CASP 10

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Old man

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Message 73007 - Posted: 6 May 2012, 17:40:32 UTC - in response to Message 73005.  

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).

CASP is for the world's scientific community. All researchers studying the subject are potential participants. It is not truly a competition. It is more done as a measure of the current state-of-the-art. At the end, the "winners" present to the others about their methods and ideas that they attribute for their superior predictions. So as the ideas are assimilated into the various other approaches and combined, the next round is always a greater challenge than the last.

When reference is made to Rosetta vs. the rest, it is just people rooting for their "home team" to do well and continue to demonstrate that science is progressing and that we're truly learning how proteins work. This leads to vaccines and treatments for many of life's diseases.

When I started with Rosetta@home, the project was graciously making good use of 15 TeraFlops of computing power. Dr. Baker said it had taken off beyond all expectation (of a campus-wide distributed system). He also said that ten times more computing power would really open new frontiers to the research he and his lab have dedicated their lives to. It is truly rewarding to now see the project churning at over 150 TFlops with people from all over the planet contributing to a common cause for the common good. Keep crunching!


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.
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Message 73071 - Posted: 16 May 2012, 9:09:25 UTC
Last modified: 16 May 2012, 9:09:52 UTC

Any news about CASP competition? How's it going?
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Message 73081 - Posted: 17 May 2012, 18:41:53 UTC - in response to Message 72964.  
Last modified: 17 May 2012, 18:48:27 UTC

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.

Yes you are absolutely right. for CASP we need results back within a day or two, as our approach is iterative: we analyze the results after one day and send out another set of wu based on these results for two days of computing, then collect the results and submit to CASP. so please do set your buffer to a shorter time, and let us know if you are running out of wu. thanks!

CASP
CASP is an international experiment to assess the state-of-the-art of the protein structure prediction field. Sequences, whose structures have been solved but which have not yet been published are sent out to participating teams and we have a 3 days to send back predictions. The whole thing is conducted in a double-blind fashion ensuring fair assessment and truly blind prediction.

You state you have 3 days to send back predictions. Can I ask a very specific question that I've raised before:

The default work buffer set is 0.25 days with a 3 hour runtime, but some of us maintain a larger work buffer in order to avoid task outages. I personally use 2.0 days, but others may use a larger amount.

The default settings allow tasks to be returned to you in good time, but is it true to say that if the work buffer+runtime totals more than 3 days, then the work we grab will not be returned to you in sufficient time for the results to count?

I will assume this is the case, so I'm reducing my work-buffer to 1.5 days - plus my 8-hour runtime - to allow a certain leeway for you to receive work back in time. Please confirm so that others can make similar adjustments.

Obviously, with reduced work buffers, there's an equivalent requirement for tasks to be reliably available at your end, so an extra degree of monitoring would be wise.

On the assumption that my guesses are correct, you may see a reduced rate of task downloads while our buffers are run-down, though tasks wil be returned a certain amount sooner after release. As long as tasks are readily available there should be no reduction in results you see back.




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.
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Message 73103 - Posted: 18 May 2012, 19:43:41 UTC
Last modified: 18 May 2012, 19:45:54 UTC

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
WARNING! cannot get file size for default.out.gz: could not open file.
Output exists: default.out.gz Size: -1
InternalDecoyCount: 0 (GZ)


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.
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Message 73148 - Posted: 24 May 2012, 15:58:02 UTC
Last modified: 24 May 2012, 16:04:03 UTC

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
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Sean Kiely

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Message 73156 - Posted: 24 May 2012, 21:18:03 UTC - in response to Message 73148.  
Last modified: 24 May 2012, 21:19:40 UTC

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


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

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Ray Wang

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Message 73411 - Posted: 9 Jul 2012, 18:42:28 UTC

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
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Message 73522 - Posted: 24 Jul 2012, 15:13:58 UTC

Thanks for the updates, please keep them coming. We like to hear what's going on behind the scenes.
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Message 73602 - Posted: 10 Aug 2012, 15:36:07 UTC - in response to Message 73071.  

Any news about CASP competition? How's it going?


I too would like to hear an update as to how it's going, what challenges you have faced this season, etc.
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svincent

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Message 73608 - Posted: 11 Aug 2012, 16:28:39 UTC - in response to Message 73602.  

Any news about CASP competition? How's it going?


I too would like to hear an update as to how it's going, what challenges you have faced this season, etc.


CASP 10 is winding down but it takes a bit of time to get the results out. See http://predictioncenter.org/news.cgi#131
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Message 73612 - Posted: 13 Aug 2012, 13:52:06 UTC

Sure, but surely there's something to talk about. The last post on the front page was over two months ago now.
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Sid Celery

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Message 73669 - Posted: 22 Aug 2012, 3:20:12 UTC
Last modified: 22 Aug 2012, 3:29:48 UTC

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.
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Message 74216 - Posted: 9 Nov 2012, 0:03:00 UTC

Can anyone tell me what the results were?
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Ray Wang

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Message 74731 - Posted: 14 Dec 2012, 0:35:21 UTC - in response to Message 74216.  

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
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Message 74736 - Posted: 14 Dec 2012, 10:29:12 UTC

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...
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Message 74741 - Posted: 16 Dec 2012, 8:16:13 UTC - in response to Message 74731.  

[quote]
1. Baker Lab is ranked first in Server Prediction (fully automated structure prediction)

2. Baker Lab is ranked second in Human Prediction (manually structure prediction):

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:

Sincerely,
Baker Lab CASP10 Team


That's great!!!
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Message 74745 - Posted: 17 Dec 2012, 0:10:36 UTC - in response to Message 74736.  

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...

Just realised I wrote bottom-left when I meant bottom-right!
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Message 74756 - Posted: 19 Dec 2012, 19:14:06 UTC

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.











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Message 74757 - Posted: 19 Dec 2012, 19:54:37 UTC

Cool!

It appears (to the untrained eye) that the Baker Lab models were not only successful, but the successful outlying models as well in many instances.
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Message 74802 - Posted: 29 Dec 2012, 4:14:22 UTC

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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