DISCUSSION of Rosetta@home Journal (3)

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Profile Hoelder1in
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Message 51903 - Posted: 12 Mar 2008, 7:12:41 UTC
Last modified: 12 Mar 2008, 7:27:33 UTC

Technology Review article on Baker lab research: Enzymes built from scratch

Check out the above Technology Review article discribing the recent successes of the Baker lab with engineering novel enzymes that has just been published in the journal Science (see David Baker's post in the Rosetta@home journal) - in my previous post I had erroneously assumed that this new research would be published in Nature (sorry for the misinformation).
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Message 51905 - Posted: 12 Mar 2008, 13:27:34 UTC

awesome :D
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Message 51910 - Posted: 12 Mar 2008, 14:24:48 UTC

That's really great - thanks for posting it, and thanks dcdc for putting the link back to the project. All good stuff.
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David Baker
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Message 51966 - Posted: 15 Mar 2008, 17:35:41 UTC - in response to Message 51903.  

Technology Review article on Baker lab research: Enzymes built from scratch

Check out the above Technology Review article discribing the recent successes of the Baker lab with engineering novel enzymes that has just been published in the journal Science (see David Baker's post in the Rosetta@home journal) - in my previous post I had erroneously assumed that this new research would be published in Nature (sorry for the misinformation).



Thanks for finding and posting this! (I would never have seen it). It would be great if a volunteer could update the list at

https://boinc.bakerlab.org/rah_articles.php

which is almost 2 years out of date now. We talked to a number of reporters about the enzyme design work, and I think there was some press on the Nature article on structure prediction last fall as well. perhaps surprisingly, we often don't get to see the final versions of the pieces, or notified when they come out, and because we are usually swamped with other things we often miss them entirely.


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Message 52035 - Posted: 20 Mar 2008, 6:20:06 UTC
Last modified: 20 Mar 2008, 6:48:03 UTC

Here is another link describing the enzyme related work that has just been published in Nature (see David Baker's post in the Rosetta@home journal):

Howard Hughes Medical Institute Reserach News (March 20): Building Enzymes from Scratch

The article specifically mentions the help from the 190,000 member Rosetta@home community!

PS: See also Designer Enzymes created by chemists at UCLA, U.of Washington (UCLA press release)
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Message 52075 - Posted: 22 Mar 2008, 11:46:07 UTC

Here's a link to a graphic of one of the designed enzymes (as given on the Nature page): http://molvis.sdsc.edu/fgij/fg.htm?mol=2rkx
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Message 52258 - Posted: 5 Apr 2008, 2:08:50 UTC
Last modified: 5 Apr 2008, 2:35:43 UTC

If you are interested in taking up Dr. Baker's request to add Ralph (the Rosetta "alpha" project) to your machine, you can simply add a second project in the BOINC Manager, the project URL for Ralph is:
http://ralph.bakerlab.org/

Once you set up an account on Ralph, you can adjust your WU runtime preference and resource shares from the "Your Account" link on the left of the Ralph homepage, which is the same URL as above, or from the "Participants" link at the top of the Ralph message boards.

[edit]
I should also point out that Ralph does not always have work available. They only crete work there when there is something specific to be tested. So you won't want Ralph to be your only BOINC project. The BOINC manager will take care of getting work when it is available, and getting it done before the due dates.

Since feedback on testing on Ralph is needed in order to bring new work and new applications to Rosetta, the deadline there is generally 72hrs (3 days) from the time of the task's download (Rosetta's deadline is generally 10 days). Other then that, it basically runs and works just like Rosetta.
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Message 52292 - Posted: 6 Apr 2008, 4:03:31 UTC

Happy to learn that Rosetta will be updated for CASP8. Will it be the traditional code or the new Minirosetta? Wouldn't it make more sense to put all new efforts into the new code, or is it not stable enough for that yet?

Either way, I'm looking forward to seeing the results of CASP 8.
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Message 52337 - Posted: 9 Apr 2008, 5:57:07 UTC - in response to Message 52292.  

Happy to learn that Rosetta will be updated for CASP8. Will it be the traditional code or the new Minirosetta? Wouldn't it make more sense to put all new efforts into the new code, or is it not stable enough for that yet?

Either way, I'm looking forward to seeing the results of CASP 8.



Yes, we are putting almost all of our efforts into the new code, and we have a lot of testing to do in the next three weeks!
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Message 52417 - Posted: 13 Apr 2008, 15:53:12 UTC - in response to Message 52337.  

Happy to learn that Rosetta will be updated for CASP8. Will it be the traditional code or the new Minirosetta? Wouldn't it make more sense to put all new efforts into the new code, or is it not stable enough for that yet?

Either way, I'm looking forward to seeing the results of CASP 8.



Yes, we are putting almost all of our efforts into the new code, and we have a lot of testing to do in the next three weeks!

Any chance of including SSE/SSE2/SSE3/... optimizations?
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Message 52645 - Posted: 21 Apr 2008, 5:33:20 UTC - in response to Message 52417.  

Hi,
I'm a member of the team BOINC.Italy; we're curious to know if the Rosetta's game (Fold it!) sole purpose is having fun or if it also has scientific goals.
How does your research advance from the protein folded by the users?
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Message 52657 - Posted: 21 Apr 2008, 21:27:39 UTC

Just an idea for anyone moving any machines over to Ralph as per DB's request:

i recommend running Ralph in a VirtualPC, with rosetta running on the real OS. That way, if the Ralph application crashes, the Rosetta thread(s) will pick up the slack and no cycles will be wasted...

MS VirtualPC 2007 download
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Message 52780 - Posted: 28 Apr 2008, 20:54:12 UTC

On the updated "Articles about Rosetta and Rosetta@home" page (https://boinc.bakerlab.org/rosetta/rah_articles.php), the link to "RCSB Protein Data Bank Molecule of the Month: Designer Proteins" (http://www.rcsb.org/pdb/molecules/pdb70_1.html) is dead. Here is a working URL: http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb70_1.html.
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Message 52781 - Posted: 29 Apr 2008, 0:54:52 UTC - in response to Message 52780.  

On the updated "Articles about Rosetta and Rosetta@home" page (https://boinc.bakerlab.org/rosetta/rah_articles.php), the link to "RCSB Protein Data Bank Molecule of the Month: Designer Proteins" (http://www.rcsb.org/pdb/molecules/pdb70_1.html) is dead. Here is a working URL: http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb70_1.html.


Thanks, incorporated. -KEL

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David Baker
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Message 52797 - Posted: 30 Apr 2008, 5:17:40 UTC - in response to Message 52645.  

Hi,
I'm a member of the team BOINC.Italy; we're curious to know if the Rosetta's game (Fold it!) sole purpose is having fun or if it also has scientific goals.
How does your research advance from the protein folded by the users?


Fold it has scientific goals. the most exciting question is whether people working together with their computers can solve hard problems in biomedical research that computers alone cannnot solve. the problems we will be sending out as puzzles for the game will be current research problems my group is working on--we will be extremely interested in the best solutions people come up with!

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Message 53019 - Posted: 12 May 2008, 20:32:05 UTC

"we are keeping our fingers crossed about our servers ever since fold it made it onto slash dot yesterday afternoon; so far we have been able to keep running most of the time although there have been some slowdowns."

Be prepared for signifigant further sign-ups. . . not only has slashdot.org posted about FoldIt, but Tycho at penny-arcade.com has linked to the game site as well. Brace yourselves!
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Message 53024 - Posted: 12 May 2008, 22:34:05 UTC

David,

Thanks for your post regarding CASP8 on May 12. Great information.

I would like to recommend though, that this particular post be copied to the front page news section as well. If added to the news section, it should then also be disseminated to all the various stats sites, as you may already know. Thereby, hopefully, encouraging others to join in the CASP fun. :-)

Anyway, just a thought.

Joel

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Message 53033 - Posted: 13 May 2008, 13:35:35 UTC - in response to Message 53024.  
Last modified: 13 May 2008, 13:36:29 UTC

David,

Thanks for your post regarding CASP8 on May 12. Great information.

I would like to recommend though, that this particular post be copied to the front page news section as well. If added to the news section, it should then also be disseminated to all the various stats sites, as you may already know. Thereby, hopefully, encouraging others to join in the CASP fun. :-)

Anyway, just a thought.

Joel

A good Thought indeed. I am (like probably many others too) connected to many projects currently so my main source for project news is the stats sites front page which gathers all the news to a one page window. Many times this news page has led me to, for example, change my resource share on projects because I have noticed that something important is going on in some project (team race, target goal etc.)
Informing on the front page gives the project A LOT of attention and therefore increase the computing power in important events such as CASP.
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Message 53094 - Posted: 16 May 2008, 21:37:16 UTC

Will CASP 8 be on mini 119 and regular research be on beta 596? (Just curious to know what I am crunching - I will crunch both.)

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Message 53097 - Posted: 17 May 2008, 5:49:32 UTC - in response to Message 53094.  

Will CASP 8 be on mini 119 and regular research be on beta 596? (Just curious to know what I am crunching - I will crunch both.)



we will continue to run both mini and regular rosetta for the next month or two. we are still finding minor problems in mini; for example you aren't seeing many mini jobs right now because of a memory leak that was causing problems for people with long work unit settings (> 18 hours). we are frantically trying to fix this as we have CASP8 targets to run. We just enlisted Rom to help us, and hopefully we will be sending out casp8 jobs with mini on Monday.
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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3)



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