Sylvain’s Panama Adventure

I’m sure many of you have heard of and even participated in the SETI@Home project. This project was all the rage in the 1990’s and it enabled the SETI program to solve its computational capacity problem; SETI was accumulating more radio data then it had the capacity to process, and it was looking at the need for decades worth of computer time to process it. The SETI program used an innovative technique to farm out pieces of work to user’s computers and leverage their unused CPU capacity to process work units. The program was so successful that SETI was actually able to process all of their data many times over. Because of this last fact, many members of SETI@Home, like me, no longer bothered carrying on with the program.

Now Stanford University is using the same distributed computing technology to address a similar but arguably more pressing and potentially very useful computing problem: protein folding. Here’s a description of this process from the project’s web site:

What is protein folding and how is folding linked to disease? Proteins are biology’s workhorses — its “nanomachines.” Before proteins can carry out these important functions, they assemble themselves, or “fold.” The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.

Moreover, when proteins do not fold correctly (i.e. “misfold”), there can be serious consequences, including many well known diseases, such as Alzheimer’s, Mad Cow (BSE), CJD, ALS, Huntington’s, Parkinson’s disease, and many Cancers and cancer-related syndromes.

Here is a list of the diseases currently being studied through protein folding:

• Alzheimer’s Disease
• Huntington’s Disease
• Cancer & p53
• Osteogenesis Imperfecta
• Parkinson’s Disease
• Ribosome & antibiotics

So you can run a small program on your computer(s), either as a background service or as a graphical screensaver, and this program will unobtrusively download and process work units using whatever unused processor capability your computer has. Please join this noble cause and help medical science by going here to download and run this software on your machines at home (you should obtain permission from your employer before running it at work!)

As an interesting corollary to this story, Sony has released an update to its PlayStation 3 machines that enables them to take part in this program. Given that the PS3s have an incredibly powerful “Cell” processor, they can chew through the work units a lot faster than PCs can. More than 20,000 PS3 owners have already joined the program and the folks at Stanford think PS3 users could double the overall throughput of the program.

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