CASP7 to start in April

Message boards : Rosetta@home Science : CASP7 to start in April

To post messages, you must log in.

1 · 2 · Next

AuthorMessage
Profile Hoelder1in
Avatar

Send message
Joined: 30 Sep 05
Posts: 169
Credit: 3,915,947
RAC: 0
Message 11373 - Posted: 25 Feb 2006, 6:48:27 UTC
Last modified: 25 Feb 2006, 6:53:53 UTC

I just came across this web page, stating that the 7th biannual protein structure predicition contest will begin in April - in just a few weeks. In some of the previous CASP rounds Rosetta seems to have come out quite a bit ahead of the pack (this is what searching for 'casp' on the Rosetta@home website brings up) and with all the Rosetta@home computing resources and recent code improvements it may do even better this time around - that is assuming that the Rosetta team intends to employ Rosetta@home's formidable resources in this year's contest. Since DC seems to be all about competition for many of us, this may be another reason to shift some more of those BOINC computing resources towards Rosetta. ;-)
ID: 11373 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
BennyRop

Send message
Joined: 17 Dec 05
Posts: 555
Credit: 140,800
RAC: 0
Message 11374 - Posted: 25 Feb 2006, 9:11:09 UTC

The worst part is waiting for the results to be published, and see how the project you've contributed to did in comparison to all the others. Casp 6 ended in Sept? and the results weren't published until mid Dec. Torture waiting so long. *grin*
ID: 11374 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
David Baker
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 17 Sep 05
Posts: 705
Credit: 559,847
RAC: 0
Message 11439 - Posted: 27 Feb 2006, 3:11:41 UTC - in response to Message 11373.  

I just came across this web page, stating that the 7th biannual protein structure predicition contest will begin in April - in just a few weeks. In some of the previous CASP rounds Rosetta seems to have come out quite a bit ahead of the pack (this is what searching for 'casp' on the Rosetta@home website brings up) and with all the Rosetta@home computing resources and recent code improvements it may do even better this time around - that is assuming that the Rosetta team intends to employ Rosetta@home's formidable resources in this year's contest. Since DC seems to be all about competition for many of us, this may be another reason to shift some more of those BOINC computing resources towards Rosetta. ;-)


Yes--CASP7 is starting soon, and yes, rosetta@home will be focused on casp once it starts. our current tests are aimed at improving the protocol we will use in casp. (we also want to resolve all the current problems/errors before casp starts). I'll keep you posted as the time gets closer.

ID: 11439 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Hoelder1in
Avatar

Send message
Joined: 30 Sep 05
Posts: 169
Credit: 3,915,947
RAC: 0
Message 12745 - Posted: 28 Mar 2006, 4:57:22 UTC
Last modified: 28 Mar 2006, 5:07:19 UTC

I wanted to share with you this figure which I came across on the Predictor@home website (section scientific update/current progress). It shows how Rosetta and Predictor were doing in the most recent (2004) protein structure prediction contest CASP6, both with respect to each other and in comparison to the mean of all competitors. This is how the figure has to be read (I think): the blue bars represent the mean score for each target protein (higher is better). The upper end of the green lines is the best result obtained for each protein, the lower end of the green line, marked in red is the Predictor result and the orange triangle corresponds to the Rosetta result. One can see that Rosetta outperforms Predictor by a wide margin. Rosetta across the board did significantly better than average and in some cases produced the best result (note that this is vintage 2004 Rosetta, not the one including the new Rosetta@home improvements that will be used for CASP7).

I think the Predictor@home team has to be given credit for openly conceding on their web page that their current algorithm does much worse than Rosetta. They even included a link to the Baker Lab Science paper from last fall. They also state on their web page that they intend to replace their current algorithm with a new one (based on PROSPECTOR/TASSER), specifically mentioning their poor results with respect to Rosetta to justify this move.
ID: 12745 · Rating: 2 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile dcdc

Send message
Joined: 3 Nov 05
Posts: 1676
Credit: 88,500,013
RAC: 37,284
Message 14764 - Posted: 27 Apr 2006, 16:06:01 UTC

Is everything on target for the CASP7 start (8th April I think)?

Also, should we be trying to get any temporary increases in production around then? I think there's probably quite a lot of people that will switch from other projects for the duration of this - should we be asking for extra help from the 8th?

cheers
Danny
ID: 14764 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sean Kiely

Send message
Joined: 31 Jan 06
Posts: 63
Credit: 43,992
RAC: 0
Message 14766 - Posted: 27 Apr 2006, 16:15:49 UTC - in response to Message 14764.  

David Baker gave us a brief update on the preparations for CASP7 in his latest post on the "David Baker's Rosetta@home journal" thread. Check it out.

Sean

Is everything on target for the CASP7 start (8th April I think)?

Also, should we be trying to get any temporary increases in production around then? I think there's probably quite a lot of people that will switch from other projects for the duration of this - should we be asking for extra help from the 8th?

cheers
Danny


ID: 14766 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
tralala

Send message
Joined: 8 Apr 06
Posts: 376
Credit: 581,806
RAC: 0
Message 14771 - Posted: 27 Apr 2006, 16:44:53 UTC - in response to Message 14764.  

Is everything on target for the CASP7 start (8th April I think)?

Also, should we be trying to get any temporary increases in production around then? I think there's probably quite a lot of people that will switch from other projects for the duration of this - should we be asking for extra help from the 8th?
cheers
Danny


CASP7 lasts from May to August - four full months. Probably too long to ask for complete switching for that time to Rosetta. Nevertheless any help even for a few weeks with more power would be good. In fact I think one might motivate quite a lot of peoples to switch over for some time to be part of the competition (and probably on the winning team). I hope David will give us a detailed list of which proteins are to be predicted and untill which deadline and how many models he wants for each protein. With this information we could make a nice short-term-Roadmap and put a progress chart somewhere. People like progress charts. ;-)
ID: 14771 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile rbpeake

Send message
Joined: 25 Sep 05
Posts: 168
Credit: 247,828
RAC: 0
Message 14775 - Posted: 27 Apr 2006, 17:31:25 UTC - in response to Message 14771.  

People like progress charts. ;-)

I agree! I love the progress chart on Einstein@home for example. A progress chart is a great idea! :)

Regards,
Bob P.
ID: 14775 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Robinski

Send message
Joined: 7 Mar 06
Posts: 51
Credit: 85,383
RAC: 0
Message 14796 - Posted: 27 Apr 2006, 21:44:04 UTC - in response to Message 14771.  

Is everything on target for the CASP7 start (8th April I think)?

Also, should we be trying to get any temporary increases in production around then? I think there's probably quite a lot of people that will switch from other projects for the duration of this - should we be asking for extra help from the 8th?
cheers
Danny


CASP7 lasts from May to August - four full months. Probably too long to ask for complete switching for that time to Rosetta. Nevertheless any help even for a few weeks with more power would be good. In fact I think one might motivate quite a lot of peoples to switch over for some time to be part of the competition (and probably on the winning team). I hope David will give us a detailed list of which proteins are to be predicted and untill which deadline and how many models he wants for each protein. With this information we could make a nice short-term-Roadmap and put a progress chart somewhere. People like progress charts. ;-)


Would be great if some Roadmap and charts are available!!!
Member of the Dutch Power Cows

Trying to get the world on IPv6, do you have it? check here: IPv6.RHarmsen.nl
ID: 14796 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Bin Qian

Send message
Joined: 13 Jul 05
Posts: 33
Credit: 36,897
RAC: 0
Message 14831 - Posted: 28 Apr 2006, 7:28:37 UTC - in response to Message 14796.  


We will definitely have a thread posting CASP7 target charts as we get them. On May 8th we will get the first target!

People like progress charts. ;-)

Would be great if some Roadmap and charts are available!!!


ID: 14831 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
tralala

Send message
Joined: 8 Apr 06
Posts: 376
Credit: 581,806
RAC: 0
Message 14846 - Posted: 28 Apr 2006, 9:48:59 UTC - in response to Message 14831.  


We will definitely have a thread posting CASP7 target charts as we get them. On May 8th we will get the first target!

People like progress charts. ;-)

Would be great if some Roadmap and charts are available!!!



Will you know on May 8th how many targets you are going to tackle with Rosetta@Home? Will you be able to tell a rough estimate how much models/target you would like to get? Could you from time to time update the information how many models/target you already got?

With this info one could set up a general CASP7-Chart which a single percentage done number. Such a reduction is great in getting people throwing in ressources to bring the "percentage done" number up.
ID: 14846 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Bin Qian

Send message
Joined: 13 Jul 05
Posts: 33
Credit: 36,897
RAC: 0
Message 14926 - Posted: 28 Apr 2006, 23:46:25 UTC - in response to Message 14846.  
Last modified: 28 Apr 2006, 23:51:09 UTC

In the previous CASPs, the targets were released throughout the period of the competition, with due dates usually several weeks after the release date.

We will post the sequences and related information of the CASP7 targets as we receive them, and give you estimation of the number of decoys we request and the number of decoys returned.

By the way I just posted casp6 target list in another thread. The "Entry date" is the target release date, and the "Expiry-date" is the target due date.


We will definitely have a thread posting CASP7 target charts as we get them. On May 8th we will get the first target!

People like progress charts. ;-)

Would be great if some Roadmap and charts are available!!!



Will you know on May 8th how many targets you are going to tackle with Rosetta@Home? Will you be able to tell a rough estimate how much models/target you would like to get? Could you from time to time update the information how many models/target you already got?

With this info one could set up a general CASP7-Chart which a single percentage done number. Such a reduction is great in getting people throwing in ressources to bring the "percentage done" number up.


ID: 14926 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Feet1st
Avatar

Send message
Joined: 30 Dec 05
Posts: 1755
Credit: 4,154,245
RAC: 1,629
Message 15199 - Posted: 1 May 2006, 18:08:19 UTC

Keep up to date with CASP7 on their NEWS page.
Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
ID: 15199 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
NorthVanMike

Send message
Joined: 30 Nov 05
Posts: 3
Credit: 43,556
RAC: 0
Message 15647 - Posted: 7 May 2006, 15:06:08 UTC

could they not pick any hotter months of the year for this? how many of us shut down during the summer, or at least know people that do? just plain stupid.
ID: 15647 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Snake Doctor
Avatar

Send message
Joined: 17 Sep 05
Posts: 182
Credit: 6,401,938
RAC: 0
Message 15650 - Posted: 7 May 2006, 15:36:32 UTC - in response to Message 15647.  

could they not pick any hotter months of the year for this? how many of us shut down during the summer, or at least know people that do? just plain stupid.


rosetta did not pick the dates for this. It is done by international agreement. Probably since most of the research is done at universities, they pick the summer because the research teams are not busy teaching at that time.
ID: 15650 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
NorthVanMike

Send message
Joined: 30 Nov 05
Posts: 3
Credit: 43,556
RAC: 0
Message 15653 - Posted: 7 May 2006, 15:46:37 UTC - in response to Message 15650.  


rosetta did not pick the dates for this. It is done by international agreement. Probably since most of the research is done at universities, they pick the summer because the research teams are not busy teaching at that time.

i realize that. your guess may have validity, but my guess is that climate was never even considered during the planning process.
ID: 15653 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Snake Doctor
Avatar

Send message
Joined: 17 Sep 05
Posts: 182
Credit: 6,401,938
RAC: 0
Message 15665 - Posted: 7 May 2006, 22:48:21 UTC - in response to Message 15653.  


rosetta did not pick the dates for this. It is done by international agreement. Probably since most of the research is done at universities, they pick the summer because the research teams are not busy teaching at that time.

i realize that. your guess may have validity, but my guess is that climate was never even considered during the planning process.



Well don't forget we are looking at this from a rather northern hemishpere centric point of view. CASP7 will run all WINTER in the Southern hemisphere.
ID: 15665 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile rbpeake

Send message
Joined: 25 Sep 05
Posts: 168
Credit: 247,828
RAC: 0
Message 15666 - Posted: 7 May 2006, 22:52:03 UTC - in response to Message 15199.  

Keep up to date with CASP7 on their NEWS page.

I was also able to sign up for their e-mail newsletter, with my affiliation I listed as being an "Interested Observer" and my source for learning about CASP as "Rosetta@home." :)



Regards,
Bob P.
ID: 15666 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Robinski

Send message
Joined: 7 Mar 06
Posts: 51
Credit: 85,383
RAC: 0
Message 15824 - Posted: 10 May 2006, 19:51:48 UTC

It looks like the first target has been set see: http://predictioncenter.genomecenter.ucdavis.edu/casp7/targets/cgi/casp7-view.cgi
Member of the Dutch Power Cows

Trying to get the world on IPv6, do you have it? check here: IPv6.RHarmsen.nl
ID: 15824 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile rbpeake

Send message
Joined: 25 Sep 05
Posts: 168
Credit: 247,828
RAC: 0
Message 15825 - Posted: 10 May 2006, 19:54:46 UTC - in response to Message 15824.  
Last modified: 10 May 2006, 19:55:45 UTC

It looks like the first target has been set see: http://predictioncenter.genomecenter.ucdavis.edu/casp7/targets/cgi/casp7-view.cgi

When can we expect to see this crunching on our machines? :)
Regards,
Bob P.
ID: 15825 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
1 · 2 · Next

Message boards : Rosetta@home Science : CASP7 to start in April



©2021 University of Washington
https://www.bakerlab.org