web site, and as someone else said below, the more you keep your contributors informed of what is going on, the better for longer term retention of participants (the point system makes it interesting for tracking one's progress and how well one is doing versus others, but after awhile there has to be more of a feeling of contributing to something worthwhile/that is going to make a difference).

Good luck!

Regards,
Bob P.
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Message 550 - Posted: 26 Sep 2005, 21:35:35 UTC - in response to Message 510.  

[Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David[/quote]



post exactly what you said here in the other forums. also, post on the homepage for those people that never read the boards. ask crunchers if they would be willing to concentrate more on your project, at least until you build up a larger user base. you have to let people know what you need.

btw, the optimized app is terrific!


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Message 566 - Posted: 27 Sep 2005, 2:49:53 UTC - in response to Message 550.  
Last modified: 27 Sep 2005, 2:50:45 UTC

[Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David




Just exactly what you said here in the other forums. also, post on the homepage for those people that never read the boards. ask crunchers if they would be willing to concentrate more on your project, at least until you build up a larger user base. you have to let people know what you need.

btw, the optimized app is terrific!


I think when you are out of Beta testing more people will come onboard, too.

I know a number of people who will not touch anything Beta. They associate Beta with being too risky.

What is your current thinking on timing for coming out of Beta? That might be a good time to make some noise on the Boinc site about Rosetta coming out of Beta, so come on and join in!
Regards,
Bob P.
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Profile David Stites

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Message 568 - Posted: 27 Sep 2005, 3:05:19 UTC - in response to Message 566.  

[Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David




Just exactly what you said here in the other forums. also, post on the homepage for those people that never read the boards. ask crunchers if they would be willing to concentrate more on your project, at least until you build up a larger user base. you have to let people know what you need.

btw, the optimized app is terrific!





Exactly, I increased Rosetta's share of my processing power due to the above quoted post. And with Predictor and now LHC down that will equal more that I have it set for, at least for now.

Also, most of us have other interests, if we spread the word in all our other hobby boards, ham radio, archery, etc... we might pick up some.

Spread BOINC like a plague, infect as many as you can.

Keep crunching,

David Stites
Mount Vernon, WA USA

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Yin Gang

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Message 570 - Posted: 27 Sep 2005, 4:33:12 UTC - in response to Message 510.  


Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David


IMHO, the most important:
1. stable & fast (both the crunching app and the project servers)
2. keep participants aware of what's going on
3. be responsive in community

(By the way, I think Einstein@home is an excellent example for all these)

Also, the less important:
n. pretty graphics
n+1. free certificate of computation, just like the one in SETI@home


Welcome To Team China!
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Message 571 - Posted: 27 Sep 2005, 4:33:43 UTC

Well, I'm a little leary spreading my resources too thing, but if you guys need a little more computation time. Besides, as some have mentioned predictor@home and LHC@home are currently down (actually the latter is up, but out of work).

BTW, I'm winding things down on this computer, so won't be downloading new work units to it for much longer. The reason is I'm upgrading from my current AXP 1900+ to an A64 3500+ when all the stuff arrives in the mail (presumably) this Wednesday. This will bring me up to 5 projects (and 6 when the planet finder project comes out). I suppose that should be fine on an Athlon 64.
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Message 589 - Posted: 27 Sep 2005, 10:42:00 UTC

There are a number of index web sites - get your project listed on these (google for "Boinc" and "distributed computing")

The BOINC home page http://boinc.berkeley.edu/ does not currently list your project!

The Boinc Wiki should get an entry as well!

Best wishes
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Message 620 - Posted: 27 Sep 2005, 15:04:56 UTC
Last modified: 27 Sep 2005, 15:05:12 UTC

Rosetta@Home *IS* in the Wiki as a "blank" entry at the moment as I have no significant knowledge of the project.

Since it is officially in "Beta" test, it is listed in the Beta test list (you have to look for it). When the project goes into "production" status we will move it to the front page.

As far as adding more material I am limited to what I can write on my own, limited, knowledge. Given permission of the project I have in the past "canabilized" material off the official site and then added things I found useful related to the project as I run across them ...

Project members are always granted accounts to the Wiki on request. But, till the project says they are production, on the beta list they stay.

I will say, that the stat sites seem to have picked up the project as they got "pressure" to do so and the fact that the projects are doing production work though in beta status.

So, in my experience, I agree, the keys to success are:

1) communication with the community.
1a) Regular monitoring of the message boards (my scan takes 1-3 hours and I only visit the NC forums for production projects
1b) News updates
1c) Timely reports when problems strike, even if it is "we don't know"
1d) Science updates, where are we, what have we done ... what are we going to do
1e) Information in the Wiki ... :)

2) Stable system
2a) this can be hard with too many participants, so, care in size allowed, see LHC@Home
2b) Work should always be available
2c) Support of all platforms (I have Rosetta on OS-X - Thanks, I needed an extra project on that machine)
2d) the application should be graceful in death, Predictor@Home can "hang" the system in a non-productive state, makes my grumpy ...
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Message 680 - Posted: 28 Sep 2005, 4:17:05 UTC - in response to Message 510.  
Last modified: 28 Sep 2005, 4:51:56 UTC

Although the growth of the project over the last week has been amazing, our efforts to predict protein structures are still limited by total computing power. Does anybody have suggestions on how to recruit more participants?

thanks,

David

I think you are already on the right track.

- Good information about the project.
- Responsiveness from the project team.
- Consistent feedback to participants
- Updates on the progress and the science.
- Links to resources and articles on the project.
- Optimized apps for the various platforms.
- When you officially get out of beta status, more will come. Looks like the number of processors has doubled in the past week.
- If problems occur, regular updates on progress, even if it is just periodic messages to say "we are working on it."
- Reliability and consistent work will attract many long term crunchers.

The word was slow getting out at first, and the first links I saw posted were incorrect. Now the word is getting out on multiple sites and in multiple forums. I think you can expect a moderate growth surge during beta, and a substantial surge after the project is out of beta. Make sure the servers are ready for it. Getting the bugs out of the Linux and Macintosh apps will also help. (remember that while these users are a minority with their platform of choice, that many of them bring substantial numbers of windows machines along with them, including yours truly)

Keep up the good work you are doing and many more folks will come. I'll speculate that the next month will see near exponential growth, just doing what you are doing now.

Oh, and once the word is out, your simplified credit system will attract many "casual" crunchers who are confused by, or don't like the multi-computer validation system required for other projects. Add a simple screensaver when you have time, and many of them will become long-term addicts.


Team MacNN - The best Macintosh team ever.
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Message 681 - Posted: 28 Sep 2005, 4:36:55 UTC

I agree completely with you Shaktai, just keep doing what you are doing and you should have boatload after boatload of people coming in. You've got me and you have also restored some of my confidence in the BOINC platform.
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Message 683 - Posted: 28 Sep 2005, 4:56:35 UTC - in response to Message 620.  

Rosetta@Home *IS* in the Wiki as a "blank" entry at the moment as I have no significant knowledge of the project.

Since it is officially in "Beta" test, it is listed in the Beta test list (you have to look for it). When the project goes into "production" status we will move it to the front page.

As far as adding more material I am limited to what I can write on my own, limited, knowledge. Given permission of the project I have in the past "canabilized" material off the official site and then added things I found useful related to the project as I run across them ...

Project members are always granted accounts to the Wiki on request. But, till the project says they are production, on the beta list they stay.

I will say, that the stat sites seem to have picked up the project as they got "pressure" to do so and the fact that the projects are doing production work though in beta status.

So, in my experience, I agree, the keys to success are:

1) communication with the community.
1a) Regular monitoring of the message boards (my scan takes 1-3 hours and I only visit the NC forums for production projects
1b) News updates
1c) Timely reports when problems strike, even if it is "we don't know"
1d) Science updates, where are we, what have we done ... what are we going to do
1e) Information in the Wiki ... :)

2) Stable system
2a) this can be hard with too many participants, so, care in size allowed, see LHC@Home
2b) Work should always be available
2c) Support of all platforms (I have Rosetta on OS-X - Thanks, I needed an extra project on that machine)
2d) the application should be graceful in death, Predictor@Home can "hang" the system in a non-productive state, makes my grumpy ...


Please use any information you find useful from our site to explain the project on your Wiki--please let us know if you would like any more info. It would be great if you could put it on your main page--we are only calling it "beta" still to be conservative, but it seems to be running well on most machines. In general, it would be great if everybody could spread the word as widely as possible!


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Message 692 - Posted: 28 Sep 2005, 13:57:00 UTC - in response to Message 680.  
Last modified: 28 Sep 2005, 13:58:41 UTC


I think you are already on the right track.

- Good information about the project.
- Responsiveness from the project team.
- Consistent feedback to participants
- Updates on the progress and the science.
- Links to resources and articles on the project.
- Optimized apps for the various platforms.
- When you officially get out of beta status, more will come. Looks like the number of processors has doubled in the past week.
- If problems occur, regular updates on progress, even if it is just periodic messages to say "we are working on it."
- Reliability and consistent work will attract many long term crunchers.

Make sure the servers are ready for it. Getting the bugs out of the Linux and Macintosh apps will also help. (remember that while these users are a minority with their platform of choice, that many of them bring substantial numbers of windows machines along with them, including yours truly)



This is a great response! You might want to consider publishing this on other BOINC project message boards. Sometimes it seems to me that some of the other projects are fairly clueless on how to run a good, long-term, productive BOINC project.
Regards,
Bob P.
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Message 695 - Posted: 28 Sep 2005, 14:40:26 UTC - in response to Message 683.  


Please use any information you find useful from our site to explain the project on your Wiki--please let us know if you would like any more info. It would be great if you could put it on your main page--we are only calling it "beta" still to be conservative, but it seems to be running well on most machines. In general, it would be great if everybody could spread the word as widely as possible!


Done, at least to the point where I used your description of purpose ...

I had also taken a few links and added them to the Also See part.

I think you will find that many BOINCers get the word by osmosis and in a small test I just did, your host count went up by 17 in less than an hour. So, you may well want to watch how many participants you allow at first. BOINC's server usage as SETI@Home has found out several times in the recent past is, um, non-linear.

Other small projects to "peek" at are LHC@Home, Predictor@Home, and Einstein@Home. All of these projects are hosted off of a small server/server pair.

Trying to be fair, if you say it is beta, I have to say it is beta. In *MY* book, ALL science projects never really get out of testing and are never super stable. And I think the majority of the participants understand this. Not all, but the vast majority. And those that have complaints would also complain about being hung with a new rope (but I digress).

The whole point of BOINC is to advance science by allowing participation of a large group of volunteers and a very tiny project staff. History says that almost all great advances are usually done on the cheap and not by a directed research project. At one point in time IBM and ATT had a dominant position because they both funded non-directed research and thereby reaped huge rewards (as far as I know the old Bell Labs was bought and sold several times and has since fallen into the directed research camp and IBM, though still committed, is not funding quite as much as they used to).

Anyway, I think that the word is out ... all I can suggest furthur is that you can take a look at what Chris C. has done for CPDN in the Wiki, if you have not already asked me for an account (p.d.buck@comcast.net - name, username desired, e-mail address to send P/W to) ask and you can add material as you please. If you don't want to do that, you can send me suggested material and I will try to get it in ...

Oh, and say that you are production ... I mean, the results you are collecting are production results, aren't they?
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Message 759 - Posted: 29 Sep 2005, 12:14:01 UTC

At the risk of triggering defensive counter-attacks, I'll posit another suggestion for encouraging users to take up the project (or at least not have them abandon inviolvement at a later date).

My suggestion is to try and keep RAM and Disk requirements as low as practical. Excessive use of these will impact the machine owners use (enjoyment) of the systems they have purchased. Using lots of unused CPU time is fine, slowing a system down (especially if no warning is given) is not. Yes I am aware of the stated requirement for 512MB RAM to run the R@H project, perhaps the implications (and symptoms) of running it on systems with overcommitted RAM could be more clearly set out.

Boinc will get a bad name and will be banned from more installations if it becomes demonstrated that clients are, in fact, causing other than trivil system degradation. When this happens, no one will win.

I'm NOT taking a swipe at R@H, I AM trying to offer suggestions to make your project one of thse that users will prefer to donate their resources to.


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Stuart Pitts

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Message 760 - Posted: 29 Sep 2005, 12:46:06 UTC

Concerning attacting new people to your project, I would recommend the following:

a) Check with your local news stations/newspaper to see if they feature a website of the week. If they do, ask them to feature your website.
b) check with the alumni magazines for the both the University that you are at and the ones that you and your team graduated from. They may be interested in an article about what their alumni are doing and will feature your website.
c) I am assuming that you have contacted all of the companies and schools running your software in their research programs to make sure that they know about your website. Hopefully they would provide some after hours cpu's to help.
d) If there are any science fairs that you and your team help with, I would recommend that you ask if you can either have a booth for your website or have your website listed on any publicity papers.
e) Longer term, I recommend that you and the other project directors contact National Geograhic to see if they would do a feature story on distributed computing. A bunch of publicity about BOINC would help your project.
f) I believe that Newsweek had an article about Seti@home two-three years ago. Maybe you can check to see who was the contact and see if they would do an article about BOINC.
g) Finally, I recommend that you add to your website home page a section on help publicize Rosetta@home. You could list all of the ideas that you receive and ask people to either provide more ideas or to contact say their local news stations about your site being site of the week or whatever they feel would help.

Good Luck!!!

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