How estimate time for rosetta completion?

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Profile 9a.robert

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Message 38403 - Posted: 26 Mar 2007, 2:32:26 UTC

hi,

I am newbie here, I just join rosetta project,
I read some information about this project online.
I like this project.

my question is
when rosetta project can be fully done (estimate time) ?

Thanks in advance.
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Keith Akins

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Message 38406 - Posted: 26 Mar 2007, 5:18:23 UTC

Hello and welcome aboard.

I like the project too. Are you new to DC projects or new to Rosetta?

As far as your question, I'm not sure what you mean. Do you mean estimated time per work unit or per model?

If you want, you can logon, go to (I think) Rosetta preferences and manually select your desired run time per WU. I have mine set at 8 hours. Also you can control how many WU's you can store in your BOINC tasks cache by selecting how many days of work you want.

Glad to have you along.
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Yaos

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Message 38410 - Posted: 26 Mar 2007, 10:00:21 UTC

He would like to know when the project will be done, when Rosetta@home no longer has a purpose.
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Message 38414 - Posted: 26 Mar 2007, 12:25:32 UTC

Rosetta is a project to improve the ability to accurately model protein (and now also RNA) folded structures, and their interactivity with other molecules. Accurate prediction for all proteins is almost certainly many years away yet, although the predictions for many protiens are now good enough to be used, there's still plenty of work to be done on this front.

Then there's putting the software to practical use, which I'm sure the bakerlab will continue to do even if the software produced perfect models for all proteins.

Then there's any new additions to the modeling abilities such as the newly added RNA function.

So I would guess there are many years of work to be done on Rosetta, but the more CPU power available at any time, the better.

HTH
Danny
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Keith Akins

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Message 38426 - Posted: 26 Mar 2007, 17:03:38 UTC

Thanks for clearing that up. The time estimate thing threw me off.

The last I heard from Dr. Baker, he's looking at 10 years minimum.

But I'd guess however long it takes to get the program as close to perfection as possible. That's how difficult this problem is.

I would say that when it's perfected to the point that no more than 10 to 20 model runs are needed to get the desired structure prediction.
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Nothing But Idle Time

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Message 38437 - Posted: 26 Mar 2007, 19:05:49 UTC - in response to Message 38426.  

The last I heard from Dr. Baker, he's looking at 10 years minimum.
But I'd guess however long it takes to get the program as close to perfection as possible. That's how difficult this problem is.
I guess the duration depends on funding, too, don't you think?
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Yaos

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Message 38481 - Posted: 27 Mar 2007, 10:39:12 UTC - in response to Message 38426.  

Thanks for clearing that up. The time estimate thing threw me off.

The last I heard from Dr. Baker, he's looking at 10 years minimum.

But I'd guess however long it takes to get the program as close to perfection as possible. That's how difficult this problem is.

I would say that when it's perfected to the point that no more than 10 to 20 model runs are needed to get the desired structure prediction.

So the total processing power only helps create the model correct?
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Message 38485 - Posted: 27 Mar 2007, 13:40:36 UTC

Yaos, I think you and 9a.robert are trying to ask if there is a fixed amount of work that needs to be done, and then Rosetta is completed. The answer is no. Rosetta is not a project with a fixed measurable amount of work that must be completed. It is a project to develop new techniques for finding protein structure. Dr. Baker and his team need many TFLOPS of power to run their new techniques and get meaningful data on whether they are effective or not.

Amongst us all, there are millions of models being computed. Generally about 100,000 per type of work unit. You can perhaps get a feeling for this if you look at the number of predictions (models) you reported for a given work unit type as compared to the number that we collectively crunched. You can see this by clicking on the link under the Returning Participants section on the homepage for "Results". If you click this link I believe it will take you to your results. You can change the user ID in the URL to see anyone's, such as mine.

Even if Rosetta were able to compute it's way to the perfect answer every time, there would still be the challenge of trying to do so with less then 40 TFLOPS of computing power. So the project has a long life ahead of it further developing this technology.
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Keith Akins

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Message 38508 - Posted: 28 Mar 2007, 1:26:49 UTC

Our donated CPU time does the model runs. Bakerlab looks at the retuned models generated by us to determine how many runs it took to get to lowest energy/RMSD for known structures. The scattergrams you see in the lower right show the clustering of energies/RMSD's. They use this information along with new ideas to make improvements to the program.

This is not to say that meaningful prediction work is not done here as well. We get plenty of unknowns with no RMSD and actual targets of interest.

So, Yaos, you might say this project is two fold. And, yes, we crunch the models.

Feet1st can probably elaborate more.
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Message 38509 - Posted: 28 Mar 2007, 3:55:43 UTC - in response to Message 38414.  

Rosetta is a project to improve the ability to accurately model protein (and now also RNA) folded structures, and their interactivity with other molecules. Accurate prediction for all proteins is almost certainly many years away yet, although the predictions for many protiens are now good enough to be used, there's still plenty of work to be done on this front.

Then there's putting the software to practical use, which I'm sure the bakerlab will continue to do even if the software produced perfect models for all proteins.

Then there's any new additions to the modeling abilities such as the newly added RNA function.

So I would guess there are many years of work to be done on Rosetta, but the more CPU power available at any time, the better.

HTH
Danny


Exactly! we are making improvements all the time, but there is still a very long way to go. the current work units are a balance of tests of new ideas and predictions for proteins and RNA of unknown structure. As Keith said, we would very much like to get to the point that structures can be computed accurately in only a fraction of the time it takes currently.


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Message 38518 - Posted: 28 Mar 2007, 8:21:22 UTC - in response to Message 38509.  

Rosetta is a project to improve the ability to accurately model protein (and now also RNA) folded structures, and their interactivity with other molecules. Accurate prediction for all proteins is almost certainly many years away yet, although the predictions for many protiens are now good enough to be used, there's still plenty of work to be done on this front.

Then there's putting the software to practical use, which I'm sure the bakerlab will continue to do even if the software produced perfect models for all proteins.

Then there's any new additions to the modeling abilities such as the newly added RNA function.

So I would guess there are many years of work to be done on Rosetta, but the more CPU power available at any time, the better.

HTH
Danny


Exactly! we are making improvements all the time, but there is still a very long way to go. the current work units are a balance of tests of new ideas and predictions for proteins and RNA of unknown structure. As Keith said, we would very much like to get to the point that structures can be computed accurately in only a fraction of the time it takes currently.



However much we know about protein structures there will always be more to find out, and therefore better ways to write computer programs. In that sense the Rosetta project is adding to something that will never be finished.

In another sense, Rosetta itself is only one part of the action. At some point Bakerlab, or/and David himself, might end the Rosetta project but similar work will go on elsewhere; probably for as long as there are humans alive. In the same way as when David started out he could build on other people's work then other people will be building on the current work.

So the question does make sense, in the sense of 'how far does the Rosetta project intend to run with its own contribution'. I think the truth here is that David et al can see so much room for improvement on the current models that, in practical terms, there is no end point in sight.


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Garry

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Message 41811 - Posted: 3 Jun 2007, 21:45:03 UTC

A project called "Rosetta" may disappear. The work that Rosetta is contributing to may, with good fortune, never be finished.
Garry DeLong
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Message boards : Rosetta@home Science : How estimate time for rosetta completion?



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