Dr. Baker wrote:

We desperately need as much CPU power as possible for the next two weeks--there are more than 25 CASP targets due, including some that are our best shots at really high resolution models. Frustratingly, we won't be able to do anywhere near as much sampling as we had planned for these proteins as there are so many coming due near the same time, and thus can't really expect the accuracy we had hoped for. So if it is at all possible for you to
increase your rosetta@home cpu time for the next two weeks please do--it will make a huge difference for our collective efforts!
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What's the big hurry Dave? Wouldn't it make sense to simply extend the processing time for them? If it takes more time, then it takes more time.

CASP is a competition - if you turn in the results late, you don't get credit for them. The deadline is not one that Dr. David Baker is arbitrarily making up.. it's one that all the participants in CASP are having to adhere to.

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It is curious. Due to whom? What exactly does he mean by due?

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All protein folding projects participate in a bi-anual CASP contest. The CASP board, composed of independent microbiologists, bio-chemists and the like, release peviously unknown protein sequences to the various projects to test the accuracy of their methods. The projects return the (best bet) five lowest energy structures back to CASP. CASP gives both soft and hard deadlines (due dates) to return project results.

Sometime in November, staffs from all projects will attend a CASP meeting at which the winner will be announced and results discussed.

Hope this helps.

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It's kinda like betting on the outcome of the world cup. Better get your "bets" (i.e. predictions of outcome) recorded before the games are over... otherwise at THAT point, EVERYONE knows.

For CASP the protein structures that are part of the competition are not yet known to mankind... but WILL be in a matter of weeks. To turn in a prediction after everyone already knows the answer do not demonstrait any ability to predict the outcome.

So it's not Dr. Baker's deadline per se. It's the deadline for reporting his teams prediction to CASP. Since all of us are an integral part of that team, we try to help by reporting results before the work unit deadlines.

After CASP is over, a late result will be just as scientifically interesting to the project team, but it will have arrived too late to prove that Bakerlab and Rosetta makes the most accurate predictions. They will review our collective prediction and compare to the known results once they are published. This is how they learn and make Rosetta better so it creates more accurate predictions and does so with less computing power over time.

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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
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What does the winner get? Are there $$$ in it?

What does the winner get? Are there $$$ in it?

I'm not sure about $, but it will determine what groups are on the best path for protein prediction. This in turn might convince other researchers to use the 'best' predictors, therefore improving their work into specific diseases.

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It is basically a test to determine what the current state-of-the-art in the field is today. The "winner" gives talks to the CASP community about how they arrived at the best prediction, and everyone learns something about how the state-of-the-art approach works and some perspective on why that approach produces the best model. They run back to their labs, incorporate some of those ideas with their own, run tests on their new combined approach, and then they do it all again in two years.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
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OK, I've switched back over to this project. I was doing some heavy Malaria Control crunching while doing some Rosetta. Now all my nine hosts will be doing Rosetta once I run out the Malaria WU's...good luck to all and Dr. Baker.

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I got the impression during the last two CASPs that those that did terribly also presented how their approach worked. Knowing what doesn't work is helpful for those working in this field.

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Dr. Baker has said that in trying to respond to people on the boards and explain how it all works to us laypersons, that he himself got ideas for improvements... so in that case, it's not even someone that entered CASP and it helped to bounce the idea around and see what sticks.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Hi Dr. Baker,
on July 15 you asked the crunching community to increase the CPU % devoted to R@H for a couple of weeks, since a lot of CASPs were due in a short time.
Since the 2 weeks are coming to an end, I would like to know whether R@H will (likely) meet the delivery deadline for those CASPs.
By the way, could you notice any increase in resources devoted to R@H?

Apart from them, a small poll:
- Did you (crucnchers) read DB's request? (I did ;)
- Did you actually increase R@H resource share? to what extent? (I prevented all other BOINC-projects from getting new tasks).

That's all folks!
darkpella

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