DISCUSSION of Rosetta@home Journal (4)

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David Baker
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Message 65778 - Posted: 20 Apr 2010, 4:28:55 UTC

Thank you all for your suggestions!

We could definitely use more compute power at rosetta@home right now. CASP9 is beginning in a couple of weeks, and the inhibitor design and structure prediction calculations will be vying with each other for compute time.

I don\'t know what the best way to spread the news is. Within two months our collaborators should have results testing whether the rosetta@home designed protein blocks the flu virus from entering cells (we expect it will). If/when this happens, I expect the news will travel pretty fast on its own.

Perhaps you could help spread the word in places where potential participants might look?

thanks!

David
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Sid Celery

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Message 65782 - Posted: 20 Apr 2010, 13:09:35 UTC

Thank you very much, David. The news message got picked up at Boincstats too, as I\'d hoped, so existing crunchers will see it and hopefully be curious at least.

I have a small team of a few friends who are interested, but I have access to others and it\'s about time I did some promoting. I guess I was waiting for something that would grab some attention.

If this isn\'t it, I don\'t know what ever will be. Let\'s all get to work on that now.
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Message 65805 - Posted: 23 Apr 2010, 14:59:26 UTC - in response to Message 65782.  

hello all,

Well, im a chemical engineer from portugal, i always liked the concept of computing @ home for a global project such as this one.

Even tough im a chemical engineer, my work days are spent dealing with energy but at a much different scale.

I have a (very very simple) question that came from what i just have read in Dr. Bakers posts:

Does this mean we all probably have made a very huge step towards irradicate conditions just like the common flu?

If so... thats huge! Am i right?
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Mod.Sense
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Message 65818 - Posted: 25 Apr 2010, 14:32:16 UTC - in response to Message 65805.  

hello all,

Well, im a chemical engineer from portugal, i always liked the concept of computing @ home for a global project such as this one.

Even tough im a chemical engineer, my work days are spent dealing with energy but at a much different scale.

I have a (very very simple) question that came from what i just have read in Dr. Bakers posts:

Does this mean we all probably have made a very huge step towards irradicate conditions just like the common flu?

If so... thats huge! Am i right?


More significantly (in my mind) it means (once confirmed in the lab) that we (mankind) are on the verge of being able to address viral threats that emerge in the future... before they take their toll on world population.

It is one thing to be able to develop a vaccine for something like polio or small pox... it is quite another to be able to create a vaccine BEFORE the disease impacts thousands of people\'s lives.

I am not certain if Dr. Baker would describe what they\'ve devised as a vaccine, or a treatment. But it shows the timeframe from disease outbreak to medical response is potentially shortening.

Even for the seasonal flu shots, the timeline from discovery of the latest strains likely to impact humans, to development and mass production of vaccine is long enough that the virus may change itself and rendure the shots ineffective. Shortening this outbreak to response window is significant.
Rosetta Moderator: Mod.Sense
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David Baker
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Message 65852 - Posted: 27 Apr 2010, 7:18:01 UTC

Being able to rapidly design proteins which bind to and neutralize viruses and other pathogens would definitely be a significant step towards being able to control future epidemics. However, in itself it is not a complete solution because there is a problem in making enough of the designed proteins to give to people--each person would need a lot of protein and there are lots of people!

We are also working on designing new vaccines, but the flu virus binder is not a vaccine, it is a virus blocker. vaccines work by mimicking the virus so your body makes antibodies in advance that can then neutralize the virus if you get infected later. the designed protein, if you had enough of it, should block the flu virus from getting into your cells after you had been exposed; a vaccine cannot do this.

One additional problem is that the designed protein may elicit an antibody response from people who are treated with it. in this case, it could be a one time treatment but not used chronically.

Finally-with CASP9 starting and more flu virus and other pathogen binder design projects ramping up--we are really limited by CPU time--please spread the word.

thanks!

David
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Message 65903 - Posted: 30 Apr 2010, 7:38:05 UTC

We got some good news today in an announcement by Vice President Biden:

http://arpa-e.energy.gov/NewsMedia/News/tabid/83/vw/1/ItemID/21/Default.aspx

We were funded to work with three other research groups to develop a completely new pathway for using solar energy to transform CO2 into the large molecules that the world has grown to depend on (fuels, etc)--this if successful could greatly reduce dependence on fossil fuels and contribute to removing CO2 from the atmosphere.

While the large majority of rosetta@home calculations will remain focused on biomedical problems, expect to see from time to time work units relating to design of enzymes for CO2 capture and conversion.


Way to undersell it! That\'s phenomenal news! I\'ve had the potential CO2 capture work mentioned in my profile for about a year now - it\'s great to see genuinely progressive action on the subject from the US government, and hopefully this news, along with the influenza work will bring a new crowd to R@H to supply the computers to help power the research. :D
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Aegis Maelstrom

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Message 65904 - Posted: 30 Apr 2010, 8:11:29 UTC - in response to Message 65903.  

Way to undersell it! That\'s phenomenal news! I\'ve had the potential CO2 capture work mentioned in my profile for about a year now - it\'s great to see genuinely progressive action on the subject from the US government, and hopefully this news, along with the influenza work will bring a new crowd to R@H to supply the computers to help power the research. :D

True, I will post a news item for my Polish folks - few people look up here, many cruchers prefer their team sites and fora.
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Tom Philippart
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Message 65908 - Posted: 30 Apr 2010, 18:04:37 UTC

what are those three teams rosetta/bakerlab is working with?

The project list only lists the university of washington at one time.

thanks!
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Message 65909 - Posted: 30 Apr 2010, 18:30:03 UTC

Will the energy WUs be handled by a separate application?
And if so, will users be able to choose which applications they receive WUs for?
And who owns the IP rights for what R@H might develop / discover in this sub-project?
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Profile Venturini Dario[VENETO]

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Message 65937 - Posted: 3 May 2010, 7:35:49 UTC - in response to Message 65909.  

Will the energy WUs be handled by a separate application?
And if so, will users be able to choose which applications they receive WUs for?
And who owns the IP rights for what R@H might develop / discover in this sub-project?


I support those questions. In my team alone there are at least other 5 users with the same doubts.
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David Baker
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Message 65952 - Posted: 4 May 2010, 5:50:48 UTC - in response to Message 65937.  

Will the energy WUs be handled by a separate application?
And if so, will users be able to choose which applications they receive WUs for?
And who owns the IP rights for what R@H might develop / discover in this sub-project?


I support those questions. In my team alone there are at least other 5 users with the same doubts.



Currently we do not plan to run many energy WUs on rosetta@home -- it will likely be less than 1% of the total. if later these calculations become more CPU demanding we will figure out how to give users the ability to choose. the IP rights for all of our research belong to public institutions like the university of washington.
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agge

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Message 65966 - Posted: 5 May 2010, 7:20:18 UTC

Baker lab is on a roll!
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Profile Venturini Dario[VENETO]

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Message 65968 - Posted: 5 May 2010, 8:19:51 UTC - in response to Message 65952.  

Will the energy WUs be handled by a separate application?
And if so, will users be able to choose which applications they receive WUs for?
And who owns the IP rights for what R@H might develop / discover in this sub-project?


I support those questions. In my team alone there are at least other 5 users with the same doubts.



Currently we do not plan to run many energy WUs on rosetta@home -- it will likely be less than 1% of the total. if later these calculations become more CPU demanding we will figure out how to give users the ability to choose. the IP rights for all of our research belong to public institutions like the university of washington.


Thanks a lot for the answer David, your (and the rest of the lab\'s team) participation in the forum and involvement with the users is what makes Rosetta my favourite BOINC project :)

Plus, the answer is satisfactory and reasonable :ok:
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Message 66054 - Posted: 10 May 2010, 20:15:21 UTC

Posted 10 May 2010 6:19:14 UTC
CASP9 is now in full swing and we need your help! We are being overwhelmed with targets and need as much CPU power as possible!

Hi David, help is on its way! SETI.Germany\'s BOINC Pentathlon challenge is crunching Rosetta@home as its 5th and last chosen project 05/14 - 05/19 as it so happens with 31 registered teams, see here: - http://www.setigermany.de/boinc_pentathlon/22_en_Welcome.html
I think I speak for everybody involved to say that we will be only too happy to assist.
Kind regards,
Susanne

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Message 66057 - Posted: 10 May 2010, 21:29:50 UTC

Hiho,

Thanks for the Info and Link to this Thread Susanne.

Yeah, I think the combined CPU-Power of 31 BOINC-Teams will torment the Rosetta-Servers soon... We\'ll do our best to get as much valid results back to you as possible.

cheers
aendgraend
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Message 66058 - Posted: 10 May 2010, 22:01:10 UTC - in response to Message 66054.  

Posted 10 May 2010 6:19:14 UTC
CASP9 is now in full swing and we need your help! We are being overwhelmed with targets and need as much CPU power as possible!

Hi David, help is on its way! SETI.Germany\'s BOINC Pentathlon challenge is crunching Rosetta@home as its 5th and last chosen project 05/14 - 05/19 as it so happens with 31 registered teams, see here: - http://www.setigermany.de/boinc_pentathlon/22_en_Welcome.html
I think I speak for everybody involved to say that we will be only too happy to assist.
Kind regards,
Susanne



Hiho,

Thanks for the Info and Link to this Thread Susanne.

Yeah, I think the combined CPU-Power of 31 BOINC-Teams will torment the Rosetta-Servers soon... We\'ll do our best to get as much valid results back to you as possible.

cheers
aendgraend

awesome ;)
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Michael G.R.

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Message 66166 - Posted: 17 May 2010, 3:39:26 UTC

Great to see the almost 34% increase in computing power for the project! I hope many of the new users will stick around even after CASP9 is over, as Rosetta@home is truly a great project with huge potential to help humanity.
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tralala

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Message 66176 - Posted: 17 May 2010, 18:31:26 UTC - in response to Message 66166.  

Great to see the almost 34% increase in computing power for the project! I hope many of the new users will stick around even after CASP9 is over, as Rosetta@home is truly a great project with huge potential to help humanity.


It\'s probably just a fluke.
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Message 66180 - Posted: 17 May 2010, 21:06:49 UTC

As far as I\'m concerned I\'m trying to help via Fold.it anyway...
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Sid Celery

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Message 66189 - Posted: 18 May 2010, 11:42:00 UTC - in response to Message 66176.  

Great to see the almost 34% increase in computing power for the project! I hope many of the new users will stick around even after CASP9 is over, as Rosetta@home is truly a great project with huge potential to help humanity.

It\'s probably just a fluke.

Yes, the mention of recent news on boincstats front page, the inclusion of rosetta in Seti.DE\'s pentathlon and the boost to recruitment has probably made no difference at all... (sigh)
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Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4)



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