Folding @ Home

[Kurz]

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:

Spoiler for FAQ:

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.

How does Folding@Home work?
The scientists behind the Folding project at Stanford have set up a system that gives out work units (which are pieces to the overall protein) to individual computers into a manageable size for them to complete. These work units are then processed on your computer while your CPU is idling (Doing nothing). Then when the work unit is complete the program, then sends the completed work unit’s data over the internet to their server for processing.

Wouldn’t running Folding@Home slow down my computer?
No, it will not slow down your system. Folding@Home identifies itself as a low priority thread to the windows operating system. This means whenever you are playing a game, watching a video, or just surfing the web; windows prioritizes what you are currently doing before giving the cpu’s resources to the lower priority programs like Folding@Home.

Example: If I want to play Battle Field 2 (A high performance hog) there is no need to turn off Folding@Home. Since Battle Field 2 takes priority, Folding@Home can’t do anything until you turn off the game. Note: Most games use 100% of the CPU’s power to produce as many Frames per Second as possible.

Wouldn't running Folding@Home use up more power?
Yes Folding@Home does increase power use however its not something you'll notice on your electricity bill. Nor is it something I can calculate since it largely depends on how effecient your CPU is. I have an AMD64, so I'll be using less power than someone with a Intel P4 processor thats for sure.

Wouldn’t running Folding@Home wear down my processor?

As long as you have a heat sink (joke: everyone has a heat sink) there shouldn’t be a problem. However, if you want to see how hot your CPU is running check out Speed Fan. It should be the hottest thing on your computer. http://www.almico.com/speedfan.php

Ideal temperature when the CPU is running full out should be less than 60 degrees Celsius. However most people dont ever reach this very high temperature, most stay around 40 - 50 degrees Celsius. In all my dealings of telling friends not one of them had an issue with temperature.

Contrary to popular belief a cpu can run at 100% all the time unlike a race car engine. Since the temperature is always in check.

Wait my computer is slow why would they want me?

The deadlines on most work pieces is about a month. It takes me about 3 days of my computer being on while doing other things to finish a work unit. They give such a huge amount of time to accomediate those with slower processors/ or those who dont turn on their computer as often.
So dont be afraid to share you CPU's cycles.

Wait why can’t Stanford just use a supercomputer?
Simple answer: Its just one computer, a very fast computer that can do the work of a few thousands machines. However, folding at home project has over 200,000 computers/CPU’s working currently, which in practice does the work of many supercomputers.

Can I install Folding@Home on other computers without their knowledge?
You may believe you are serving the greater good. However doing so can put you under provision of the law. Instead, talk to the owners of the computers about Folding@Home and explain its purpose, and its harmless nature, and persuade them to supporting it.



Wait it uses the internet? Doesn’t that mean there could be security Breach?
If you download it directly from their site it won’t be an issue. It’s a very secure program and it won’t open holes to your system.

If you have any other questions don’t be afraid to ask here or PM me.

II.
Choosing a Client

1.
http://folding.stanford.edu/download.html

This link takes you to the client download page. At the top, you can see if your desired username is taken. Do Not Download the Beta. Also, pay attention to the OS version the client you download supports.

Next, stop choosing a client format.

There are 2 forms of the client for the Windows operating system. (Mac OS X and Linux are equally supported, however since most people (including myself) use Windows. I’ll just be explaining Windows install and its options.

Graphical client:

Allows you to see the protein you are currently working on. Its pretty 3D render of the protein. However, I don’t recommend it since it takes a bit more processing time to draw those pretty objects. When I had it installed it was usually minimized to keep out of my way.

Pros: Easy to install. Also you have a more personal way of interacting with the program. They had this option to appeal to more people since it is easy to install and run.

Cons: Takes up an Icon space near the system clock. Also because of the graphics take up a bit of processing time which is detrimental to the folding project.

*IMPORTANT TO NOTE* Some programs do not get along with the Graphical Client. It can cause conflicts. Its not in every case, however if you play video games, video capture, or any other programs dealing with video do not install this verison, instead use the Console client.

Console client Recommended:

Its’ setup has a few more steps to it, however if you want it to take the smallest amount of space on your hard drive, and not intrude on your desktop space this is the best way to fold. Also, you can have it run as a service, which I believe, is the easiest way to handle it.

Pros: Gives you more options when setting it up. It allows for the fastest folding possible. Ability to run as a background service is a definite plus.

Cons: Previously was hard to set up, however I now have my hands on a Installer.


III. Installing Console Client as a Service
Previously I had a guide to set it up through console. However, I found a simple Installer that will making setting up a breeze.

FAH installer

1. First download the FAH installer i have linked.
2. Unzip
3. In the new folder click on servicegui.exe and run it. Options should pop up. Steps A - H tell about which settings you should put.




a. Pick any username you wish. If you want to check to see if anyone is using it currently Check here

b. The Team number for Animesuki is already there so you dont need to change it.

c. If you are behind a proxy enable the option. However if you are not behind a proxy, or dont know what a proxy is dont worry (I dont really understand Proxies myself).

d. If you have at least a 1.5ghz CPU (in other words you can play h.264 just fine) "Work units with deadlines is the best option". If you have CPU slower than 1.5ghz choose "Work units without deadlines" is best for you.

*Basically what this option does is weed out slower processors from faster ones. So it enables Stanford to send only harder Work units to the faster processors.

e. Core Priorty sets the thread Priorty for FAH. I suggest "Low" since idle waits until the cpu isnt doing a thing before it starts doing it. With Idle I just cant get any work units done that way.

f. Do not change the options I have crossed out.

g. If for some reason you want to change how much CPU % is used for FAH you can change the value.

h. Checkpoint interval is just fine.

4. Click Next





*Advanced* If you wish to see what other flags you can add. Go here. Remember between parameters put a space with -. Example " -forceasm". You dont need a space on the first parameter though.

Read what I've wrote on the image, then install. Since you dont have FAH install before it'll download the client and install it with all the options you've set up eariler.

5.Now just Restart your computer and Folding@Home will begin as a service. You can see it taking CPU priority in the Task Manager. There you have it you’ve began to fold for science.





7. *Optional* if you like to check on how the task is proceeding. http://fahmon.silent-blade.org Just install and follow its read me. Its a Third party program that reads the Log file to see; how much there is left before finishing, how fast your folding based on points per day scale, and it tells you how many points you'll be making when you send it in. It also says what protein your working on.

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.

[physics223]

So that's why I see molecules twisting and turning around at some school computers... some techs installed FAH on the lib computers.

[Kurz]

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.

[Kurz]

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.

[TougeSil80]

Is this project still going? Is F@H already considered obsolete?

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.

[Kurz]

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.

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 ^^

[TougeSil80]

Cool, thanks for the info.

[Kurz]

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.

[Kurz]

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

[Zero Shinohara]

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

[Kurz]

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. ^^

[Ending]

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.

[Kurz]

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.

[Hyral]

I'm in too now =)

[Kurz]

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.

[Kurz]

Spoiler:

III. Installing Console Client as a Service
Previously I had a guide to set it up through console. However, I found a simple Installer that will making setting up a breeze.

FAH installer

1. First download the FAH installer i have linked.
2. Unzip
3. In the new folder click on servicegui.exe and run it. Options should pop up. Steps A - H tell about which settings you should put.




a. Pick any username you wish. If you want to check to see if anyone is using it currently Check here

b. The Team number for Animesuki is already there so you dont need to change it.

c. If you are behind a proxy enable the option. However if you are not behind a proxy, or dont know what a proxy is dont worry (I dont really understand Proxies myself).

d. If you have at least a 1.5ghz CPU (in other words you can play h.264 just fine) "Work units with deadlines is the best option". If you have CPU slower than 1.5ghz choose "Work units without deadlines" is best for you.

*Basically what this option does is weed out slower processors from faster ones. So it enables Stanford to send only harder Work units to the faster processors.

e. Core Priorty sets the thread Priorty for FAH. I suggest "Low" since idle waits until the cpu isnt doing a thing before it starts doing it. With Idle I just cant get any work units done that way.

f. Do not change the options I have crossed out.

g. If for some reason you want to change how much CPU % is used for FAH you can change the value.

h. Checkpoint interval is just fine.

4. Click Next, then the next screen of options will come up.





Read what I've wrote on the image, then install. Since you dont have FAH install before it'll download the client and install it with all the options you've set up eariler.

*Advanced* If you wish to see what other flags you can add. Go here. Remember between parameters put a space with -. Example " -forceasm". You dont need a space on the first parameter though.


5.Now just Restart your computer and Folding@Home will begin as a service. You can see it taking CPU priority in the Task Manager. There you have it you’ve began to fold for science.


7. *Optional* if you like to check on how the task is proceeding. http://fahmon.silent-blade.org Just install and follow its read me. Its a Third party program that reads the Log file to see; how much there is left before finishing, how fast your folding based on points per day scale, and it tells you how many points you'll be making when you send it in. It also says what protein your working on.

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.

[Jinto]

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

[Kurz]

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.

[Kurz]

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!

[Jinto]

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.