Message boards : Rosetta@home Science : CASP 10
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Old man Send message Joined: 10 Nov 07 Posts: 25 Credit: 1,122,372 RAC: 0 |
CASP has one side of things for automated structure prediction, but there is another side for human predictions (many of which are done with various degrees of automated tooling behind them). You have been here for about 6 years if I concluded the date of accession correctly. Now I will wait with interest to see if the performance are ~1500 TFlops after next 6 years. |
![]() Send message Joined: 1 Dec 05 Posts: 1963 Credit: 9,099,488 RAC: 551 ![]() |
Any news about CASP competition? How's it going? |
![]() Send message Joined: 16 Jun 08 Posts: 1227 Credit: 14,140,275 RAC: 238 |
I would recommend that you post an item under "News" on the homepage (and also a new thread in the number-crunching forum) asking participants to check their work buffer settings and reduce them to no higher than 1.5 days? This might reduce the number of CASP units that are processed but not returned quickly enough to be useful. One of my computers (the slowest one) seems to stop downloading any workunits at all unless I tell it to maintain a 3-day work buffer, even if it's totally out of workunits. I usually don't have Rosetta@Home enabled on that one. 0.1 days seems adequate for the other two, in order to make them finish downloading new workunits before they finish the old ones. Otherwise, they would waste time finishing a workunit, then doing almost nothing on that CPU core except downloading the next workunit. |
HW&JC Send message Joined: 2 May 08 Posts: 21 Credit: 7,870,114 RAC: 354 ![]() |
FYI: Something going very wrong with these CASP10 jobs Task rb_05_16_31351_62365__round2_t000__0_C1_SAVE_ALL_OUT_IGNORE_THE_REST_50188_1160_0 did not checkpoint at all and only completed due to the watchdog cutting in BOINC:: CPU time: 25596.7s, 14400s + 10800s[2012- 5-18 19:45:20:] :: BOINC Task rb_05_16_31351_62365__round2_t000__0_C2_SAVE_ALL_OUT_IGNORE_THE_REST_50188_1074_0 is still in progress but doing exactly the same. Currently at 5hours 58m of processor time (not wall-clock) into a preferred runtime of just 3 hours. |
THESPEEKER Send message Joined: 21 Sep 08 Posts: 3 Credit: 6,891 RAC: 0 |
https://boinc.bakerlab.org/rosetta/workunit.php?wuid=462919979 This has also happened to this one... as below post. Also why am I receiving these casp9 benchmark WU'S still?? https://boinc.bakerlab.org/rosetta/result.php?resultid=508171512 |
Sean Kiely Send message Joined: 31 Jan 06 Posts: 64 Credit: 43,992 RAC: 0 |
These casp9 benchmark workunits are normal and expected. There was a post (by TJ) in this thread back on May 2 discussing this. https://boinc.bakerlab.org/rosetta/workunit.php?wuid=462919979 |
Ray Wang Send message Joined: 9 Mar 09 Posts: 8 Credit: 230,454 RAC: 0 |
Hello everyone!! Apologies! I am Ray Wang, one of the protein structures predictors of Baker Lab CASP10 team. Few days ago, there were massive error submissions which caused the success rates to be zero. That was due to a remiss update of the CASP working pipeline. We were very sorry about causing the inconvenience for you all, and for sure will be doing more meticulous checking before we trigger the pipeline! Again Sorry about this, and THANKS you all for the contribution to the Rosetta@home! We couldn't accomplish these scientific feats without your participation!!!!! Sincerely yours, Baker Lab CASP10 team |
Polian![]() Send message Joined: 21 Sep 05 Posts: 152 Credit: 10,141,266 RAC: 0 |
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Polian![]() Send message Joined: 21 Sep 05 Posts: 152 Credit: 10,141,266 RAC: 0 |
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svincent Send message Joined: 30 Dec 05 Posts: 219 Credit: 12,120,035 RAC: 8 |
Any news about CASP competition? How's it going? CASP 10 is winding down but it takes a bit of time to get the results out. See http://predictioncenter.org/news.cgi#131 |
Polian![]() Send message Joined: 21 Sep 05 Posts: 152 Credit: 10,141,266 RAC: 0 |
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Sid Celery Send message Joined: 11 Feb 08 Posts: 2059 Credit: 40,463,815 RAC: 1,453 ![]() |
From this link the following message has been posted: 1. Just three days ago we received the last CASP10 prediction, and today we start collecting methods abstracts... From that I will assume no more CASP10 tasks are being issued here, so I'll now revert to my usual share between Rosetta & WCG and restore my work buffer to what it was before (not that there's been any shortage for quite some while - thanks) Edit: now that I look, I notice I'm still getting "rb" tasks. I'll assume this is some kind of post-CASP10 re-test, but if I've misunderstood and you're still needing to run tasks for submission, please do put me right. ![]() ![]() |
![]() Send message Joined: 10 Feb 10 Posts: 35 Credit: 51,915 RAC: 0 |
Can anyone tell me what the results were? |
Ray Wang Send message Joined: 9 Mar 09 Posts: 8 Credit: 230,454 RAC: 0 |
Can anyone tell me what the results were? Hi ALL ROSETTA@HOME participants, Good new from CASP10 meeting, which just ended yesterday at Italy!!! Having your contribution to Rosetta@Home project, the Baker lab did really good this time. With a lot of exceptional scientists' effort, in CASP10 we have improved our template-based modeling (TBM) method. And here are those results: Let's focus on TBM easy/hard using "best model" (best out of five submission) as the criterion. 1. Baker Lab is ranked first in Server Prediction (fully automated structure prediction) --------------------------------------------------- [1] [2] [3] [4] [5] --------------------------------------------------- 1. 330 s BAKER-ROSETTASERVER 111 79.614 2. 035 s Zhang-Server 111 79.365 [1] rank [2] server id [3] server name [4] proteins count [5] Z-score (how well you did compared to others using GDT-TS as metrics) website: http://www.predictioncenter.org/casp10/groups_analysis_best.cgi?type=server&tbm=on&tbm_hard=on&submit=Filter 2. Baker Lab is ranked second in Human Prediction (manually structure prediction): --------------------------------- [1] [2] [3] [4] [5] --------------------------------- 1. 237 zhang 56 56.832 2. 477 BAKER 56 54.482 [1] rank [2] server id [3] server name [4] proteins count [5] Z-score (how well you did compared to others using GDT-TS as metrics) website: http://www.predictioncenter.org/casp10/groups_analysis_best.cgi?type=all&tbm=on&tbm_hard=on&submit=Filter 3. Baker Lab is ranked first in Human Contact-assisted Prediction (given few native contacts, to predict protein structure) with a tremendous distance to the group ranked second: Here is the preliminary results the CASP organizer posted on website: http://predictioncenter.org/casp10/results.cgi?view=targets&model=all&tr_type=others&groups_id=4 , where for each graph with orange-color lines into it, you need to compare the black line to the rest- that's us. The main predictor, David Kim, will come here, explaining it clearly to you all with a summary table. With the help and contribution to Rosetta@HOME from you all, we are able to make significantly progress to predict more accurate protein structures, which ends up would impact the real world by tackling human deseases, like, therapeutics protein design. Please let me know if I said something unclear. Again, thank you so much for the support. We will keep you updated about our triumph in contact-assisted protein structure prediction in CASP10. Sincerely, Baker Lab CASP10 Team |
![]() Send message Joined: 3 Nov 05 Posts: 1829 Credit: 119,133,504 RAC: 2,487 ![]() |
That's great news! Well done to everyone there. It's obvious from the thumbnails on the link you've given http://predictioncenter.org/casp10/results.cgi?view=targets&model=all&tr_type=others&groups_id=4 that the bakerlab's results are consistently to the bottom-left on the charts and often by some distance! You should definitely send this message out on the R@H twitter account, and get this post on the website's front page... |
![]() Send message Joined: 1 Dec 05 Posts: 1963 Credit: 9,099,488 RAC: 551 ![]() |
[quote] That's great!!! |
![]() Send message Joined: 3 Nov 05 Posts: 1829 Credit: 119,133,504 RAC: 2,487 ![]() |
That's great news! Well done to everyone there. Just realised I wrote bottom-left when I meant bottom-right! |
![]() Volunteer moderator Project administrator Project developer Project scientist Send message Joined: 1 Jul 05 Posts: 1018 Credit: 4,334,829 RAC: 0 |
Hi all, As Ray posted below, we did well! Here are a couple plots and images of our results from the contact assisted category. Points above the line are best. The y-axis is the GDT (how close we are to the correct structure, higher is better) of our best models for each of the contact assisted targets vs on the x-axis for the left plot, the GDT of the best models of all predictions without using contact information, and for the right plot, the best models of other predictors using contact information. As you can see we are above the line for many of the targets. An outstanding prediction was for T0680o, which is a tetramer. There were other outstanding predictions. See below. Thank you all for contributing to this effort. I'll see if I can find users who provided the actual predictions that led to the final submitted models. It might be tough though. ![]() ![]() ![]() ![]() ![]() ![]() |
Polian![]() Send message Joined: 21 Sep 05 Posts: 152 Credit: 10,141,266 RAC: 0 |
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![]() Send message Joined: 18 Mar 08 Posts: 5 Credit: 32,225 RAC: 0 |
Is there any point in running the work named "rb" now? Since we are past August, that was put up as deadline in the first post. |
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