CASP9

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Mike Tyka

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Message 65811 - Posted: 25 Apr 2010, 1:04:17 UTC
Last modified: 25 Apr 2010, 1:14:10 UTC

Hey everyone !

As some of you may know CASP9, a community wide experiment in structure prediction, is starting in less then 10 days. As usual we are participating with both a human prediction group and a brand new automatic server, called RosettaServer. We will be utilizing BOINC heavily during the next 4 months, as you can see we already have nearly 4 million workunits lined up.
We have been very busy getting everything ready in time!

CASP 9
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 limited amount of time to send back predictions. The whole thing is conducted in a double-blind fashion ensuring fair assessment and truly blind prediction.

We will be testing a number of new strategies during this period, these will be carried out by the human prediction group and crunched on BOINC.

In the automatic category we have modernized out old prediction server (Robetta, created more then 6 years ago) and replaced it\'s heart with Rosetta\'s most modern implementation. Among many scientific improvements, we have also, for the first time, connected the public structure prediction server to BOINC for both ab initio prediction and homology modeling.

For the community, by the community:
After CASP this server will go public and provide Rosetta\'s Abinitio and Homology modelling capabilities to the scientific community (and to the public). The computation for this will be conducted on BOINC meaning that you guys will be crunching protein structure prediction jobs for real scientific studies conducted by researchers all over the world!


Thanks again everyone for crunching, we wouldn\'t be able to do this stuff without you !

Excitedly yours,

Mike
http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Profile Chilean
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Message 65812 - Posted: 25 Apr 2010, 1:41:22 UTC

Awesome! Winter just started here... Meaning my PCs will be both crunching and making the winter a bit less cold. :)
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Michael G.R.

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Message 65822 - Posted: 25 Apr 2010, 18:46:09 UTC
Last modified: 25 Apr 2010, 18:46:35 UTC

Great, I\'ll try to throw more computing power your way for the duration! It will be interesting to see how Rosetta has improved since the last CASP.

btw, this announcement should probably linked from the frontpage news.
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Matthew Lei
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Message 65847 - Posted: 27 Apr 2010, 3:09:04 UTC

Guess I\'ll relocate more CPU time for this event. :)
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Profile JChojnacki
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Message 65848 - Posted: 27 Apr 2010, 3:53:42 UTC

Very excited about CASP9 this year.

And Mike, a double \"WOW\" goes out to you all for the \"For the community, by the community\" section of your post. That is very cool news!

Happy CASP9-ing.

~Joel



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Matthew Lei
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Message 65886 - Posted: 29 Apr 2010, 7:51:12 UTC

Just wondering, it is possible tell whether the WU is a CASP task just by looking at the WU name?
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Message 65887 - Posted: 29 Apr 2010, 8:22:54 UTC - in response to Message 65886.  

Just wondering, it is possible tell whether the WU is a CASP task just by looking at the WU name?

Some of the WUs in my queue have CASP in the name now - I don\'t know if they all will though.
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Tom Philippart
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Message 65907 - Posted: 30 Apr 2010, 17:59:50 UTC - in response to Message 65811.  



We will be utilizing BOINC heavily during the next 4 months, as you can see we already have nearly 4 million workunits lined up.
We have been very busy getting everything ready in time!

Mike


Those 4 million WUs are no CASP WUs???

It says the first targets will be released on may 3rd...
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Profile Ed and Harriet Griffith
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Message 65977 - Posted: 5 May 2010, 13:15:25 UTC

The team BOINC Synergy has selected Rosetta to be its project of the month for May! I hope the extra computing helps with CASP.

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David Baker
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Message 65992 - Posted: 6 May 2010, 5:57:56 UTC - in response to Message 65977.  

The team BOINC Synergy has selected Rosetta to be its project of the month for May! I hope the extra computing helps with CASP.



THANKS!!
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billy ewell 1931

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Message 66010 - Posted: 6 May 2010, 20:38:34 UTC
Last modified: 6 May 2010, 20:39:30 UTC

Are we now operating in a primarily CASP9 mode? I have over 220 work tasks queued-up in direct support of R@H and to be crunched by my 20+ cpus but I cannot tell from reviewing the tasks if they are CASP related. I feel very strongly about the efforts of this research program and I intend to fully support the scientific effort with all my resources for the indefinite future.
Thanks to David and Mike and all other operatives who make this project posssible.

Bill
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Evan

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Message 66011 - Posted: 6 May 2010, 21:09:35 UTC

Are we now operating in a primarily CASP9 mode
I have recently downloaded a batch with the wording \'casp9\' in the description
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David Baker
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Message 66014 - Posted: 7 May 2010, 3:49:07 UTC

Yes--the first CASP9 target was released a few days ago, and you will be seeing primarily CASP targets for the next month or so. thanks for your contributions to this effort!
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Tom Philippart
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Message 66030 - Posted: 8 May 2010, 10:19:43 UTC

Hello, 2 basic questions:

1. are our casp deadlines the \"human\" or \"server\" deadlines?

2. where can I find out which target I\'m running? I remember on the last CASP challenges, the target name was in cluded in the WU name in this format tXXX_rest_of_the_WU_name. Right now I see a WU with casp9 in the name on my computer, but it says t000...
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Mike Tyka

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Message 66053 - Posted: 10 May 2010, 20:10:03 UTC

Hi all!

First of all thanks for all your computing effords!

In answer to some of the questions:

The jobs ending in \"casp9\" and containing t000_ are homology modelling jobs ones submitted by our automated new rosetta server. Sadly the way it\'s set up they do not contain the original casp target name but instead are numbered internally so you can\'t tell from the name what target they are. But you can probably guess from the length and the day they were submitted (the submit day should match up with the target release date).
These targets are operating under the Server deadline, not the human deadline, which means only 3 days from release time to deadline !

OTOH jobs that do not contain casp9 in the name are not necessarily not related to casp. THe human group will be submitting various jobs relating to casp but will use custom names.

Basically a very large fraction of the jobs you\'ll see on your machines will be relaated to casp in one way or another - i\'d say at least 60-70%.


Mike


http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Profile JChojnacki
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Message 66056 - Posted: 10 May 2010, 21:22:18 UTC - in response to Message 66053.  


Basically a very large fraction of the jobs you\'ll see on your machines will be relaated to casp in one way or another - i\'d say at least 60-70%.

Mike


Thanks for the info, Mike.




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Tom Philippart
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Message 66067 - Posted: 11 May 2010, 7:34:14 UTC

hmmm 3 days doesn\'t seem a lot given the long deadlines of this project.

In this case: @Bakerteam: what\'s your prefered WU runtime?

I think the goal is to have as many predictions as possible in this time frame...
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Murasaki
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Message 66071 - Posted: 11 May 2010, 15:16:19 UTC - in response to Message 66067.  

hmmm 3 days doesn\'t seem a lot given the long deadlines of this project.


Definitely. I just noticed my slow computer has a \"CASP9\" task that it has been chugging away on for 4 days. Is the result still valuable? It still has 6 days left before the \"official\" BOINC deadline.

Would it be worth me cutting the work time in my preferences to force results to come back sooner?
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Mike Tyka

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Message 66076 - Posted: 11 May 2010, 22:18:51 UTC

Indeed. For jobs that contain _casp9 in their name, we need the results back within about 18hrs. Everything that comes back after that will ikely not make it into the final analysis - the reason is that we need some time for post analysis here before we can send the final models (we have to choose 5!) to the CASP organisers. So, for those kind of WUs it would help us tremendously if you could set your runtimes to 12-16hrs, even if you only end up crunching a single decoy (sometimes we get fairly large structures from CASP).
These deadline restrictions are only for the server predictions - the human team have about 3 weeks per target, but they use a different naming scheme.

Mike


http://beautifulproteins.blogspot.com/
http://www.miketyka.com/
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Sid Celery

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Message 66078 - Posted: 12 May 2010, 2:45:13 UTC - in response to Message 66076.  

Indeed. For jobs that contain _casp9 in their name, we need the results back within about 18hrs. Everything that comes back after that will ikely not make it into the final analysis - the reason is that we need some time for post analysis here before we can send the final models (we have to choose 5!) to the CASP organisers. So, for those kind of WUs it would help us tremendously if you could set your runtimes to 12-16hrs, even if you only end up crunching a single decoy (sometimes we get fairly large structures from CASP).
These deadline restrictions are only for the server predictions - the human team have about 3 weeks per target, but they use a different naming scheme.

Mike, unless I\'m misunderstanding something here, doesn\'t this also mean that the work buffer needs to be adjusted too? If, for example, I have a 2.5 day work buffer, it\'ll be about that amount of time before a WU gets to the top of the pile to even start running. Then, if I have an 8-hour runtime, the completed WU won\'t be ready to return until 2.83 days after being received.

If I understand you right, 18 hours (=0.75 days) is the maximum that will fall within this window. So anything more than a 0.5 day buffer and 6-hour runtime (or some combination > 0.75days\\18 hours) is guaranteed to be late.

An early reply will be appreciated. I\'ll be out of town in 12 hours until late Sunday and won\'t have an opportunity to change my local settings between those dates. It sounds like everything I\'m crunching will be of no use at all. Please tell me I\'m wrong!
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