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Grid Computing & Protein Folding

What are Distributed Computing and Grid Computing?

Distributed computing is a means by which computer resources at more than one physical location can be tied together to perform a task. The Worldwide Web is perhaps the best example of distributed computing. Distributed computing systems range in size from global computing to local intranets.

Grid computing is a method by which the computing power of individual PCs or other computer resources throughout the world can be harnessed to perform large-scale projects. Grid computing joins these resources together through special software to simulate a single large computer or virtual computer. Previously, such massive computing power was available only through use of supercomputers. You can participate in these projects; become a partner with us! The projects are largely non-profit; you donate your idle computing time to help forward progress in scientific research that might otherwise not be possible.

The Folding@home Protein Folding Project

Folding@home is a protein folding grid computing project being conducted by Stanford University. Protein folding is the method by which proteins in the body assemble themselves. Learning how proteins fold is extremely important because diseases such as Alzheimer’s, BSE (Mad Cow disease), cystic fibrosis and cancer may be the result of faulty protein folding. The Stanford Folding@home project studies protein folding, misfolding, aggregation, and diseases that may result when proteins do not fold properly.

How Does Folding@home Work?

The Folding@home application that runs on your PC is known as a distributed client — a standalone program that runs independently on a PC or workstation under direction of a central server. In this case, each Folding@home client is fed data from and returns results to a Stanford University server. The Folding@home client runs in the background on your PC and uses what would otherwise be idle CPU time, so it is out of the way and unnoticed unless you choose to invoke its display function, which shows the protein you are modeling and can be rather cool to watch.

Under Windows, control of the Folding@home client is available via an icon in your Windows system tray. (Folding@home client is also available for Linux and Mac OS X operating systems.) A nice control feature is the ability to manually adjust the maximum percentage of CPU usage devoted to Folding@home. You can also set the client to inform you when it needs to connect to the Stanford servers; this is necessary if you need to establish a dial-up connection or reconfigure your firewall. (I’ll talk more about firewalls in a moment.)

Folding@home spends most of its time performing mathematical calculations; it is a number cruncher. Once installed and configured (a relatively simple task), the Folding@home client downloads a processing core and work unit. Thereafter, it will merrily crunch away in the background for hours or days, depending upon the speed of your CPU and amount of memory, how many hours per day you run your computer, the percentage of CPU usage you have allocated to the client, and the size of a particular work unit being processed. When finished, the Folding@home client will attempt to upload its results to one of the Stanford servers and download another work unit.

The Folding@home client appears to be a safe and highly reliable program which should not affect normal computer use. I have run (and continue to run) the Folding@home distributed client on several different PCs under both MS Windows® XP and MS Windows 98 operating systems more or less continuously for over three years. During that time I have experienced no negative interactions with hardware or other software with the exception of components of the Corel™ WordPerfect® Office suite, which for some odd reason seem to not want to run when Folding@home is present. If I wish to run these, I simply quit Folding@home temporarily.

IMPORTANT:  As with any program, our results do not guarantee that you will not experience problems with Folding@home on your own system, either now or in the future. Use your own best judgement and read the FAQs (Frequently Asked Questions) on the Folding@home website before proceeding with installation.

WARNING:   Never install or run Folding@home or any other distributed computing client at your place of employment without first receiving written permission from your employer to do so, and do not install it on any computer or workstation other than those for which you have been authorized to do so. Because they transfer data to and from an outside server, some employers consider distributed computing clients to be invasive software and could levy punitive actions for unauthorized use which could include termination of employment.

If you have a firewall in place, you will need to configure one or more rules to allow Folding@home to download work units and upload results. I suggest that you disable your firewall protection during initial Folding@home installation. Once installation — including core and work unit download — is complete, you can reenable the firewall. In my experience, our firewall has prevented download of Folding@home cores. While you can reconfigure your firewall to permit core download, it may become a laborious task depending upon your level of expertise.

Folding@home presently appears to be using three to four processing cores, with specific cores being utilized by different work units. Each core will be downloaded only when called upon by a work unit you have been assigned. Once the cores are in place, the only core downloads that will take place are new cores or updates to old ones. Cores updates are very infrequent, on the order of months to a year.

Who Benefits from Folding@home?

Folding@home is run by an academic institution (specifically, the Pande Group at Stanford University’s Chemistry Department), which is a non-profit organization dedicated to science research and education. The Pande Group and Stanford University will not sell the data or receive monetary compensation for it.

Results derived from Folding@home will be made available for others to use on several levels. Most importantly, analysis of the simulations will be submitted to scientific journals for publication. Journal articles will be posted on the Folding@home website following publication and the raw data upon which analysis for such articles is based will be made available to everyone, including other researchers, on the Folding@home website.

We hope you will decide to participate in this worthwhile scientific effort and urge you to join our team. You can find sign-up, download and Team Ten Spider information to the right. Welcome aboard!

Authored by Kenneth L. Anderson.  Original article published 21 October 2003, updated 18 January 2006.

Follow links to the right to learn more about grid computing, protein folding and Stanford University’s Folding@home distributed protein folding project. At the left margin, Related Links address topics of interest pertaining to computer and internet resources. View the Computer & Internet SiteMap for a complete list of computer and internet-related topics.

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