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LanDroid
Prince
Joined: 11 Jun 2002
Posts: 4476
Location: Cincinnati, OH U.S.
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 Posted: Wed Apr 18, 2012 9:19 am Post subject: CASP 10 Competition |
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Every two years, Critical Assessment of protein Structure Prediction (CASP) competitions analyze the current state of the art in protein structure prediction. The winners have the most accurate predictions of the actual folded protein shape.
I think KWSN should support this effort as it pits several Boinc projects against quite a few independent labs. In the last competition 2 years ago, Rosetta made one of the best predictions of the entire experiment. POEM tried something different that didn't work very well and have learned from that. Perhaps Boinc projects can do better against independent labs this time with more power. Essentially this would involve KWSN shrubbing several Boinc projects during May - July of this year. This involves Rosetta, POEM, and possibly Docking, Folding (non-boinc) and others.
What do you think - should KWSN support Boinc projects in this competition? It's our last chance for two years!
| Quote: | The main goal of CASP is to obtain an in-depth and objective assessment of our current abilities and inabilities in the area of protein structure prediction. To this end, participants will predict as much as possible about a set of soon to be known structures. These will be true predictions, not ‘post-dictions’ made on already known structures.
CASP10 will particularly address the following questions:
Are the models produced similar to the corresponding experimental structure?
Is the mapping of the target sequence onto the proposed structure (i.e. the alignment) correct?
Have similar structures that a model can be based on been identified?
Are comparative models more accurate than can be obtained by simply copying the best template?
Has there been progress from the earlier CASPs?
What methods are most effective?
Where can future effort be most productively focused?
http://predictioncenter.org/casp10/ |
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LanDroid
Prince
Joined: 11 Jun 2002
Posts: 4476
Location: Cincinnati, OH U.S.
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| Posted: Wed Apr 18, 2012 9:20 am Post subject: |
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Rosetta needs help gearing up for CASP 10:
| Quote: | In the last two months we believe we have made quite a breakthrough in structure prediction, and are excited to test the new method in CASP10. We need your help though--we are now testing many aspects of the new approach and are seriously limited by available CPU cycles. There are now so many flu inhibitor design and structure prediction jobs queued up on Rosetta@Home that there is an eight day wait before they are getting sent out to you. This would be a great time to temporarily increase Rosetta@Home's share on your computers and/or recruit new users--we need all the help we can get!
Thanks!
David Baker
3/30/12
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#72628 |
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Plomos
Prince
Joined: 26 Apr 2011
Posts: 859
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| Posted: Wed Apr 18, 2012 9:30 am Post subject: |
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I am game for supporting this. I can do Rosetta no problem and possibly some poem as well. When i get home I'll switch to running Rosetta and ABC or maybe just finish up what is running currently and then just run rosetta.
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LanDroid
Prince
Joined: 11 Jun 2002
Posts: 4476
Location: Cincinnati, OH U.S.
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| Posted: Wed Apr 18, 2012 9:39 am Post subject: |
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| I'm trying to find out if POEM or any other projects (in addition to Rosetta) are competing in CASP10. Haven't seen much info, this may turn out to be Rosetta only? However this shakes out, KWSN needs to consider this in a broader context as BOINC Vs. The World! |
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Plomos
Prince
Joined: 26 Apr 2011
Posts: 859
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| Posted: Wed Apr 18, 2012 2:40 pm Post subject: |
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Ok sounds good. Also do we need to register our computers on the CASP site or is rosetta doing that automatically?
Another note: I have picked up one of these CASP9 benchmark WUs and so far after an hour of crunching I am at 19% done so that means it will take roughly 4+ additional hrs to finish it, give or take
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Blurf
Prince
Joined: 03 Jan 2011
Posts: 1090
Location: Upstate NY
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| Posted: Wed Apr 18, 2012 3:07 pm Post subject: |
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Maybe this should be the automatic PoTM for May...?
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Plomos
Prince
Joined: 26 Apr 2011
Posts: 859
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| Posted: Thu Apr 19, 2012 1:01 pm Post subject: |
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An update from my end on the CASP9 WUs that are running right now. It seems that for my comp they run in 4 hrs so not too long at all. I'm sure others can speed through them
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LanDroid
Prince
Joined: 11 Jun 2002
Posts: 4476
Location: Cincinnati, OH U.S.
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| Posted: Fri Apr 20, 2012 8:37 pm Post subject: |
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POEM is participating in CASP10, but actual WU's may not materialize until the 2nd half of May...
http://boinc.fzk.de/poem/forum_thread.php?id=660
So that's two Boinc projects, still checking on Docking... |
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LanDroid
Prince
Joined: 11 Jun 2002
Posts: 4476
Location: Cincinnati, OH U.S.
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| Posted: Sat Apr 21, 2012 11:37 am Post subject: |
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I probably should have emphasized this more in the intro, but keep in mind this competition is a 3 month deal: May - July. Not sure how that affects PotM, may have to form a sub-team to shrub just CASP10 knowing our problems with atten... - hey there goes a Volkswagen!
FYI: POEM app for Nvidia GPU should be coming out soon... |
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Sir Cracked of the Mind
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| Posted: Sat Apr 21, 2012 1:10 pm Post subject: |
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Just tell me when and were, at the time and Im in.
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