CASP8

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Profile carp

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Message 52897 - Posted: 7 May 2008, 14:10:34 UTC

Can someone please let us know when to back off Ralph and change resource share back to Rosetta.
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David Baker
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Message 52928 - Posted: 9 May 2008, 5:14:10 UTC - in response to Message 52897.  

Can someone please let us know when to back off Ralph and change resource share back to Rosetta.



please switch back to rosetta now--thanks! David
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Profile Jack Shaftoe
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Message 52975 - Posted: 10 May 2008, 14:06:46 UTC - in response to Message 52928.  

Can someone please let us know when to back off Ralph and change resource share back to Rosetta.



please switch back to rosetta now--thanks! David


Is CASP8 running now? If not, when does it start/finish?
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Profile Jack Shaftoe
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Message 52976 - Posted: 10 May 2008, 14:14:00 UTC - in response to Message 52975.  

Is CASP8 running now? If not, when does it start/finish?


Just found this:

http://predictioncenter.gc.ucdavis.edu/casp8/index.cgi#timetable

Timetable:
Registration for the experiment will start in the last week of March. The first prediction targets will be released not earlier than May 5; the last prediction targets will be released not later than July 18; prediction season will end not later than August 1. The CASP meeting will take place on December 3-7, and approximately one month before that, groups with the most accurate and interesting predictions will receive invitations to give talks. There will also be discussion of predictions and methods on the FORCASP web site.

Does this mean it's running now? There was no announcement on the Rosie homepage.
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Profile Jack Shaftoe
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Message 53026 - Posted: 12 May 2008, 23:08:50 UTC - in response to Message 52976.  

Please put an announcement up on the Rosetta homepage when CASP8 begins.

I look forward to joining the push.
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Message 53042 - Posted: 13 May 2008, 19:39:30 UTC
Last modified: 13 May 2008, 19:40:07 UTC

I have been posting the CASP 8 news releases in this thread since February.
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 53104 - Posted: 17 May 2008, 14:04:32 UTC - in response to Message 53042.  
Last modified: 17 May 2008, 14:07:57 UTC

Thank you Dr. Baker for the announcement on the homepage. I set all my other projects to "No New Work" and will be running Rosetta exclusively for the remainder of the CASP8 competition. I hope many other BOINC members will join us.

I look forward to hearing how Rosetta is doing in the competition. Good luck!
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Profile David E K
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Message 53132 - Posted: 18 May 2008, 15:50:21 UTC
Last modified: 18 May 2008, 15:58:12 UTC

Many of you have already contributed to the Robetta automated structure prediction server for a couple CASP8 targets, T0397 and T0405 so far. We've been getting 2 targets each weekday and are given 3 days for our Robetta server to return results. Only the small ab initio domains are being run on R@h and so far there have been 4 domains among the two targets mentioned above.

We post the R@h userids in the final Robetta results/models that are submitted to CASP as a REMARK. For example, the very first model submitted has the following:

REMARK SOURCE ROSETTA@HOME BOINC USER: 252498

I'll post more information soon about this along with some images of the models and the users who contributed.
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Michael G.R.

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Message 53136 - Posted: 18 May 2008, 18:12:44 UTC

Thanks for the update, David. I currently have 11 T0405 WUs in my queue (crunching 8 of them at the same time with my two quads). Good to know that they are CASP 8.
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Message 53175 - Posted: 19 May 2008, 19:19:19 UTC - in response to Message 53132.  

Many of you have already contributed to the Robetta automated structure prediction server for a couple CASP8 targets, T0397 and T0405 so far. We've been getting 2 targets each weekday and are given 3 days for our Robetta server to return results. Only the small ab initio domains are being run on R@h and so far there have been 4 domains among the two targets mentioned above.

We post the R@h userids in the final Robetta results/models that are submitted to CASP as a REMARK. For example, the very first model submitted has the following:

REMARK SOURCE ROSETTA@HOME BOINC USER: 252498

I'll post more information soon about this along with some images of the models and the users who contributed.


are you restricting R@H to the small tasks because they're too big for most people's PCs? If so, would it be useful to be able to send out big jobs to certain computers that can handle them?

I would be happy to put my two more powerful ones forward for this and i'm sure plenty of other people would too.
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Profile David E K
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Message 53176 - Posted: 19 May 2008, 19:54:51 UTC
Last modified: 19 May 2008, 20:00:56 UTC

The length cutoff is in place to not waste cpu time on R@h for targets that are just too hard given the 3 day turnaround time.

edit: so far there have not been any ab initio domains that are longer than 150 residues on Robetta
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Message 53216 - Posted: 21 May 2008, 6:05:48 UTC

What application is the CASP8 structures been run under rosie mini or rosie 5.96?
Cheers
Jarod

Have a crunching good day!!
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Message 53247 - Posted: 21 May 2008, 19:03:00 UTC

Should be MiniRosetta from now on as the compiler issue that was causing the earlier problems would seem to have been resolved.
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 53261 - Posted: 22 May 2008, 2:55:35 UTC

When CASP8 starts are we going to be able to tell how many work unit are left to be done until CASP8 will finish?
Cheers
Speedy
Have a crunching good day!!
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Message 53262 - Posted: 22 May 2008, 7:38:34 UTC - in response to Message 53261.  

When CASP8 starts are we going to be able to tell how many work unit are left to be done until CASP8 will finish?
Cheers
Speedy

i'm fairly sure it'll be as many as can be crunched before the deadlines...
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Message 53263 - Posted: 22 May 2008, 7:45:52 UTC - in response to Message 53262.  


i'm fairly sure it'll be as many as can be crunched before the deadlines...

Thank you I gess you are right.
Speedy

Have a crunching good day!!
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Message 53287 - Posted: 22 May 2008, 23:46:35 UTC

F.Y.I.

I've got a CASP8 task for the 5.96 app, i geuss the old saying of

(don't put all your eggs in one basket) is still true! :)

pete.
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Message 53423 - Posted: 28 May 2008, 21:09:39 UTC

I tought CASP was a blind prediction test, why do I see native structures in my WU 's? wuid=152643758 for example
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Message 53439 - Posted: 29 May 2008, 15:26:17 UTC - in response to Message 53423.  

I tought CASP was a blind prediction test, why do I see native structures in my WU 's? wuid=152643758 for example


This is just a guess, but it's possible that not all WUs that have CASP8 in the name are actually CASP8 targets; some might be new optimizations that the team are doing for CASP8 and first testing on proteins with known shapes before moving them over to the real deal.

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Message 53441 - Posted: 29 May 2008, 18:10:09 UTC - in response to Message 53439.  

I tought CASP was a blind prediction test, why do I see native structures in my WU 's? wuid=152643758 for example


This is just a guess, but it's possible that not all WUs that have CASP8 in the name are actually CASP8 targets; some might be new optimizations that the team are doing for CASP8 and first testing on proteins with known shapes before moving them over to the real deal.

Can anyone confirm this?
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