CASP12

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Profile [VENETO] boboviz

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Message 79939 - Posted: 26 Apr 2016, 12:20:00 UTC
Last modified: 26 Apr 2016, 12:20:52 UTC

This is the timetable:

April 2016 - Start of the registration for CASP12 prediction experiment.
April 20, 2016 - Start of the testing of server connectivity (\"dry run\" for server predictors).
May 1, 2016 - Release of the first CASP12 prediction target.
July 15, 2016 - Last date for releasing regular prediction targets.
July 31, 2016 - End of the regular prediction season.
August 18, 2016 - End of the refinement and data-assisted prediction season.
July/August 2016 - Early bird registration for the December predictors\' meeting.
September 2016 - Collection of abstracts describing the methods tested in CASP12.
October/November 2016 - Invitation of groups with the most accurate predictions and interesting methods to give talks at the meeting.
Novermber 2016 - Publishing of the program of the meeting.
December 2016 - Predictors\' meeting to discuss the results of the experiment.


Will Rosetta release, like others casp, wus with _casp_ name? Which is R@H timetable??
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Sid Celery

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Message 79943 - Posted: 26 Apr 2016, 23:30:46 UTC

And what will be the turnaround requirements for released tasks.

What adjustments need to be made in settings given variations from default 6 hour run times, and default 0.25 day buffer sizes so we can be sure of returning tasks in accordance with Rosetta\'s expectations.
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Message 79946 - Posted: 27 Apr 2016, 2:50:23 UTC - in response to Message 79943.  

And what will be the turnaround requirements for released tasks.

What adjustments need to be made in settings given variations from default 6 hour run times, and default 0.25 day buffer sizes so we can be sure of returning tasks in accordance with Rosetta\'s expectations.


+1
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Profile [VENETO] boboviz

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Message 79949 - Posted: 27 Apr 2016, 15:42:13 UTC - in response to Message 79943.  

What adjustments need to be made in settings given variations from default 6 hour run times, and default 0.25 day buffer sizes so we can be sure of returning tasks in accordance with Rosetta\'s expectations.


Good question.
(I hope that one of admins read this thread)
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Profile [VENETO] boboviz

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Message 79995 - Posted: 1 May 2016, 13:14:03 UTC

From Casp site:

1. As of today, more than 150 groups have registered for the CASP12 experiment and we are set to start the prediction season. If you are planning to participate, but have not registered yet - please do this as soon as possible. Today and tomorrow is also the last chance for server curators to resolve any remaining issues with connectivity of their servers to CASP distribution/ verification servers.

We will start CASP12 gently and release two short targets (one on a slightly harder side and another - on the easier) on May 2. Two more targets constituting a dimer of heterodimers complex will be released the next day. Please follow the submission instructions provided in the Additional Information section of target-specific webpages and remember that predictors of complexes and quaternary structure should submit their models for all submitted targets (please see a more detailed explanation and the example of the coming T0861/862 complex at our Q&A page: http://predictioncenter.org/casp12/index.cgi?page=QandA). There will be only one (but large and difficult) target on Wednesday, followed by two targets (one harder and one easier) on both, Thursday and Friday.

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Message 80006 - Posted: 3 May 2016, 15:57:31 UTC

First target is released
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krypton
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Message 80009 - Posted: 3 May 2016, 18:00:21 UTC

YEP, it has begun!

We have some pretty cool new tools to test. I\'ll post more info as casp progresses.

Usually what happens is that server (automated) takes part in the first 3 days, then \"humans\" try stuff (this is when we start submitting lots of experimental jobs!) Later we are given more information (experimental data) and we try combine that with rosetta@home sampling.
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Profile [VENETO] boboviz

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Message 80080 - Posted: 13 May 2016, 8:32:06 UTC - in response to Message 80009.  

YEP, it has begun!
We have some pretty cool new tools to test. I\'ll post more info as casp progresses.


No news? No _casp_ wus?
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Message 80094 - Posted: 18 May 2016, 9:53:29 UTC - in response to Message 80080.  

Hi boboviz,

We are still in the server stage of CASP and so jobs are run through the robetta platform which gives the jobs a rb_* prefix. The CASP jobs have been running with this prefix.

I\'ve started to submit CASP jobs, I\'ll be sure to give them names so everyone can recognize them!

YEP, it has begun!
We have some pretty cool new tools to test. I\'ll post more info as casp progresses.


No news? No _casp_ wus?

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Sid Celery

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Message 80099 - Posted: 18 May 2016, 18:51:30 UTC - in response to Message 80094.  

Hi boboviz,

We are still in the server stage of CASP and so jobs are run through the robetta platform which gives the jobs a rb_* prefix. The CASP jobs have been running with this prefix.

I\'ve started to submit CASP jobs, I\'ll be sure to give them names so everyone can recognize them!

YEP, it has begun!
We have some pretty cool new tools to test. I\'ll post more info as casp progresses.


No news? No _casp_ wus?

rb_* jobs are coming through with a 2-day turnaround, which is great. Presumably this gets back to you in time to process them.

What is your actual turnaround requirement? Those who keep a larger buffer than 2 days run the risk of not getting them back soon enough.
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krypton
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Message 80101 - Posted: 19 May 2016, 6:27:48 UTC - in response to Message 80099.  

Hi Sid,

That is a good point! I\'ll check with DK about the automated server.

For the server we are only given 3 days, but for the human group we are given up to 15 days. Models generated after the 3 day limit could still be useful for the human group, especially if they happen to sample better scoring models.

For the human group, we typically try increase the amount of sampling, or try restrict sampling to regions of the protein where we think there might be an error.

-krypton

Hi boboviz,

We are still in the server stage of CASP and so jobs are run through the robetta platform which gives the jobs a rb_* prefix. The CASP jobs have been running with this prefix.

I\'ve started to submit CASP jobs, I\'ll be sure to give them names so everyone can recognize them!

YEP, it has begun!
We have some pretty cool new tools to test. I\'ll post more info as casp progresses.


No news? No _casp_ wus?

rb_* jobs are coming through with a 2-day turnaround, which is great. Presumably this gets back to you in time to process them.

What is your actual turnaround requirement? Those who keep a larger buffer than 2 days run the risk of not getting them back soon enough.

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Sid Celery

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Message 80112 - Posted: 21 May 2016, 4:14:07 UTC - in response to Message 80101.  

Great. I\'m in the clear as I keep 2 days, but I might still knock it down a little to make sure I stay on the right side of things. I noticed one or two tasks got returned a few hours after the deadline when some WCG tasks got in the way.

Others here may need to take note and adjust their buffer accordingly.
Hi Sid,

That is a good point! I\'ll check with DK about the automated server.

For the server we are only given 3 days, but for the human group we are given up to 15 days. Models generated after the 3 day limit could still be useful for the human group, especially if they happen to sample better scoring models.

For the human group, we typically try increase the amount of sampling, or try restrict sampling to regions of the protein where we think there might be an error.

-krypton
Hi boboviz,

We are still in the server stage of CASP and so jobs are run through the robetta platform which gives the jobs a rb_* prefix. The CASP jobs have been running with this prefix.

I\'ve started to submit CASP jobs, I\'ll be sure to give them names so everyone can recognize them!

YEP, it has begun!
We have some pretty cool new tools to test. I\'ll post more info as casp progresses.

No news? No _casp_ wus?

rb_* jobs are coming through with a 2-day turnaround, which is great. Presumably this gets back to you in time to process them.

What is your actual turnaround requirement? Those who keep a larger buffer than 2 days run the risk of not getting them back soon enough.


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Profile David E K
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Message 80194 - Posted: 17 Jun 2016, 18:18:41 UTC

There\'s a 3 day turnaround for the server groups but the human groups have much more time so the results that come in late are still helpful. Also, we are providing all the models to the WeFOLD group which we are participating in. It\'s a community effort.
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Profile [VENETO] boboviz

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Message 80659 - Posted: 16 Sep 2016, 7:09:20 UTC
Last modified: 16 Sep 2016, 7:09:35 UTC

Yesterday:
To be included in the CASP12 Abstract Book, your abstract(s) should reach us not later than tomorrow, September 15.


And:
12th CASP Meeting
December 10-13th 2016, Gaeta (Italy)

Subject: State of the art of methods for predicting protein structure, assembly, and function from sequence.

Scientific context: Results of the 12th international CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiment.

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Profile [VENETO] boboviz

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Message 80822 - Posted: 2 Nov 2016, 10:30:50 UTC
Last modified: 2 Nov 2016, 10:31:23 UTC

Some batches of _casp12_ on Ralph....
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Message 80829 - Posted: 8 Nov 2016, 19:59:59 UTC - in response to Message 80822.  

Some batches of _casp12_ on Ralph....


Hi bobviz,
There are some test related to casp12.

-krypton
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Profile David E K
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Message 80893 - Posted: 9 Dec 2016, 4:35:12 UTC

The official CASP12 automated evaluation is available and we are attending the conference in Gaeta, Italy this weekend. The official rankings will be released at the meeting. We did well! Thanks everyone!

http://predictioncenter.org/casp12/zscores_final.cgi

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Message 81095 - Posted: 27 Jan 2017, 17:46:58 UTC

It would be nice to hear a little more about the CASP 12 results. Were there any interesting insights into the state of the art in protein folding from the meeting last month?
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Message 81096 - Posted: 27 Jan 2017, 19:15:30 UTC - in response to Message 81095.  

It would be nice to hear a little more about the CASP 12 results. Were there any interesting insights into the state of the art in protein folding from the meeting last month?


Hi svincent,

If you are interested I uploaded slides from our CASP12 presentation here:
https://docs.google.com/presentation/d/1ZQ3Uvh-PPGz9VBJlohKlMHuW7FceAGQEgvpSsvBBy1A

But in short:
1) we have a method (GREMLIN:co-evolution) for predicting contact from given a multiple sequence alignment.
2) we used boinc before casp to precompute protein families with unknown structure. At least one of the targets (T0866) matched a precomputed model and was used by the server! This was a highlight this casp.
3) we developed a new method \"map_align\" that can take predicted co-evolution contacts and search the entire PDB. Sometimes two proteins may have VERY different sequences (beyond anything you would call homologs) but have very similar structures. If we find a hit in the PDB that matches the contacts, we can use it as a starting point in modeling. We had some great sucess using this method on target T0886.


Tell me if you have any quesionns

-krypton (aka sergey)
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Profile [VENETO] boboviz

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Message 81537 - Posted: 26 May 2017, 7:30:45 UTC - in response to Message 81096.  

Tell me if you have any quesionns

-krypton (aka sergey)


Just a curiosity. From CASP\'s abstract of Bakerlab\'s presentation:
The refinement method used in CASP12 is a composite of Rosetta software applications and AMBER software. Rosetta software is freely
available for academic users, and all of the applications newly developed for CASP12 will be available by end of this year.


Are you implementing this new protocols/functions/applications in Rosetta@Home??

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