Thursday, August 21, 2008

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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.

Pandora Could Be First Major Casualty of New Royalty Rates

By Eliot Van Buskirk

For over a year, publications including have warned that the U.S. Copyright Royalty Board's new rates for webcasters would end online radio as we know it. Now, those chickens are coming home to roost.

Pandora -- practically the poster child for online radio -- says it will shut down if royalty rates enacted in March of 2007 are not altered soon.

Despite all of those warnings, the rates remain intact and must be observed by webcasters, even as the battle over them continues. Aside from a few concessions to small webcasters and those with lots of unique streams, Washington lawmakers have not altered the rates, which currently require Pandora to fork over 70 percent of its revenue to labels and artists.

"We're losing money as it is," founder Tim Westergren's told The Washington Post. "The moment we think this problem in Washington is not going to get solved, we have to pull the plug because all we're doing is wasting money," adding, "We're funded by venture capital. They're not going to chase a company whose business model has been broken. So if it doesn't feel like its headed towards a solution, we're done."

Westergren agreed to a hasty interview on Monday but was unavailable to talk due to a family engagement. However, a Pandora spokeswoman said the company has been paying the new royalty fees to SoundExchange since July 2007 and that there's no specific day on which Pandora will go offline, assuming the rates are not changed. "It's an ongoing judgment call based on the trajectory of the negotiations," she said.

If Washington lawmakers want to ensure that legal music services cannot compete with under-the-radar alternatives that pay nothing to artists, they're doing a bang-up job.

Record labels and artists have nothing to gain by killing off services that pay them royalties. In fact, a source close to the situation told us last year that SoundExchange, which represents many labels and artists, was as surprised as anyone else that the U.S. Copyright Royalty Board accepted SoundExchange's proposed rates without altering them substantially. What may have been a negotiating tactic has become law, much to the detriment of webcasters, music fans and a flagging industry that desperately needs legitimate music services like Pandora.

While all forms of U.S. radio pay royalties to songwriters and publishers through rights organizations such as BMI and Ascap, record labels and recording artists have not received performance royalties from radio in this country, because radio was thought to have a promotional effect on sales. With sales flagging, labels and artists are trying to collect licensing fees from all uses of their music, including radio. Satellite radio stations must pay a small percentage of revenue, while terrestrial radio stations currently pay no royalty to labels and recording artists.

Rep. Howard Berman (D-California) is reportedly trying to broker a new deal between SoundExchange and webcasters to reduce the per-song, per-listener rates handed down by the Copyright Royalty Board last year. But he doesn't appear optimistic.

"Most of the rate issues have not been resolved," Berman told The Washington Post. "If it doesn't get much more dramatic quickly, I will extricate myself from the process."

Due to rates Westergren called "far too high to allow ad-supported radio to operate," Pandora ceased webcasting to the United Kingdom on January 15. Unless these rates change, the United States is next.