CASP 8

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Message 51122 - Posted: 2 Feb 2008, 9:12:06 UTC

Rather then resurrect the old CASP thread, I\'ll start a new one for news from this years compo.

Dear prospective CASP8 participants,

Happy New Year :) ! Yes, it is an even year again, which means
that new CASP is coming. Wanted to let you know that the organizers
have finalized the arrangements for the conference venue. The next
CASP meeting will take place in Sardinia, Italy, in December 2008.
Please, check CASP8 web page for details:
http://www.predictioncenter.org

Also, together with CNIO, Madrid, we are organizing the next
between-CASP meeting (CASP7.5). It is going to take place in Madrid,
Spain in April 2008. The idea of the between CASP meetings is to
update the progress of structure prediction as measured by the
CASP experiments. In contrast to the full CASP meetings that are
exclusively for participants and developers, this meeting will be
open to all interested scientists. All interested please check the
meeting web page:
http://ubio.bioinfo.cnio.es/casp/index.html

--
Andriy Kryshtafovych
for CASP organizers

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Message 51496 - Posted: 19 Feb 2008, 6:43:42 UTC

One for the team really, but I did say I\'d post everything I got...
Dear prospective CASP participants,

We have an outstanding candidate for template based assessor in CASP8,
who also wishes to predict in the template free category. In the opinion
of the organizers, given this person’s integrity and experience with
CASP, this can be done without overlap or other complications. And of
course there is no question of the assessor assessing their own
predictions! And also, absolutely no chance that an assessor can assess
the data while a target is still live.

However, the candidate would like to know what the prediction community
feels about this, and so is requesting comments. If you have a view you
wish to express, please post it at the FORCASP website or send us a
message.

John Moult
for CASP organizers

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Message 51606 - Posted: 25 Feb 2008, 10:20:30 UTC

Prediction season will run from early May through early August 2008. The first prediction targets will be released not earlier than May 5, 2008; the last prediction targets will be released not later than July 18, 2008; prediction season will end not later than August 1, 2008.

According to the recommendations of the CASP7 predictors meeting, we will be releasing about 50 targets for evaluation in the human and server track and as many targets as we can for evaluation in the server-only track (including \"human and server\" targets). The human-expert groups wishing to take the challenge and predict all of the released targets (including the \"server-only\" ones) are welcome to do so but the evaluation accent will be placed on the selected targets. Subject to the availability, we will give priority to targets containing low homology domains for inclusion in the human-expert modeling experiment.
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Message 52085 - Posted: 22 Mar 2008, 22:25:34 UTC

Dear prospective CASP8 participant,

The registration for CASP8 experiment is now open.

To register for the experiment, you will need to register with the Prediction Center (PC) first (if you haven\'t done this yet). At this step we will collect the basic registration information to be used for your participation in CASP8, all subsequent CASP experiments, between-CASP initiatives, and local services. The information provided by you will not be shared with anyone outside of the CASP system.

After you register with PC and login to our website, you will be able to register for the CASP8 experiment (a separate registration form under the CASP8 menu). You will find five separate registration forms there. Please, read the registration instructions and use the appropriate form.

We ask that you register with the Prediction Center at your earliest pportunity as we plan to release future CASP8-related news mainly through our website. We recommend that you select an option \"Subscribe for Prediction Center newsletters\" as in this case you will be receiving emails every time the news are posted on our website. This functionality was just recently added to our registration form. So, if you have registered earlier, please go to \"My personal Data\" link and select this option.

Also, we ask server group leaders to register as soon as possible as we are planning on testing the connectivity with the registered CASP8 servers starting April 14, 2008. Server participation rules and the details of the dry run will be posted in the Message Board section of our website shortly (this section is available from both the Prediction Center home page and the CASP8 home page).

If you have any questions concerning the registration procedure - please let us know at casp@predictioncenter.org.

Let the CASP8 ball roll!

--
Andriy Kryshtafovych
for CASP organizers

Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 52706 - Posted: 25 Apr 2008, 12:19:42 UTC
Last modified: 25 Apr 2008, 12:20:31 UTC

Can anyone here point me in the proper direction?

I have a friend who is working at the NLM in the NIH, and has asked around about CASP, and no one seems to know anything about it.

Just what is the involvement (\"sponsored by\") of NIH/NLM in CASP? Can you pm me some contact names for my friend to follow up with?


CASP8 web page for details:
http://www.predictioncenter.org


Protein Structure Prediction Center
Sponsored by the US National Library of Medicine (NIH/NLM)
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Message 52712 - Posted: 25 Apr 2008, 16:44:55 UTC

I\'ve just asked Andriy at Davis, I\'ll report back when I get a reply.
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Message 52719 - Posted: 25 Apr 2008, 20:42:34 UTC

e-mail and telephone details sent by PM.
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Message 52830 - Posted: 2 May 2008, 3:37:50 UTC

How do you guys feel about progress/advance in a resulted quality of models generated by current Rosetta/Robetta compare to version that participated in CASP7?

Lab finished second place in \"free\" models, i.e. ones that luck any homologies information and number 5 overall. Do you think you can do better this time?

Is it safe to say, that you would secure second place in CASP7, if you successfully submitted two models that you manage to miss somehow? Score is cumulative and rest top 10 teams submitted all models... I\'m talking TM and GDT-TS based benchmarks.

TestPilot, AKA Administrator
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Message 52840 - Posted: 3 May 2008, 0:09:39 UTC

Does the project have any plans to decrease the report deadlines of workunits at the start of CASP?
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Message 52862 - Posted: 4 May 2008, 16:01:15 UTC

Gentlepeople, start your cpu\'s...

Although I have some philosophical differences with the Project staff, I will be switching all my crunchers over to Rosie 100% during CASP 8.

May 5 - Here we come !!!
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Message 52864 - Posted: 4 May 2008, 18:55:05 UTC

I\'ll definitely be doing as much crunching as possible for CASP 8. Would be awesome for Rosetta to finish first.
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Message 52867 - Posted: 5 May 2008, 3:13:30 UTC

The last CASP this project went through, there was much more fanfare and many more announcements leading up to the event. How come I don\'t see this now?
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Message 52873 - Posted: 5 May 2008, 17:17:43 UTC - in response to Message 52867.  
Last modified: 5 May 2008, 17:20:05 UTC

The last CASP this project went through, there was much more fanfare and many more announcements leading up to the event. How come I don\'t see this now?


It\'s kind of sad, since we had the huge member increase which more than doubled the project Tflops, the project became much more silent. Dr Baker still has his blog, but the project team doesn\'t reply on the forums that much anymore.

They even systematically ignore some questions, like CPU optimization/Xbox development/specific disease research.
It really depressed me because I see/saw a huge potential in this project. I\'d be glad if they finally restart talking actively to their contributors.

That\'s a reason why some people are severely holding back their crunching power to support other projects (like POEM, which also participates at CASP. (but nobody seems to mind this bad public image that has begun to spread)

CASP7 was an awesome crunching time, everybody loved it and many teams suspended other projects in order to support rosetta.

I once got an excuse for the lack of communication lately saying that the team was too budy with the user increase... Still communication is crucial in DC imo.

I hope the project can recreate the fun and enthusiasm it once had through a CASP announcement in the news section and an attempt to answer the most frequent questions (noted above)

sincerely
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Message 52880 - Posted: 6 May 2008, 12:29:12 UTC - in response to Message 52873.  

hmm...
May 05, 2008
The minirosetta application has been updated to version 1.19. This version introduces several bugfixes for our CASP8 abinitio and template-based modeling protocols. We\'ll be testing small batches of workunits this evening and tomorrow morning. For details, see this thread, and please report bugs in this thread.


Thanks for reading my post ;)
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Message 52888 - Posted: 6 May 2008, 23:02:23 UTC
Last modified: 6 May 2008, 23:13:24 UTC

2 Tom P.:

Bad image? What are you talking about? Just right after BakerLab was behind major breakthrough in the field? After they reportedly successfully applied protein designing technique to HIV vaccine? By \"successfully\" I mean some artificial proteins produced by BakerLab worked as predicted in vitro. Technology that came directly from scifi, one that eventually will let us cure virtually all diseases, including aging. We not there yet, and getting there will require understanding most if not all of the genetic pathways on molecular level, but ability to be able to design proteins/ribozymes with predefined properties in a fast and accurate manner would also be crucial. Look at published papers. The only scientific team that have comparable publication record is a Pande Group, one behind F@H. And if you would take a closer look - BakerLab wins hands down, considering that there is correlation in importance of paper and prestigiousness of journal it is published in. And no other science team behind distributed projects can come anywhere close to this two.

And, you seriously not kidding, there is projects with better feedback from scientists (better and more frequent compare to: 1, 2, 3) then R@h? Can you please point me out - I will definitely check that project(s) out.

As to Xbox 360 and PS3 - client will never happens for that platforms. The main reason is that both consoles luck fullprecision FPUs and because of that slow in most scientific calculations. PS3 have only one \"smart\" core - one that can use conditional execution, plus seven \"damn\" vector units. Xbox 360 processor somewhat better -it got three smart cores assisted by three SSE-like vector units. And actual usefulness of vector units depends on algorithm. Vector supercomputers of the past gone extinct partly because of that - and they were designed for double precision from start... But anyway, the whole point of R@h project it to improve software. And porting code to highly specialized and slow architectures is not in the best interest of project. It would take a lot of resources and what? After each new version project would need to port code again and again. It is not likely that it would be possible to keep same codebase among such a different platforms. And don\'t forget, Rosetta is written on FORTRAN. With Mini it looks like they are trying to port it on some sort of object oriented language (c++?)actually. And same go for processor specific optimizations. The main focus of project is improving algorithms behind Rosetta suit - and for that reason on the long run it is better to keep code as simple and clear as possible. Few percent of project speed increase you can squeeze from optimizations not worth it.
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Message 52892 - Posted: 7 May 2008, 5:46:51 UTC - in response to Message 52888.  
Last modified: 7 May 2008, 5:47:50 UTC

Let\'s not start a fight, let me just point out a few points:

I\'m talking about a \"bad\" public image that slowly begins to spread in the DC community, others wouldn\'t even know what POEM is.

I\'ve been reading these message boards every day since 2006 and I really noticed a slowdown in communication from the team (not Dr Baker).

CASP7 was a fun time, we knew what WUs were CASP WUs and the project team announced the major and minor events from the start to the end. If you don\'t visit these message boards regularly and only visit the startpage for the news you would barely know that rosetta participates in CASP. I remember people saying something like \"einstein can wait for his thesis to be proven, CASP and mankind cannot\".

So far I\'ve only seen approximate answers from crunchers concerning the XBOX, SSE issue and nobody was really sure, there hasn\'t been a statement from the project team in any thread.

I really appreciated it, when somebody from the team recently posted the \"help me explain the science behind rosetta\" and I actively contributed to it.

Yes, I\'ve read the papers and compared them to the F@H papers. I clearly noticed the difference and I fully support rosetta on that end.

In summary:
The DC image has become a bit worse through the fact that the most urging questions (like what are we crunching and which disease/research field is currently targeted, the thread is rarely ever updated, I check a protein data base to see what I\'m crunching) noted above. Furthermore the optimization and platform questions even get worse through the fact that there is no statement on these forums. F@H now supports PS3s, GPUs and people only see a game being born on this end.

I still like the project, but I fear and that\'s why this is intended to be a warning, that the lack of communication in this domain could harm rosetta (from a contributor count point of view)
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Message 52927 - Posted: 9 May 2008, 5:12:07 UTC - in response to Message 52892.  

Let\'s not start a fight, let me just point out a few points:

I\'m talking about a \"bad\" public image that slowly begins to spread in the DC community, others wouldn\'t even know what POEM is.

I\'ve been reading these message boards every day since 2006 and I really noticed a slowdown in communication from the team (not Dr Baker).

CASP7 was a fun time, we knew what WUs were CASP WUs and the project team announced the major and minor events from the start to the end. If you don\'t visit these message boards regularly and only visit the startpage for the news you would barely know that rosetta participates in CASP. I remember people saying something like \"einstein can wait for his thesis to be proven, CASP and mankind cannot\".

So far I\'ve only seen approximate answers from crunchers concerning the XBOX, SSE issue and nobody was really sure, there hasn\'t been a statement from the project team in any thread.

I really appreciated it, when somebody from the team recently posted the \"help me explain the science behind rosetta\" and I actively contributed to it.

Yes, I\'ve read the papers and compared them to the F@H papers. I clearly noticed the difference and I fully support rosetta on that end.

In summary:
The DC image has become a bit worse through the fact that the most urging questions (like what are we crunching and which disease/research field is currently targeted, the thread is rarely ever updated, I check a protein data base to see what I\'m crunching) noted above. Furthermore the optimization and platform questions even get worse through the fact that there is no statement on these forums. F@H now supports PS3s, GPUs and people only see a game being born on this end.

I still like the project, but I fear and that\'s why this is intended to be a warning, that the lack of communication in this domain could harm rosetta (from a contributor count point of view)


Hi Tom,

thank you for your comments. we would of course very much like to make advances on the xbox/ SSE/ gpu fronts, we are limited by the large number of problems we are tackling right now and the relatively small number of people working on the project. One of the complicating features is that even the new version of rosetta is now over 500,000 lines of code, with quite a number of different fundamental algorithms, so unlike folding@home and seti@home, where the core algorithm is quite compact, getting substantial speed increases through the GPU and SSE optimization for example are very large tasks. I spoke again with Dan Fay from the technical computing initiative at Microsoft, which has helped us out a huge amount over the past two years, about the issues you have brought up, and we will have a more complete report for you soon.

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Message 52930 - Posted: 9 May 2008, 5:36:13 UTC - in response to Message 52927.  

Thank you very much for your reply! I see other threads (number crunching section) got answers too, thanks so much for taking time to adress the vulenteers.

Now that I finally understand the problem behind, I\'ll be happy to support rosetta during CASP with some additional computers and I\'m in the process of organizing a TeAm AnandTech Rosette CASP team race!

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Message 52962 - Posted: 10 May 2008, 4:10:38 UTC - in response to Message 52930.  

Thank you very much for your reply! I see other threads (number crunching section) got answers too, thanks so much for taking time to adress the vulenteers


I\'d like to second this!
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Message 52996 - Posted: 12 May 2008, 1:24:33 UTC - in response to Message 52962.  
Last modified: 12 May 2008, 1:33:25 UTC

CASP8? great! I\'ll be switching some PCs back to help (from F@H)

A few things I\'ve noticed while reading up on some posts in this thread:

The front page mentions but doesn\'t really advertise CASP8 is back - (and in general perhaps consider making the front page more engaging/interesting?). Perhaps to refresh the project image, especially with the game bringing in new people to check out the project.

As I\'m quite familiar with it, I can update some of the comments made about F@H in this thread (and another linked thread).
1) Nvidia GPU is likely to be supported within the next year (they have commented on finally making good progress).
2) Staff and project manager posts are way higher than most other projects, usually with several posts per day in their forums. Plus an ongoing news \"blog\" from the project leader at http://folding.typepad.com/ Of course the staff at F@H is quite a bit larger and with several different areas to cover especially all their beta clients. But in any case their presence is very appreciated.
3) Because their project mix can permit them, they have both simpler projects that their PS3 and GPU clients can work on as well as more complex project handled by their SMP client (as well as their standard client).
As a final comment on F@H, I wonder if there is way for the two project to cooperate more (even if it is just such as to suggest people to people in both projects that have an ATI HD2000 or HD3000 series card to run the GPU2 folding client and have their other core working on R@H?)

I am looking forward to CASP8 ... and I do hope there are lots of updates! ;)
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