Rosetta@home and World Community Grid

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Steven Dunn

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Message 32254 - Posted: 8 Dec 2006, 4:18:12 UTC

From what I understand Rosetta makes the "draft" of all the protiens and what ever else than World Community Grid comes in and takes what Rosetta has done and does more "fine/precise" work on it to get a result that will help people/scientist. Is this correct?

If I am correct would it not be more benificial for more people to go to World Community Grid since Rosetta has about 7x-10x more people or atleast dedicate more time to World Community Grid?
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Message 32257 - Posted: 8 Dec 2006, 8:14:55 UTC - in response to Message 32254.  

From what I understand Rosetta makes the "draft" of all the protiens and what ever else than World Community Grid comes in and takes what Rosetta has done and does more "fine/precise" work on it to get a result that will help people/scientist. Is this correct?

If I am correct would it not be more benificial for more people to go to World Community Grid since Rosetta has about 7x-10x more people or atleast dedicate more time to World Community Grid?



I wouldn't put it like that.

One of the main aspects of Rosetta@Home currently is to improve the algorithms and process the scientist use with the Rosetta software (which is much more than just Rosetta@Home). But that is not all, for instance there is the current HIV docking research going on and hte Alzheimers reseach.

HPF & HPFII at WCG is all about humane pretome folding and is just using it to at the (I think) Robetta database.
It uses an older snapshot of Roestta than we are using here. So no we don't make a 'draft' protiens for WCG's HPF.

The problem they have there is they are competing with the Cancer and AIDS as well so all WCG gets split up. Maybe it would be better to run HPF under the Rosetta banner....
But then you would loose the extra market theat WCG brings.

I believe what we are doing here takes more computer crunching resources than HPFII. Though it would take someone who knows a lot mote about what they are doing there (like David Baker) to give an exact answer.
I also know we are still well below an ideal processing power here and more computers are needed.
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Message 32265 - Posted: 8 Dec 2006, 12:13:19 UTC

Rosetta@Home is a project to improve the accuracy of the modelling process. The models need to be accurate to be useful, and although for some proteins the models are relaively accurate (take a look at the CASP7 results here to see how well the Bakerlab do against some of the other best predictions - they're either one of the best or the best, sometimes by a long way).

Basically, WCG-HPF is running an old version of the Rosetta software and using it for some real-world testing. The problem is that the models produced by the software need improving - they're adding features like being able to test how proteins interact with each other and modelling the protein side-chains, and that's the point of this project.

In 5 years there might be some useful results from the WCG tests, but I have no doubt that the improved accuracy from the improved Rosetta algorithms produced by this project will be massively more useful.

I'm not saying that the WCG-HPF project won't produce useful results, but IMO the R@H will be far more beneficial for the future.

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Message 32299 - Posted: 8 Dec 2006, 21:35:19 UTC

In terms we can all understand... think of it this way, Rosetta@Home is building a microscope. WCG is using that microscope to learn about microscopic objects. Rosetta continues working on building a BETTER microscope, and WCG will continue sticking different things under the latest available microscope to learn more about microscopic objects. So, WCG is applying the tools created and improved by Rosetta.

To further the analogy, unless the microscope is good enough to see the baterium, the scientists using microscopes won't be able to cure ... <insert your favorite disease caused by bateria here>. At this point, Rosetta is approaching "good enough" for use in some applications. I believe it is still difficult to know ahead of time which applications are appropriate though. So WCG, by applying Rosetta to different applications is actually helping to prove where it works well, and where further improvements are still needed.

WCG is a valueable project, and changes over time as new applications are brought online, and others complete their task. It is not just working on protein study.

Since Rosetta is now also sending work units that directly relate to the search for cures for Alzheimers and AIDS, in addition to the pure science, I am comfortable with my 100% Rosetta position being the best possible use of my machines for mankind.
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Profile Dimitris Hatzopoulos

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Message 32425 - Posted: 10 Dec 2006, 21:19:03 UTC

I have a relevant part on this in my http://www.hyper.net/dc-howto.html page on DC projects. To quote Bonneau (head scientist for HPF/WCG) on "HPF or R@H" (19-Sep-05):

"How does the human proteome folding project (HPF) on the world community grid (WCG) relate to Rosetta@home?

[CASP6 Target T281] It is important to differentiate Rosetta@home from the HPF project (the one currently running on the WCG and grid.org), so I'll take a few lines to explain each from the perspective of motivation. The two grids HPF and Rosetta@home are not competing grids and we would like to see them both thrive.

Rosetta@home is run by the bakerlab as a way to accelerate development of the Rosetta code. With the focus on all-atom refinement and protein design even their benchmarks (to see if they broke the code or improved the code) are taking a large amount of time. Thus, Rosetta@home is primarily for testing/developing new versions of the Rosetta code and making Rosetta better. Also the robetta server could be hooked up to this project. This grid meets the spikes in the compute demands of the robetta server and the bakerlab. Rosetta@home does not aim to produce databases that will in turn be used by biologists but it helps to make the code better, which in turn helps efforts, like HPF, that use the code to give biologists usable fold and function predictions. In that way it is an essential part of the field-wide effort to fold proteomes.

Conversely, our project, HPF on the WCG, aims to use stable versions of Rosetta to make predictions that can be presented to biologists and biomedical researchers in comprehensive databases with intuitive front ends. HPF on the WCG can be thought of as the production phase of the project, where we produce function annotation for many genomes and then distribute this product to biologists. Due to the large number of proteins we're folding (comprehension is essential) we need a great deal of computer time if we want to make our databases comprehensive and availiable to biologists.

We are working with the bakerlab on HPF on the WCG and think of the two grids as very different parts of the solution of getting function out of fold prediction: one using Rosetta and one improving Rosetta (D Baker is involved in both projects)."


Btw, nowadays Rosetta@home isn't just building the tools (Rosetta sw) but also applying them (e.g. vaccines).

There has also been some concerns on HPF usefulness at grid.org's forums in the past.

Personally, I was a bit disappointed with technical aspects of WCG (not HPF which is one of WCG's 3 projects) because they ran it at too high initial replication, didn't compress data at all (under BOINC) etc. Maybe they've fixed things recently.
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Message 74671 - Posted: 5 Dec 2012, 16:09:53 UTC
Last modified: 5 Dec 2012, 16:10:27 UTC

So now that it's 5 years later, and Rosetta and WCG are further along, is it now worth the time to crunch for WCG as well, if not exclusively?
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Message 74673 - Posted: 6 Dec 2012, 12:10:19 UTC - in response to Message 74671.  

So now that it's 5 years later, and Rosetta and WCG are further along, is it now worth the time to crunch for WCG as well, if not exclusively?


Since Rosetta is having SOOOO many problems ALOT of people have gone elsewhere with WCG being a good choice. But there are other medical type projects too and of course a ton of math ones, Science ones, etc, etc.
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Message 74692 - Posted: 9 Dec 2012, 5:04:13 UTC

What kind of problems is Rosetta having?
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Message 74695 - Posted: 9 Dec 2012, 11:56:15 UTC - in response to Message 74692.  

What kind of problems is Rosetta having?


The units finish but then fail when sent back to Rosetta. It happens to some people but NOT to everyone, frustrating for those it does happen to!
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Message boards : Rosetta@home Science : Rosetta@home and World Community Grid



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