DISCUSSION of Rosetta@home Journal (4)

Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4)

To post messages, you must log in.

Previous · 1 · 2 · 3 · 4 · 5 · 6 · 7 · 8 · Next

AuthorMessage
agge

Send message
Joined: 14 Nov 06
Posts: 63
Credit: 432,341
RAC: 0
Message 63384 - Posted: 17 Sep 2009, 10:32:55 UTC

I\'m not sure what to put as a heading for the latest post in the twitter feed, any suggestions?
ID: 63384 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile dgnuff
Avatar

Send message
Joined: 1 Nov 05
Posts: 347
Credit: 24,023,248
RAC: 0
Message 63431 - Posted: 23 Sep 2009, 8:12:27 UTC

Without any knowledge of previous headings on Twitter, I\'m going to suggest the following:

\"Fine tuning Rosetta\'s energy function\"
ID: 63431 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Michael G.R.

Send message
Joined: 11 Nov 05
Posts: 264
Credit: 10,087,366
RAC: 4,872
Message 63857 - Posted: 27 Oct 2009, 18:00:57 UTC

It\'s been 40 days since the last update. What\'s going on? Working on anything new and exciting?
ID: 63857 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 689
Credit: 9,329,683
RAC: 4,612
Message 63868 - Posted: 28 Oct 2009, 4:52:32 UTC - in response to Message 63857.  
Last modified: 28 Oct 2009, 5:03:11 UTC

It\'s been 40 days since the last update. What\'s going on? Working on anything new and exciting?


Looks like the project team is considerably less responsive than they were back in 2006; I recently caught up on reading posts from that year.

They might be planning to add a Nvidia GPU application, and therefore attending the GPUGRID meeting in or near Barcelona, Spain. Don\'t expect any GPU version of minirosetta to run much faster on a GPU than on a CPU very soon, though; that would take a major rewrite to allow each GPU core to run with much less a share of memory than the current minirosetta application, even if Nvidia\'s plans to make more compilers available soon allow the project team to avoid rewriting the new version in an entirely different computer language.

I\'ve already found a few articles saying that at least one copper-binding protein is very relevant to Alzheimer\'s research, and posted links to them in a separate thread, so there could be some resulting activity in the background.
ID: 63868 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Michael G.R.

Send message
Joined: 11 Nov 05
Posts: 264
Credit: 10,087,366
RAC: 4,872
Message 63871 - Posted: 28 Oct 2009, 17:26:13 UTC - in response to Message 63868.  

They might be planning to add a Nvidia GPU application, and therefore attending the GPUGRID meeting in or near Barcelona, Spain. Don\'t expect any GPU version of minirosetta to run much faster on a GPU than on a CPU very soon, though; that would take a major rewrite to allow each GPU core to run with much less a share of memory than the current minirosetta application, even if Nvidia\'s plans to make more compilers available soon allow the project team to avoid rewriting the new version in an entirely different computer language.


I kind of doubt it.

From what I know, Rosetta@home takes too much RAM for current GPUs. Though I suppose that it would be possible to only run multiple instances of very small proteins on a GPU to keep the RAM requirements low while taking advantage of the many cores, but I\'m not sure if such small proteins would be useful scientifically.

In any case, every time the project has been asked about GPUs they said that it\'s not in the plans for now.


ID: 63871 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 689
Credit: 9,329,683
RAC: 4,612
Message 63874 - Posted: 29 Oct 2009, 1:20:48 UTC - in response to Message 63871.  
Last modified: 29 Oct 2009, 1:22:29 UTC

I kind of doubt it.

From what I know, Rosetta@home takes too much RAM for current GPUs. Though I suppose that it would be possible to only run multiple instances of very small proteins on a GPU to keep the RAM requirements low while taking advantage of the many cores, but I\'m not sure if such small proteins would be useful scientifically.

In any case, every time the project has been asked about GPUs they said that it\'s not in the plans for now.


Note that if they DON\'T try to use all the GPU cores at once, they should have much less trouble fitting it into graphics memory. However, this idea has at least one problem: Much less speedup than if all the GPU cores could be used.

It does not, however, have a problem with proteins of the size currently handled in the CPU application.

It would, however, probably mean that my 9800 GT Nvidia card with 1 GB graphics memory would not achieve even twice the speed of the CPU minirosetta application.
ID: 63874 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Michael G.R.

Send message
Joined: 11 Nov 05
Posts: 264
Credit: 10,087,366
RAC: 4,872
Message 63939 - Posted: 3 Nov 2009, 16:58:25 UTC

So we can\'t quantify our progress by giving you a % complete. Instead, the project\'s contributions and progress can be evaluated by the many scientific publications it has produced, some of which I\'ve tried to summarize in these posts. (the current issue of Nature for example has the article I described below on designing new enzymes to ultimately repair disease causing mutations).


Thank you for the update Dr. Baker.

Speaking of publications, this page:

http://boinc.bakerlab.org/rosetta/rah_publications.php

Doesn\'t include anything from 2009. Will it be updated to include the latest publications?
ID: 63939 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Sean Kiely

Send message
Joined: 31 Jan 06
Posts: 62
Credit: 43,992
RAC: 0
Message 63944 - Posted: 3 Nov 2009, 21:07:30 UTC

Here\'s a link to the (free) editor\'s summary of the article in \"Nature\" that Dr. Baker mentioned.

http://www.nature.com/nature/journal/v461/n7268/edsumm/e091029-15.html

Please note that the first author listed on the article is Summer B. Thyme, which makes me question the reliability of the judgment of certain parents.
ID: 63944 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile rochester new york
Avatar

Send message
Joined: 2 Jul 06
Posts: 2738
Credit: 1,698,169
RAC: 277
Message 63948 - Posted: 3 Nov 2009, 23:56:19 UTC

ID: 63948 · Rating: 0 · rate: Rate + / Rate - Report as offensive
David Baker
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 17 Sep 05
Posts: 705
Credit: 559,847
RAC: 0
Message 63950 - Posted: 4 Nov 2009, 5:27:38 UTC - in response to Message 63948.  

excuse me if this was already posted somewhere http://online.wsj.com/article/SB10001424052748703816204574483481567116994.html



Thanks--I hadn\'t seen that!
ID: 63950 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Otto

Send message
Joined: 6 Apr 07
Posts: 27
Credit: 3,141,606
RAC: 4,327
Message 64062 - Posted: 17 Nov 2009, 6:07:59 UTC

I sometimes get the impression that real, actual, concrete progress in medicine - and energy, for that matter - requires infinite computing power and/or infinite money, neither of which are obtainable. Since these barriers cannot be broken, progress is constrained by the level of intelligence which is in itself limited by biology (talk about irony!). But what\'s worse, progress in IT is not good enough all alone because all the data need to be analysed... but there is too much data for a human being or even a group of human beings. I\'m pessimistic about the possibility of great or even any progress without advanced artificial intelligence.
ID: 64062 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Michael G.R.

Send message
Joined: 11 Nov 05
Posts: 264
Credit: 10,087,366
RAC: 4,872
Message 64069 - Posted: 17 Nov 2009, 19:08:22 UTC - in response to Message 63939.  

Thank you for the update Dr. Baker.

Speaking of publications, this page:

http://boinc.bakerlab.org/rosetta/rah_publications.php

Doesn\'t include anything from 2009. Will it be updated to include the latest publications?


It seems like the page was updated with 2009 papers since I wrote. Thanks to whoever updated it!
ID: 64069 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 979
Credit: 21,591,898
RAC: 14,660
Message 65713 - Posted: 9 Apr 2010, 10:54:42 UTC

Does this mean what I think it means?

I think we got another \'wow\'.
ID: 65713 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Aegis Maelstrom

Send message
Joined: 29 Oct 08
Posts: 61
Credit: 1,758,491
RAC: 4,447
Message 65714 - Posted: 9 Apr 2010, 10:59:28 UTC - in response to Message 65713.  

Does this mean what I think it means?

I think we got another \'wow\'.


Congratulations for the whole team and keep us informed! :)
ID: 65714 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Sean Kiely

Send message
Joined: 31 Jan 06
Posts: 62
Credit: 43,992
RAC: 0
Message 65716 - Posted: 9 Apr 2010, 19:50:12 UTC

Dr. Baker, can you estimate when more details will be published?
ID: 65716 · Rating: 0 · rate: Rate + / Rate - Report as offensive
David Baker
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 17 Sep 05
Posts: 705
Credit: 559,847
RAC: 0
Message 65727 - Posted: 11 Apr 2010, 2:41:04 UTC

Hi Sean,

We are doing a series of tests and control experiments in my lab in the next 2-3 weeks to rule out various possible artifacts. If, as we expect, the design passes with flying colors, we will send it to Scripps research institute where the ability of the design to neutralize the virus in cell based tests and the extent to which the design neutralizes different strains of virus will be measured. I would expect we would know the results of this in several months. We will also work to solve the crystal structure of the design bound to the virus to confirm the design binding mode. This hopefully will not take more than a few months as well.

I will keep all of you posted in my journal about the results from these experiments. I am very optimistic, but one should be cautious about getting to excited too early about results like these--there are very many places where things can go wrong just with the biochemistry, and after this there are very many steps to actually make a protein into a drug--this is why there are so few new drugs for curing diseases being discovered.

For those of you who would like to try your hand at improving designed binders to the influenza virus, we are now posting virus inhibitor design challenges on foldit.

David
ID: 65727 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 979
Credit: 21,591,898
RAC: 14,660
Message 65728 - Posted: 11 Apr 2010, 3:26:08 UTC - in response to Message 65727.  

I am very optimistic, but one should be cautious about getting to excited too early about results like these--there are very many places where things can go wrong just with the biochemistry, and after this there are very many steps to actually make a protein into a drug--this is why there are so few new drugs for curing diseases being discovered.

Far be it for me to contradict you(!) but you did say it was an \"extremely exciting result\" and I kind of trust you, of all people, to be able to tell the difference between an exciting result and an \"extremely\" exciting result ;)

A successful drug is obviously #1, but making a step change toward an exciting result is also pretty good news and at the very worst, if it doesn\'t turn out successful at all, you may be able to work out just where it went \'wrong\' and fine-tune your methodology.

So if it\'s ok with you I\'ll be getting a little more excited than I ought to.

Out of casual interest, has there ever been a breakthrough that\'s had a direct link to discoveries from a distributed computing project? Or is that too vague a question or is the process too multi-sourced for anyone to be able to point at something and say \"that\'s when it happened\"?
ID: 65728 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Profile dcdc

Send message
Joined: 3 Nov 05
Posts: 1617
Credit: 62,914,447
RAC: 30,065
Message 65769 - Posted: 19 Apr 2010, 12:46:49 UTC

The latest news is awesome. I don\'t want to jump the gun and know there\'s a great deal of clinical trialling to be done it the binding proves successful, but getting this far is amazing.

Hopefully, this will not only be successful, but will let more people know about how they can help such research just by an install-and-forget program on their computers...
ID: 65769 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 979
Credit: 21,591,898
RAC: 14,660
Message 65776 - Posted: 20 Apr 2010, 0:39:21 UTC
Last modified: 20 Apr 2010, 0:48:22 UTC

Still not excited? Me neither.

(I\'m such a bad liar...)

Edit: Switching my resource priority even more to Rosetta.

Editx2: At what point is it worth mentioning this as news on the Rosetta front page? And does that transfer over to places like Boincstats frontpage so people get to read about something a little more important than downtime?

Little news from here gets propogated to where people might be interested to contribute more. Even if nothing comes of this, the potential for a major result is significant enough to be called real news. Don\'t you think?

Take a chance and do yourselves a favour - please.
ID: 65776 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Nickhorsky

Send message
Joined: 11 Mar 07
Posts: 10
Credit: 134,214
RAC: 0
Message 65777 - Posted: 20 Apr 2010, 3:30:14 UTC

Get a little more proactive on spreading the news and bionic users will switch.
Beats looking for noise from space! Personally SETI is a waste of power. Once we solve our problems here on earth we can then look for little green people.
ID: 65777 · Rating: 0 · rate: Rate + / Rate - Report as offensive
Previous · 1 · 2 · 3 · 4 · 5 · 6 · 7 · 8 · Next

Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (4)



©2019 University of Washington
http://www.bakerlab.org