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World Community Grid Forums
Category: Retired Forums
Forum: The New Members Forum [Read Only]
Thread: Just Wonderin' |
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Thread Status: Active Total posts in this thread: 6
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I gots a buncha questions... hopefully someone from WCG reads these questions from us compu-data newbies.
1. When I watch the screensaver, I see all the pretty-colored molecules (atoms?) all rotating on an axis... BUT... every once in awhile the animation will jump from a basketball-shaped glob of protein stuff to a little stringy doohickey... 1b. Just curious... how do the data sets process? Is my computer processing several discrete partial data sets at random... to be recompiled with other partial sets processed by other WCG participants? OR are the full data sets just that small? 2. Also, the process is "protein folding"... however, rotating on an axis doesn't constitute "folding" (to make a paper airplane, one does not rotate a piece of paper in mid-air). :-) How does the animation jibe with "folding"? 3a. It would be nice if someone would design some settings for the screen saver... maybe a few different skins or an option to go full-screen... (my dog barks her fool head off at the movement of the half-window around the screen with the current config...)  3b. (Still much happier with this project than I was with SETI... although they had a nice config where you could track the specific part of the sky for each data set...) How about adding something similarly educational about the specific data set that one is currently processing on WCG? (I have already clicked around the "generic" pages that the client software allows...) PERSONAL NOTE: (Get that data analysis done quickly, please ... I have Diabetes and sure would like to see a "cure" before I croak or lose any more of my foot/leg from this insidious disease!) |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Well, earlier posts have touched on questions 1 and 2. Every once in a while, a snapshot is taken of the actual configuration of the protein molecule being tested on your computer. This is converted into a 3D schematic which is then rotated in the view of your application screen / screen saver. This allows you to see how it looks from various angles yet takes minimal CPU time. Almost all your CPU time is devoted to trial configurations of the protein that are not displayed on your screen. If the screen saver annoys your dog, you can change it or get rid of it. It is just an optional toy to keep people interested.
Question 1b has not been definitively answered. If you read the news release on the Institute for Systems Biology site at http://www.systemsbiology.org you will see that they have split up the work into millions of Work Units. Since the .pdb file in the World Community Grid directory is named like a standard protein base file, I am assuming they have another file in the download that assigns a range of variables for testing, but who knows. This is a startup, we are working as crunchers for computer systems people who are trying to develop a system to feed the Institute for Systems Biology while also [Laugh Out Loud] trying to deal with the public. The worst kind of startup! So much easier to deal with other businesses. The Institute for Systems Biology people will hopefully answer some of our specific questions someday. In the mean time, keep on crunching!! |
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joatmon
Senior Cruncher Joined: Nov 17, 2004 Post Count: 185 Status: Offline Project Badges: 
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while the screen saver is interesting to watch, it is not required. It takes up processing power (read somewhere here 25-30%?) that could be used to fold proteins fasters, so if you change your screensaver to something simple that does not use the CPU (mine is "blank screen") then when your computer is idle, it uses all the CPU to crunch the workunit. If you still want to watch the protein fold some, you can either switch back to the screensaver for a while or just open up the WCG agent and hit the "i" button.
Of course, if you have the preference set to only work in screensaver mode, and then set a different screensaver, then it will never crunch any of the work unit. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
THANK YOU BOTH VERY MUCH for taking the time to answer my questions... I really appreciate it.
I was unaware that the screensaver used so much of the free CPU... I have changed mine to "blank screen" and will watch to see if I am processing the units any faster. As for dealing with the "public".... alot of times I would rather deal with a random "John Q Public" than try to deal with a corporate muckity muck. At least you have a 50-50 chance of running into a "good guy" in the public realm. I think the latter runs about 90-10 against. :-) (Now THERE'S some data that doesn't need crunchin'!) THANKS AGAIN! |
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Viktors
Former World Community Grid Tech Joined: Sep 20, 2004 Post Count: 653 Status: Offline Project Badges: 
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1. The screen saver shows a snapshot of the molecule during the folding process and then shows it for a minute +- some period of time. When it looks stringy, it means the snapshot was taken near the beginning of a folding iteration while it was not yet highly folded.
1b. Each work unit works on one particular gene sequence and therefore one protein. It folds the protein many times, each time using a different random number seed so that many subtle alternatives are tried during the folding process. The results of all of the foldings that your computer processed are combined with those computed by many other computers. This gives a sufficiently large statistical sample to produce useful final results. 2. The rotation is just to give you an idea of the 3-dimensional shape of the protein taken at the time of the snapshot. Showing the live folding process would consume far more CPU time than actually doing the useful computations. On the average computer, the molecule rendering takes just a very few percent of the CPU time. However, on slower computers, this fraction can quite a bit higher. We are considering having the rotations occur less often on slower machines to counter this. Keeping the agent minimized and not running as a screen saver actually makes it contribute the most CPU time to useful work. 3a. We will note your suggestion, however the current software infrastructure does not permit us to offer configuration options for the screen saver. 3b. Thank you for participating. Go look at http://www.worldcommunitygrid.org/projects_showcase/human_proteome.html and http://www.systemsbiology.org/Default.aspx?pagename=humanproteome for more interesting information about the project. World Community Grid - tech |
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Dataman
Ace Cruncher Joined: Nov 16, 2004 Post Count: 4865 Status: Offline Project Badges: 
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Thanks Viktors!
----------------------------------------As the all time points total leader. And project member. http://www.worldcommunitygrid.org/stat/viewStatsByMemberAT.do?sort=results Your response is most appreciated! <dataman>  |
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