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Old 2006-03-03, 02:12   Link #1
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
Folding @ Home

Team: Animesuki
Team Number: 49362
Team Page: Team page

I.
Behind the folding

Folding@Home (http://folding.stanford.edu )

Before anyone begins to think I am talking about Origami, Folding@Home is a scientific study (backed by the University of Stanford) on the folding of proteins in cells. This research studies how proteins fold, why do they misfold, and for a miss folding might cause a developement of a disease. Diseases such as cancer, Alzheimer’s, Parkinson’s, can be caused by a misfolding of a protein within an affected cell. All this data is given to biological research facilities to develop treatments and possibly even cures. If you are interested continue reading on how you can contribute to the research.

Folding@Home does this by actually simulating the numerous atoms in the protein structure. Then it simulates the processes of intermolecular bonding to begin the folding process. This is how they find how a protein folds while in the process of folding. When you send in your work unit you are actually just sending in a small part of the overall folding process.

Every time you completed a work unit, your team receives a specified amount of points towards your team’s overall score. Thus increasing the rank of the team, this is just a competitive side to folding.

I have set up a Folding Team so if you choose you can donate to Team Animesuki. The Team number is 49362. You can enter this whenever instructions prompt you.

Spoiler for Guide for Folding:


FAH installer
I've had this in my guide But I decided to make it more... Visible.
Just download and unzip the app and click to install its that simple. So simple a Caveman who is interrested in folding can do it.

For a guide on how to set it up visit my FAQ which is hidden and is in section 3/III.

Last edited by Kurz; 2006-11-14 at 15:26.
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Old 2006-03-03, 10:18   Link #2
physics223
In the Tatami Galaxy ↓
 
 
Join Date: Feb 2006
So that's why I see molecules twisting and turning around at some school computers... some techs installed FAH on the lib computers.
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Old 2006-03-03, 10:37   Link #3
Kurz
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Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
http://folding.stanford.edu/FAQ-diseases.html

Are some more indepth about the dieases they are researching.


The more CPU's the better in this type of project.
Since a Typical SuperComputer has around 5,000 cpus,currently there are over 200,000 CPUs folding. Thats about 40 Supercomputers right there by this system of distrubition of CPU's all connected by the internet. The Human Gnome was decoded by using this same method. (Trying to find the site...)

I thought since Animesuki's fanbase is so large the more cpu's will be a definate impact on the project.

Plus we can bring a bit of celebrity to Anime Watchers. While we watch our anime we fold proteins


P.S. I've gotten Premission from GHDpro to do this.

Last edited by Kurz; 2006-03-03 at 15:20.
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Old 2006-03-04, 18:04   Link #4
Kurz
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Join Date: Nov 2003
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Age: 27
Added "why do I want to contribute."

Copied from above.

Why would I want to contribute?
I am not saying you need to contribute. However, after reading their published papers it inspired me to be part of this project. Then I got the idea maybe those of animesuki might want to lend a hand in this project.

I see this project for the betterment of man kind, since it could speed up development for cures for the mentioned diseases. Instead of having your brain decay to alzhiemers or lying in bed dying from cancer. You could be playing tennis after taking medicine that was developed from this research.

The work is going to be done one way or another. However, if you put forth a little bit of your own time (in this case CPU cycles) the research will precede faster.

When you look back you'll see it was well worth being part of this project.
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Old 2006-03-05, 03:06   Link #5
TougeSil80
I have enough, I'm gone.
 
 
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Is this project still going? Is F@H already considered obsolete?

Quote:
Originally Posted by Wikipedia
Recent developments in the protein folding world by both David Baker's research group at the University of Washington and Rama Ranganathan's research group at the University of Texas Southwestern Medical Center have demonstrated that the folding of proteins, as well as protein-protein interactions and protein engineering can be best solved using principles of cooperative evolutionary conservation. This is not the approach taken by Folding@home, which has rendered it somewhat obsolete. This recent work is tied to the Rosetta@Home distributed computing protein modeling effort.
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Old 2006-03-05, 18:00   Link #6
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
Wikipedia is a place where anyone can make a change to it and often isnt a good source of info.

This is quote is from the Vijay Pande of the Pande Group, at Folding@Home. After I asked the question.

Quote:
I know Baker and Ranganathan and their work very well and (like the rest of the protein community) find their work very important and impressive. However, Rosetta and Folding@Home are addressing very different problems.

Rosetta only predicts the final folded state, not how do proteins fold (and Rosetta has nothing to do with protein misfolding). Thus, those methods are not useful for the questions we're interested in and the diseases we're tackling (Alzheimer's Disease and other aggregation related diseases).

Also, one should note that accurate computational protein structure prediction is still very challenging compared to what one can do experimentally, whereas the information obtained from Folding@home on the nature of folding and misfolding pathways matches experiment (eg with quantitative validation in rates, free energy, etc) and then goes beyond what experiment can tell us in that arena.

While Rosetta has gone a long way and is a very impressive project, given the choice between a Rosetta predicted structure and a crystal structure, one would always chose the crystal structure. I bet that will be changing due to their great efforts, but that may still be a ways off for that dream to be realized.

So, both are valuable projects IMHO, but addressing very different questions. I think there are some misunderstandings out there, though. Some people think FAH is all about structure prediction (which it is not -- that's Rosetta's strength) and some think Rosetta is about misfolding related disease (which it's not, that's Folding@Home's strength). Hopefully this post helps straighten some of that out.
I still ally my CPU time to Folding@Home since its about finding the cause of diseases in protein misfolding. Rosetta like said above seeks different answers in the relm of proteins.

Work at Folding@home is still going. So join up an contribute points to Animesuki ^^
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Old 2006-03-05, 18:05   Link #7
TougeSil80
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Cool, thanks for the info.
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Old 2006-03-05, 21:54   Link #8
Kurz
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Join Date: Nov 2003
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Age: 27
No problem http://forum.folding-community.org has alot of intelligent people there. So if you ask they will answer.

http://en.wikipedia.org/wiki/Folding%40home is their Wikipedia site.

http://forum.folding-community.org/v...ic.php?t=13821
Is a link to more information about the results they are creating.

Last edited by Kurz; 2006-03-05 at 22:09.
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Old 2006-03-16, 20:47   Link #9
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
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Age: 27
Update

We have just completed 14 Work units with a grand total of 3146 points so far. We currently rank 9961 of 43282 of all the current teams. Not bad record to accomplish in only 13 days.
Animesuki Team Page

I guess I should stop gaming so much and leave the computer alone to fold. Or else I get overtaken by my team mates.

If anyone has any questions regarding Folding@Home and their pursuit for cures, I am more than able to help answer your questions.

I appreciate any suggestions on editing the guide I have writen up.



*More Info*
Here is more information to the Advanced options. http://forum.folding-community.org/viewtopic.php?t=6057
Its basically saying if you are getting errors and are not able to complete a work unit with -forceasm on, take it off.


Here is a link for the list of projects and the diseases for each project they are researching.
http://fahwiki.net/index.php?title=Projects

Last edited by Kurz; 2006-03-16 at 21:20.
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Old 2006-03-16, 21:51   Link #10
Zero Shinohara
I'll keep walking.
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I'll be installing that on my grandmother's comp. It's less used for gaming than mine, so it's gonna do a better job. Also, I'll see if I may install them at my college comps, though I think I already know the answer to that :P
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Old 2006-03-19, 22:21   Link #11
Kurz
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Join Date: Nov 2003
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Age: 27
The more the better I always say.

Btw to those who noticed I've put the guide in Spoiler tags it shouldn't be a pain just get to the bottom now. ^^
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Old 2006-03-20, 07:09   Link #12
Ending
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Quote:
Wikipedia is a place where anyone can make a change to it and often isnt a good source of info.
Actually, it has been reported to be as reliable as Encyclopedia Britannica, even though there still are many people who disagree.
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Old 2006-03-20, 08:57   Link #13
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
Well the fact I can go on Wikipedia and change something on a topic makes it less creditable.

Though I will agree most of it can be reliable. Infact its a way for me to quickly research a topic which is nice.
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Old 2006-03-20, 12:10   Link #14
Hyral
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I'm in too now =)
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Old 2006-03-20, 17:49   Link #15
Kurz
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Join Date: Nov 2003
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Age: 27
Welcome to the fold *pun intended*

I wonder If Animesuki's userbase can get up to the level of a certain other sites.
Our rank is steadly passing other new teams as well as inactive ones. Still I wonder how high we can get before hitting the first Block.

Hmm... Maybe I should put FAH on my mom's labtop.
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Old 2006-03-24, 16:54   Link #16
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
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Age: 27
Quote:
Spoiler:


An updated install guide. This time I have an installer for those who hate Command Prompt. Now there shouldn't be any excuse about it being too hard to install.

Last edited by Kurz; 2006-03-30 at 11:32.
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Old 2006-04-02, 02:53   Link #17
Jinto
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Join Date: Feb 2004
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I want to point out, that Kurz has a good reason to promote the console client here. Because the nice looking graphical client has an issue with OpenGL and maybe Games (or TV applications in my case). Just wanted to let you know
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Old 2006-04-02, 16:05   Link #18
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
Yes a serious oversight on my part... I forgot to mention it in my guide. The graphical client is good, however it can cause conflicts with curtan graphical programs such as video games or Jinto's case, "TV recording". Its not the fault of the Folding@Home program, the coding of certain programs are a little touchy. They dont like to share resources of directX and openGL.

Console client from my experience doesnt effect the performance of my machine in any form. This is why I recommend it over the graphical program.
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Old 2006-05-08, 16:58   Link #19
Kurz
Gao~ a sound for the ages
 
 
Join Date: Nov 2003
Location: I live in a relm of swirling of thought and emotion, Ever lost in the relm of infinite possiblities.
Age: 27
UPDATE:
As we Press on Folding for a cure.
Team Stat Page
The Team folded over 100 Workunits and a respectable score of 18752. And a team Ranking of 5801 of 43974 total teams.

To also add you dont need to fold at a constant 100% of your computer. There is an option for the FAH installer that limits the program's use of your CPU to any percentage you wish. Example I currently fold at 90%.

I must say this yet again. This program doesnt make your computer slower since it runs at a lower priorty of your main stream programs. So while you fold, you can play games, surf the web without ever feeling a sign of Slowdowns.

So please join Team Animesuki and fold on for a cure.

-Kurz

Honorable Mentions for both "Jinto Lin" and "Kwngy"
For turning out tons of work units for the team!
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Old 2006-05-08, 17:50   Link #20
Jinto
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Age: 33
In summer I wont be able to submit that many workunits. I can't let it run all the daytime, because it will heat up my room too much.
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