CASP9

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Mod.Sense
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Message 66082 - Posted: 12 May 2010, 3:53:13 UTC

Certainly correct, good catch Sid. If all of the tasks you download are CASP9 tasks, then a large download buffer defeats the purpose of the shorter deadline.
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Profile Venturini Dario[VENETO]

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Message 66086 - Posted: 12 May 2010, 10:10:36 UTC - in response to Message 66082.  

Certainly correct, good catch Sid. If all of the tasks you download are CASP9 tasks, then a large download buffer defeats the purpose of the shorter deadline.


So, do we really need to set cache at 0, connection "always on" and "target run time" at 12 hours, else our WUs will be useless?
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Message 66087 - Posted: 12 May 2010, 10:15:14 UTC - in response to Message 66078.  

It sounds like everything I'm crunching will be of no use at all. Please tell me I'm wrong!


You are wrong. ^_^

I took a look at the tasks you received. Only 1 has "casp9" in the description and will be restricted to the 18 hour window. From what Mike has said the rest should be under the human prediction deadline and have a few weeks to get the results back.
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Max DesGeorges

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Message 66088 - Posted: 12 May 2010, 12:10:13 UTC - in response to Message 66087.  

Mike, if you need the casp9 WUs to be finished within a day, why you don't set for this WUs a different deadline (one day or less if possible) and send them only to users that give back results rapidly?
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billy ewell 1931

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Message 66097 - Posted: 12 May 2010, 19:22:00 UTC

Based on my reading and interpretation of the preceding posts, I am resetting my account "Computing Preferences" to "0" for the option that says: "Maintain enough work for an additional _______days". My previous setting was 1.5 days so to hopefully guarantee my computers would not be deprived of work during server down-times; and in so doing I was unknowingly guaranteeing that many of my random casp9 units would exceed the 18-hour time restraint from download to upload.

Secondly; wouldn't it be practical for admin to post clear casp9 processing time limitations to the Home news section.

I appreciate the feedback from the previous posters.

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Sid Celery

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Message 66098 - Posted: 12 May 2010, 22:37:03 UTC - in response to Message 66097.  
Last modified: 12 May 2010, 22:38:50 UTC

Certainly correct, good catch Sid. If all of the tasks you download are CASP9 tasks, then a large download buffer defeats the purpose of the shorter deadline.

Nice that I understood it. Not nice that I left home before checking what the answer was :( I can adjust the dual-core laptop I'm using now but that's just 13 of my processing.

You are wrong. ^_^

I took a look at the tasks you received. Only 1 has "casp9" in the description and will be restricted to the 18 hour window. From what Mike has said the rest should be under the human prediction deadline and have a few weeks to get the results back.

:) Thanks for checking for me. I wasn't sure what to look at - I wasn't following the discussion above very well. Fortunately (or not) BOINC was going through another phase of not grabbing WUs when you looked at my quad desktop. Now there are over 20 8-hour WUs (still only 1 CASP9) - I'm just lucky that's the case.

Mike, if you need the casp9 WUs to be finished within a day, why you don't set for this WUs a different deadline (one day or less if possible) and send them only to users that give back results rapidly?

This makes sense. People can't be expected to micro-manage their tasks, nor to identify which task is of which type - this is best set by the project when a certain batch of tasks are released. Changing the work-buffer is a very blunt instrument, as is changing the runtime.

Based on my reading and interpretation of the preceding posts, I am resetting my account "Computing Preferences" to "0" for the option that says: "Maintain enough work for an additional _______days". My previous setting was 1.5 days so to hopefully guarantee my computers would not be deprived of work during server down-times; and in so doing I was unknowingly guaranteeing that many of my random casp9 units would exceed the 18-hour time restraint from download to upload.

On the plus side, BOINC defaults are for a 0.25 day buffer and a 3-hour runtime, so the majority of users won't have a problem. And if there are a whole bunch of tasks available (which there are) we'll only run dry if the server goes down.

The problem is for all us inveterate tinkerers. I'm cutting back to 0.33 days buffer to go with my 8 hour runtimes (in case of over-runs and to give time to get the WUs back to base).
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billy ewell 1931

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Message 66100 - Posted: 13 May 2010, 2:25:56 UTC

That is one hell of a fine post Sid; great job.
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Murasaki
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Message 66111 - Posted: 13 May 2010, 22:50:37 UTC

I just spotted that the graphics of a casp 9 task I have is showing both energy levels and RMSD. As CASP9 targets are unknown I had thought the RMSD comparison was impossible.

Is this really a CASP9 target or just a non-casp target with a poor choice of name?

If it is CASP have you guys come up with some idea for estimating the RMSD and trying to track against it?
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Message 66430 - Posted: 3 Jun 2010, 1:05:18 UTC - in response to Message 66111.  

I just spotted that the graphics of a casp 9 task I have is showing both energy levels and RMSD. As CASP9 targets are unknown I had thought the RMSD comparison was impossible.


Ditto, I've been wondering that as well.

Aren't CASP targets supposed to be blind?
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Message 66433 - Posted: 3 Jun 2010, 3:50:37 UTC

CASP, while in progress, issues blind targets. Or targets that noone on earth knows the structure for. If someone solves the structure during the period of time when submissions can still be made to CASP then the protein is thrown out (sometimes scientists elsewhere in the world happen to be working on solving the same protein that CASP is following and finish before the folks that CASP is working with).

Sometimes targets from prior CASP exercises are studied to see if more insight can be gleaned. These might say casp8 in the name.

I am most accustomed to tasks with no known solutions not displaying an RMSD at all. But from Mike's post here it sounds like some tasks show a flat line for RMSD instead when the target's structure is unknown.
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Message 66446 - Posted: 3 Jun 2010, 19:53:19 UTC - in response to Message 66433.  

I am most accustomed to tasks with no known solutions not displaying an RMSD at all. But from Mike's post here it sounds like some tasks show a flat line for RMSD instead when the target's structure is unknown.


No, the ones I was watching at the time of my last post definitely had known structure with a "native" graphic and changing RMSD. However, a few days later I stopped getting casp9s with RMSD and instead started picking up tests using casp8 models.

I suspect what I saw was just some casp8 targets with a typo in the batch name.
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Message 66557 - Posted: 12 Jun 2010, 10:28:30 UTC - in response to Message 65992.  
Last modified: 12 Jun 2010, 10:28:46 UTC

The team BOINC Synergy has selected Rosetta to be its project of the month for May! I hope the extra computing helps with CASP.

our team (BOINC.Italy) yesterday was the most productive team worldwide relating to BOINC credits...
wooo!
let's help Baker team and their great research effort in this CASP challenge!
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Jeff Gilchrist

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Message 66857 - Posted: 12 Jul 2010, 13:52:56 UTC

Does anyone know how long Rosetta@Home will be handing out CASP9 WUs? Will they be coming out until the end of July, mid-August, end of August?

Thanks.

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Message 66865 - Posted: 12 Jul 2010, 23:19:33 UTC - in response to Message 66857.  

Does anyone know how long Rosetta@Home will be handing out CASP9 WUs? Will they be coming out until the end of July, mid-August, end of August?


From the first post, CASP9 started around the beginning of May and the team will be sending work out through BOINC for 4 months. That would suggest the CASP work should be tailing off towards the end of August/start of September.
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Message 67157 - Posted: 10 Aug 2010, 11:42:22 UTC - in response to Message 66865.  

Does anyone know how long Rosetta@Home will be handing out CASP9 WUs? Will they be coming out until the end of July, mid-August, end of August?

From the first post, CASP9 started around the beginning of May and the team will be sending work out through BOINC for 4 months. That would suggest the CASP work should be tailing off towards the end of August/start of September.

I'm guessing this is why we're now seeing the queue of jobs dropping from 4m+ to 3m.

Can we have a statement of where we stand on CASP9 jobs now? Are the deadlines still at 18 hours? Are we keeping up with the schedule of remaining jobs?

And after it's all over, will the project look to maintain a large queue for ongoing work? It seems to have been very successful these last few months.
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Message 67159 - Posted: 10 Aug 2010, 19:40:22 UTC

It looks like the deadline for submitting CASP9 results was the first week of August. I assume that we are now back to normal crunching operations, but it would be nice if we could get confirmation from the project team.
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Message 67166 - Posted: 12 Aug 2010, 3:20:57 UTC

0
Server groups: CLOSED on July 24, 2010

Human groups: OPEN until August 20, 2010

Server groups: CLOSED on July 24, 2010

Human groups: CLOSED for regular predictions on July 31, 2010. OPEN until
August 20, 2010 for the refinement experiment.

Will start collecting on August 30, 2010.

Deadline for submission - September 20, 2010.

Registration will open on September 21, 2010
Financial support application deadline - October 6.
Notification of the fellowship recipients - October 15.
Early registration deadline - October 22.
Meeting - December 5-9, 2010, Pacific Grove, California, USA.

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Mark

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Message 67522 - Posted: 1 Sep 2010, 15:55:47 UTC - in response to Message 67166.  
Last modified: 1 Sep 2010, 15:56:18 UTC

Do we have any results on how well rosetta did compared to UW's human team or compared to Foldit, or other research teams?
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Message 67605 - Posted: 6 Sep 2010, 6:43:15 UTC

The results are trickling in and looking pretty good, but the definitive analysis won't be available until December at the CASP meeting
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Message 67669 - Posted: 9 Sep 2010, 21:58:13 UTC

Hi.

I'm seeing more tasks with casp9 marked in them now, then when CASP was running how come.

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