Thursday, August 21, 2008

Join Folding@Home Team 33258 Folding@Home Thread
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A quick FAQ
What is Folding@home? What is protein folding?

Folding@home is a distributed computing project, that very simply stated, studies protein folding and misfolding. Protein folding is explained in more detail in the scientific background section.

What is distributed computing?

Distributed Computing is a method of computer processing in which different parts of a program, or different portions of data, are processing simultaneously on two or more computers that are communicating with each other over a network or through the Internet.

Who "owns" the results? What will happen to them?

Unlike other distributed computing projects, Folding@home is run by an academic institution (specifically the Pande Group, at Stanford University's - Chemistry Department), which is a nonprofit institution dedicated to science research and education. We will not sell the data or make any money off of it.

Moreover, we will make the data available for others to use. In particular, the results from Folding@home will be made available on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication, and these journal articles will be posted on the web page after publication. Next, after publication of these scientific articles that analyze the data, the raw data of the folding runs will be available for everyone, including other researchers, here on this web site.

How can I see how many other people are participating?

What has been "folded" so far, and how much have I folded?

We keep many types of statistics of users and work accomplished in our Stats section. You can check your Individual stats, Team stats, and overall Project stats. Please also review the Results and Awards sections.

What has the project completed so far?

We have been able to fold several proteins in the 5-10 microsecond time range with experimental validation of our folding kinetics. This is a fundamental advance over previous work. Scientific papers detailing our results can be found in the Results section. We are now moving to other important proteins used in structural biology studies of folding as well as proteins involved in disease. There are many peer-reviewed and published in top journals (Science, Nature, Nature Structural Biology, PNAS, JMB, etc) that have resulted from FAH. Currently, the FAH project has published more papers than all of the other major distributed computing projects combined!

Why not just use a supercomputer?

Modern supercomputers are essentially clusters of hundreds of processors linked by fast networking. The speed of these processors is comparable to (and often slower than) those found in PCs! Thus, if an algorithm (like ours) does not need the fast networking, it will run just as fast on a supercluster as a supercomputer. However, our application needs not the hundreds of processors found in modern supercomputers, but hundreds of thousands of processors. Hence, the calculations performed on Folding@home would not be possible by any other means! Moreover, even if we were given exclusive access to all of the supercomputers in the world, we would still have fewer computing cycles than we do with the Folding@home cluster! This is possible since PC processors are now very fast and there are hundreds of millions of PCs sitting idle in the world.

Can I run Folding@home on a machine I don't own?

Please only run Folding@home on machines you either own or on which you have the permission of the owner to run our software. Any other use of Folding@home violates our license agreement (and just isn't a good idea in general).

What are the minimum system requirements?

All computers can contribute to Folding@home. However, if the computer is too slow (e.g. wasn't bought in the last 3-4 years or so), the computer might not be fast enough to make the deadlines of typical work units. A Pentium 3 450 MHz or newer equivalent computer (with SSE) is able to complete work units before they expire.

Why don't you post the source code?

Most of the critical parts of FAH are publicly available. The Tinker and Gromacs source codes can be downloaded and run. Unlike many computer projects, the paramount concern is not functionality, but the scientific integrity, and posting the source code in a way that would allow people to reverse engineer the code to produce bogus scientific results would make the whole project pointless.

However, we stress that the vast majority of our code is already open source. We have an Open Source FAQ with more details.