Posted:
in General Discussion edited January 2014
<a href="http://folding.stanford.edu/"; target="_blank">http://folding.stanford.edu/</a>;



Who of you have heard of this project? I am guessing more than half.



[quote]From the Folding WebSite<strong>

What are proteins and why do they "fold"? Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out their biochemical function, they remarkably assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, remains a mystery. Moreover, perhaps not surprisingly, when proteins do not fold correctly (i.e. "misfold"), there can be serious effects, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, and Parkinson's disease.



What does [email protected] do? [email protected] is a distributed computing project which studies protein folding, misfolding, aggregation, and related diseases. We use novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously acheived. This has allowed us to simulate folding for the first time, and to now direct our approach to examine folding related disease</strong><hr></blockquote>



Which of you currently run [email protected]? If so, why not run [email protected] instead?



And for all of you OS X loving mac users, you can join <a href="http://statsman.org/folding2stats/html/1971.html"; target="_blank">TeamMacOSX</a>



When you load Folding enter 1971 for the team number.



Why look for ET when you can look for the cure for Alzheimers, cancer, and other devastating diseases?
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Comments

  • Reply 1 of 45
    Maybe if we find ET he can just give us the cure. Then we win two fold
  • Reply 2 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by M3D Jack:

    <strong>Maybe if we find ET he can just give us the cure. Then we win two fold </strong><hr></blockquote>



    Yeah, in return for what?
  • Reply 3 of 45
    Out of the kindness of his heart of course
  • Reply 4 of 45
    noahjnoahj Posts: 4,502member
    Something they have already accomplished.



    <a href="http://www.sciencedaily.com/releases/2002/10/021022070813.htm"; target="_blank">http://www.sciencedaily.com/releases/2002/10/021022070813.htm</a>;



    From the article:



    Now, for the first time, a distributed computing experiment has produced significant results that have been published in a scientific journal. Writing in the advanced online edition of Nature magazine, Stanford University scientists Christopher D. Snow and Vijay S. Pande describe how they ? with the help of 30,000 personal computers ? successfully simulated part of the complex folding process that a typical protein molecule undergoes to achieve its unique, three-dimensional shape. Their findings were confirmed in the laboratory of Houbi Nguyen and Martin Gruebele ? scientists from the University of Illinois at Urbana-Champaign who co-authored the Nature study.



    It is for a good cause and it is getting real results. What more could you want?
  • Reply 5 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by M3D Jack:

    <strong>Out of the kindness of his heart of course </strong><hr></blockquote>



    Would that be the glowing red one? Coooool!



    But seriously, what do you truly think of the project? Do you think [email protected] is of greater or equal value than [email protected] in the long run? <img src="confused.gif" border="0">
  • Reply 6 of 45
    mcqmcq Posts: 1,543member
    I've just started to run [email protected] after reading about that report a week or so ago... seems like a worthy project, and it seems like not a lot of people working on it.
  • Reply 7 of 45
    stevesteve Posts: 523member
    [quote]Originally posted by NoahJ:

    <strong>



    Yeah, in return for what? </strong><hr></blockquote>



    Reses' Pieces, silly. Didn't you watch the movie?



    I've been running SETI since around April of this year. I have about 80 units, and I even have it doing my dirty work on some of the computers in the various tech labs on campus.



    I heard that the Google toolbar for Windows IE has its own Folding client in it. Thought that was pretty cool--it's a great way to get more people to participate while they're doing something as simple as surfing the web.



    It's also a worthy cause. My mother died of breast cancer last year, and it would make me happy to find a cure this decade.
  • Reply 8 of 45
    I've run [email protected] I think it's a bit more productive currently, but it is nowhere near is neat when compared to [email protected] The cute little graph graphics and stuff in [email protected] beat 3d molecules any day
  • Reply 9 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by M3D Jack:

    <strong>I've run [email protected] I think it's a bit more productive currently, but it is nowhere near is neat when compared to [email protected] The cute little graph graphics and stuff in [email protected] beat 3d molecules any day </strong><hr></blockquote>



    Well I guess if you spent all your time looking at the graphics and such I would agree, however, those who want to get real speed out of either system know it is best to hid the graphics and disable as much of them as possible to get full speed out of the client. So now you are left with either pretty pictures or raw speed. Most go for the speed and bragging rights. You may not be one of those. However if you are what are you going to brag about?
    • My computer is looking for aliens, oh and it is really fast doing it.

    • My computer is looking for the cure for incurable diseases, and it is really fast doing it.

    • My computer has a neato screensaver, look!

    For me #2 wins out in the long run. #3 is no big deal and #1 really does not impress me anymore. Even if we "find ET", what is to say he wants to talk to us? Just knowing he is there does not a conversation make.



    However, if we find the cure for Alzheimers, we get that as soon as we find it. Seti's case gets weaker and weaker as time goes by for me. However, I do have 787 units done on Seti so I have put in my time there as well. I guess I just felt that it was time for something meaningful to me.
  • Reply 10 of 45
    Wow! Congratulations, Noah! You're really up there in the ranks of TeamMacOSX. I just joined the team. How long did it take you get that high? I wish there was an option of using a higher portion of processor power...
  • Reply 11 of 45
    ast3r3xast3r3x Posts: 5,012member
    i feel [email protected] is better, but i have to admit, i like putting up [email protected] as my screen saver...haha makes me feel more productive. I am normally at school during the day, so i think that I will get the console version of [email protected] and run that while [email protected] runs as my screen saver during the day...they can both run at the same time right?
  • Reply 12 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by ShawnPatrickJoyce:

    <strong>Wow! Congratulations, Noah! You're really up there in the ranks of TeamMacOSX. I just joined the team. How long did it take you get that high? I wish there was an option of using a higher portion of processor power...</strong><hr></blockquote>



    Took a few months. And you can use a higher portion of processor power. renice works in OS X now. Welcome to the team, we can use all the help we can get...
  • Reply 13 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by ast3r3x:

    <strong>i feel [email protected] is better, but i have to admit, i like putting up [email protected] as my screen saver...haha makes me feel more productive. I am normally at school during the day, so i think that I will get the console version of [email protected] and run that while [email protected] runs as my screen saver during the day...they can both run at the same time right?</strong><hr></blockquote>



    If you run DP then you can run both at full speed with no speed hit. If you are Single Proc then you can run both, but they will take a lot longer to finish. You might renice [email protected] to 20 and set [email protected] to 10 or so. That way you can still run SETI and folding will get more of your Proc time.
  • Reply 14 of 45
    I'm at 4% on p166_villin right now. What does that mean?
  • Reply 15 of 45
    telomartelomar Posts: 1,804member
    Sorry I just find this funny when talking about what to brag about.



    [quote]Originally posted by NoahJ:

    <strong>
    • My computer is looking for the cure for incurable diseases, and it is really fast doing it.

    </strong><hr></blockquote>



    Does anybody else see the irony in bragging about searching for a cure for an incurable disease? Incurable isn't the right word but when phrased like that it sruck me as a funny thing to brag about
  • Reply 16 of 45
    ast3r3xast3r3x Posts: 5,012member
    how exactly do you use the renice command?
  • Reply 17 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by Telomar:

    <strong>Sorry I just find this funny when talking about what to brag about.







    Does anybody else see the irony in bragging about searching for a cure for an incurable disease? Incurable isn't the right word but when phrased like that it sruck me as a funny thing to brag about </strong><hr></blockquote>



    <img src="graemlins/lol.gif" border="0" alt="[Laughing]" /> Perhaps I should have phrased it differently.



    My computer is looking for the cure for currently incurable diseases, and it is really fast doing it.



    But I think that the point is made either way.
  • Reply 18 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by ShawnPatrickJoyce:

    <strong>I'm at 4% on p166_villin right now. What does that mean?</strong><hr></blockquote>



    <a href="http://folding.stanford.edu/psummary.html"; target="_blank">http://folding.stanford.edu/psummary.html</a>;



    Check there for information about the different work units.



    4% means you have finished 4 steps in the 100 step process. A villin is usally an easier unit. Your machine should finish it in about a half day to a day depending on how much processing power you have, and how much you use your machine.
  • Reply 19 of 45
    noahjnoahj Posts: 4,502member
    Perhaps I should post some speed tips here for those who have decided to do [email protected]



    First tip. Use the command line client, that way you can make it a background process and if you log out it does not stop working. You have to sart it from the terminal (Unless someone here could write us up a nice applescript to start it ) and if you put the & symbol after the command to start it e.g:



    ./[email protected] &



    It will allow you to exit from the terminal and will continue to run as a background process. If you do not want to run it as a background process or from the terminal just use the graphical app and leave it in the dock. It will not stay running if you logout, but it will run about as fast so long as you keep the protein hidden.



    Once you have it running you can use the renice command to give it a higher processor priority. The way I do this is to use top to get the PID.



    Folding uses different cores, but on the Mac all it uses right now is FAHCORE_65. Find that in the list and write the number down that is in front of it, that is the PID.



    on the command line type:



    sudo renice (fahcore_65's PID here) (some number between 20 and -20) &lt;then press enter&gt;



    e.g.:



    sudo renice 321 10 &lt;then press enter&gt;



    After you enter your password it should tell you that the new priority for the PID is 10.



    when using renice 20 is the lowest priority, this is default for [email protected] -20 gives it all the processor all the time. I usually recommend about 10 or so. Anything more and your systems performance in other things, like Photoshop, iTunes and such starts to suffer.



    If any part of this is wrong, someone please correct me.
  • Reply 20 of 45
    noahjnoahj Posts: 4,502member
    [quote]Originally posted by ShawnPatrickJoyce:

    <strong>I'm at 4% on p166_villin right now. What does that mean?</strong><hr></blockquote>



    What is your username on the team? I will be looking for you.
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